ismb-2008.json

{ "_id" : "e/00f61fa46ab6440cbfc6e4941c426852", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The abstract linked above is out of date - he modified his talk in light of what other speakers earlier in the program talked about. Paper about the AMD biofilm: <a rel=\"nofollow\" href=\"http://www.orau.gov/gtl2008/abstracts/thelan_2.pdf\" title=\"http://www.orau.gov/gtl2008/abstracts/thelan_2.pdf\">http://www.orau.gov/gtl2008...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/c04e8187605841d0b3fa02287876e22f", "date" : "2008-07-19T17:58:22Z" }, { "body" : "Main point: many of existing GO annotations are simply wrong, or at best inaccurate. Need better annotations.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/49d8dfe3aa5248ab8d782400c0f26295", "date" : "2008-07-19T17:59:43Z" }, { "body" : "Audience member: should GO reach out to experts to help?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/f037f8360cd64afa9cb92ebbc061d87b", "date" : "2008-07-19T17:59:57Z" }, { "body" : "Steve: they've tried, but the experts don't reach back - expert curation takes time and there's no incentive to help.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/455f3fe946bb4612832c70da9f028af2", "date" : "2008-07-19T18:00:28Z" }, { "body" : "Steve: take wiki-based community annotation. This has failed, there are more wikis than there are annotations.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/7f86b2447ba74bb69f98d605ecd5a588", "date" : "2008-07-19T18:01:18Z" }, { "body" : "Kimmen Sjolander asks: is it possible to do automatic error detection, is there a solution for this problem of inaccurate annotations?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/d0d5af3348054e1d80e25ec2fb79c771", "date" : "2008-07-19T18:02:03Z" }, { "body" : "Steve says: something needs to change at the institutional level with how scientists are credited. Contribution to databases and value-added activities should factor in, not just papers. Also not all data is considered publishable; if the researcher doesn't put it into a database then the knowledge is often lost. Perhaps we should count citation of databases entries.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/629cfcb050e64838aff2d725f8644e76", "date" : "2008-07-19T18:03:44Z" }, { "body" : "Audience member: how do we then determine the quality of these entries (for evaluating a scientists) if they're not peer-reviewed?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/48a7bd614a0e45feae0f6031a9cf8886", "date" : "2008-07-19T18:04:27Z" }, { "body" : "Steve says: there will be review in the sense that good entries will be cited more frequently than spam entries. But the bigger problem is that the current reward system doesn't reward many activities that will benefit science greatly, like doing your part to ensure that scientific databases are complete and accurate.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/e4f5945c25524c5b9939b9a5ee4d9d6e", "date" : "2008-07-19T18:05:57Z" }, { "body" : "He ends with a call to arms for the Automated Function Prediction SIG group - since we depend so much on databases and annotations, we should motivate to enact change. (Sorry for the lengthy thread. Wish I could do line breaks in my comments for dialogue type reporting!)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/00f61fa46ab6440cbfc6e4941c426852/c/8091761bb81f42d98e4a88ecde4343b4", "date" : "2008-07-19T18:07:37Z" } ], "body" : "Steve Brenner talked about the state of functional annotation using a case study, plus an open call for predictions for new proteins in oganisms found in an acid mine drainage community - <a rel=\"nofollow\" href=\"http://compbio.iupui.edu/afp/2008/node/47\" title=\"http://compbio.iupui.edu/afp/2008/node/47\">http://compbio.iupui.edu/afp...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/00f61fa4/steve-brenner-talked-about-state-of-functional", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T17:55:27Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Jason Stajich", "id" : "stajich", "type" : "user" }, "date" : "2008-07-21T03:48:40Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T02:50:23Z" } ] }
{ "_id" : "e/012deb4aabf3481e8d777533874b7acc", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Based on the meetup at ISMB.  Greg suggests a set of standards that could be used to determine whether a piece of research is open, and the use of a badge to indicate when it is.", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/012deb4aabf3481e8d777533874b7acc/c/4c7398c7a90b4251810c608a18471bd0", "date" : "2008-07-20T01:29:03Z" }, { "body" : "It'd be interesting to convene a group of open scientists and people from the journals to talk about this, and perhaps come to some preliminary agreement. Imagine if, e.g., Nature authors had the option to say at the end of their paper &quot;This paper meets the standards of the Open Science Initiative for reproducibility and disclosure.&quot;", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/012deb4aabf3481e8d777533874b7acc/c/56992a7846c94e479b38995d26fcbaf0", "date" : "2008-07-20T01:29:24Z" } ], "body" : "Greg Wilson: &quot;This research is certified open&quot; - <a rel=\"nofollow\" href=\"http://pyre.third-bit.com/blog/archives/1677.html\" title=\"http://pyre.third-bit.com/blog/archives/1677.html\">http://pyre.third-bit.com/blog...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/012deb4a/greg-wilson-this-research-is-certified-open", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T01:28:05Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "date" : "2008-07-20T04:44:30Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T04:22:23Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-20T03:29:29Z" }, { "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "date" : "2008-07-20T03:21:19Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-20T03:08:24Z" } ] }
{ "_id" : "e/01cef01ba06b4263bda26ad0704c378f", "feed_id" : "ismb-2008", "comments" : [ { "body" : "if anyone can pick a mystery giveaway for me I'd appreciate. Dinner is on me.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/01cef01ba06b4263bda26ad0704c378f/c/d175032badc745d7bc2f74c3b64f8348", "date" : "2008-07-10T02:01:36Z" } ], "body" : "BioMed Central Blog : BioMed Central - on location at ISMB - <a rel=\"nofollow\" href=\"http://blogs.openaccesscentral.com/blogs/bmcblog/entry/biomed_central_on_location_at\" title=\"http://blogs.openaccesscentral.com/blogs/bmcblog/entry/biomed_central_on_location_at\">http://blogs.openaccesscentral.com/blogs...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "url" : "http://friendfeed.com/ismb-2008/01cef01b/biomed-central-blog-on-location-at-ismb", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-10T01:37:51Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-10T02:12:55Z" }, { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-10T01:49:05Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-10T01:42:41Z" } ] }
{ "_id" : "e/02110ba3fc1741a196ceee114c8adaf7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Reinhard Schneider approached me if I was interested in organizing a hackathon at next year's ISMB. I couldn't say for sure that I'd come next year, but I told him that there was community interest for some sort of Open Science hackathon. I think this would be an interesting thing to put together. We should discuss this at Tuesday's BOF meeting, but I just wanted to put this here to get you thinking about it.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/02110ba3fc1741a196ceee114c8adaf7/c/da176de62bcd4af7bf39feb27de24184", "date" : "2008-07-21T14:41:23Z" } ], "body" : "Hackathon at ISMB 2009", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/02110ba3/hackathon-at-ismb-2009", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T14:35:07Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "date" : "2008-10-20T13:11:48Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T15:44:41Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T15:00:15Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-21T14:43:39Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T14:36:01Z" } ] }
{ "_id" : "e/021d7bf33472447ba72dc4e26df53fb0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "&quot;ISCB is looking for a few aspiring reporters, who also happen to be attending ISMB 2008 in Toronto. (...)This year we are also seeking a select corps of students and Jr. Scientists to take on the role of writing about the vast scientific content of the conference and the personal experience of participating in this large, international bioinformatics event. Submissions will be reviewed for posting to the ISMB website, and will be considered for publication in the designated ISCB pages of PLoS Computational Biology, the Society's official journal, as a single author report or as part of a larger report compiled from the contributions of multiple authors.&quot;", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/3b1e28d630e44dfaa886482e835d222f", "date" : "2008-07-15T20:59:37Z" }, { "body" : "Hmm, shouldn't we (the ususal suspects) grab the bull by horns and write a decent conference report, compiled from multiple sources?", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/8ab44115e2b34663b8172deab6c6fa5a", "date" : "2008-07-16T08:09:35Z" }, { "body" : "I'm up for some reporting, once my brain has adjusted :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/d1b53f121f01462680dacc583d511ab7", "date" : "2008-07-17T18:45:44Z" }, { "body" : "folks: another one of those: spent a lot of energy in vain hoping to get something similar to what you guys pulled off: totally impressed!!! Thanks. write it up, we'll put it onto our journal pages if we'd find it ok. other than that: we'll like a blog at a central place in stockholm and will link to this one as soon as steven leard is back from his deserved break. burkhard", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/ddf12138703e4f5c8ec37b410c9db114", "date" : "2008-07-27T01:40:03Z" }, { "body" : "Hi Burkhard , I am glad you find this experiment interesting. It ended up being a useful way not only to gather notes about the conference but to set up events on the fly. It would be great to have something like this set up from the beginning at the next ISMB.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/54e400c5b1d84952a5776409d9488848", "date" : "2008-07-27T01:53:50Z" }, { "body" : "Just add my voice to the fact that I think this was really impressive grass roots reporting. I felt like I was actually at two meetings at the same time, one where I was physically present, and one where I was just a fly on the wall. Great example of what can be done (with enough people and the right tools)", "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/f7dbee5b85384a19b98691396afd5cc9", "date" : "2008-07-27T09:50:35Z" }, { "body" : "again: have tried to find you guys before; now that i found you i will do whatever i can to support this for future ISMBs; let me give you another impression: i saw the blog for the first time during the wed morning keynote, after the keynote i stood up and thanked Lars &amp; Neil (those were the ones i had seen in the 20 secs i spent on this); at least 30 people walked up to me after that announcement and asked how to get at that blog!", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/ebb43d8e2a8844099825b38d88dbf0a7", "date" : "2008-07-28T16:25:17Z" }, { "body" : "Thanks Burkhard! I think that it would be a great idea to improve the visibility of the live blogging from the official ISMB web site. However, it is also important that we don't try to formalize it too much as this would likely kill a grassroot effort like this. I find that FriendFeed worked remarkably well (much better than my personal attempts on Tumblr), so I suggest that we try to stick to that but somehow tie it in with the ISMB web site.", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/56bc7dd2860840b7a3c6c2874f68ca9e", "date" : "2008-08-02T06:27:16Z" }, { "body" : "One possibility would be to set up an ISMB2009 room ahead of the conference and prefill it with one thread per presentation. These can then be used to comment on each talk. By making them ahead of time, we could link to the thread in an iframe on an official ISMB page with the speakers abstract. This would allow people to work in an almost unchanged manner, yet it would structure the comments slightly better and hook it up with the official web site.", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/0dbf9c0cd34346d1976f5dcfb5bc58af", "date" : "2008-08-02T06:31:56Z" }, { "body" : "Another wild idea: virtual poster sessions. Could we somehow get people to upload a high-resolution bitmap of their poster? These could then again be linked with a FriendFeed thread to allow commenting. Perhaps the posters could even go on Flickr and be fed directly into FriendFeed?", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/7856fa0d85aa47b18f255ae71e1ba46a", "date" : "2008-08-02T06:35:40Z" }, { "body" : "Roland &amp; Neil, I'm also up for helping out on writing a conference report. Burkhard, where would the conference report be published - in PLoS Comp Biol or Bioinformatics?", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/a61430316aec47658e356cd493e553a0", "date" : "2008-08-02T06:41:19Z" }, { "body" : "Lars, we are in touch with BJ Morrison. There is a Googledoc with 5 minutes worth of scribbles by me but I wonder whether a fresh start - or sketch - wouldn't be advantageous. 2000 - 5000 words, I guess, the rest is up to us. Oh and yes, PLoS Comp Bio.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/29d091d70dc946f4ac9dc134e206d6f6", "date" : "2008-08-02T08:59:59Z" }, { "body" : "Roland, excellent - can you email me an invitation to join the Googledoc? I can try to take a look at it later today.", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/0a43e73d7060446888fa2eaa6782b68a", "date" : "2008-08-02T09:15:36Z" }, { "body" : "Hi Burkhard - I've been on the road since ISMB, just got back to this conversation.  I'm glad you found the FriendFeed coverage valuable and I think we're all looking forward to contributing again at future ISMBs.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/76b7cfc6bd14440087698229e93ca420", "date" : "2008-08-03T13:09:06Z" }, { "body" : "neil: you did not see this because you had obviously left already; i saw your feed first on wed. morning; i stepped up after hannah's talk and announced it and was bombarded by questions: 'how to find that' for the rest of the day, literally at least 20 people approached me. Will anybody write for journals?", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/021d7bf33472447ba72dc4e26df53fb0/c/653c195e83d447078d623458060d6ad4", "date" : "2008-08-06T01:52:07Z" } ], "body" : "ISMB News - <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/ismbnews.php\" title=\"http://www.iscb.org/ismb2008/ismbnews.php\">http://www.iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "url" : "http://friendfeed.com/ismb-2008/021d7bf3/ismb-news", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-15T20:59:37Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-08-02T06:56:52Z" }, { "from" : { "name" : "Pawel Szczesny", "id" : "freesci", "type" : "user" }, "date" : "2008-07-28T16:28:20Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-22T18:24:16Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-16T13:10:31Z" } ] }
{ "_id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9", "feed_id" : "ismb-2008", "comments" : [ { "body" : "you are too fast you know !", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/f5ce8f43906045e3b1fbee5d912a0143", "date" : "2008-07-22T13:02:48Z" }, { "body" : "challenge w/ breast cancer: heterogenous disease linked to different clinical outcomes; lack of relaible prognostic markers", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/5103ee22dfa94dae9c240c86c7de06b1", "date" : "2008-07-22T13:07:26Z" }, { "body" : "there exist already a few assays (estrogen receptor status, Her2 amplification, ...) that given hints ofr treatment. However, 30% of lymph node negative patients develop aggressive disease within 5 yrs", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/11c5bba89c6d4996a92bb1ec4f51e9ba", "date" : "2008-07-22T13:08:51Z" }, { "body" : "Breast cancer heterogeneous, complex; difficult to customise individual treatments", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/01ef265f80a44c9295f113c1535f205a", "date" : "2008-07-22T13:10:09Z" }, { "body" : "gene expression profiling to identify subtypes (2004)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/1eebdedef235420d95dfb8a53952b832", "date" : "2008-07-22T13:11:22Z" }, { "body" : "Gene expression profiling of tumors identifies molecular subtypes; these arise from transformation of different cell types", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/0161da97bead40dba3b0ea0528e21ceb", "date" : "2008-07-22T13:11:34Z" }, { "body" : "some patients with negative ER and Her2 state, so they can't be diagnosed well --&gt; worst outcome (basal type, thought to derive from a stem-cell lineage). Studies were done on whole tissue.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/52adc15488e14c98a4c6d68126676564", "date" : "2008-07-22T13:12:55Z" }, { "body" : "mammary ducts contain stem cells and epithelial cells, breast cancer derives from these cells", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/15b8a145bf8c47eeb2bd9e0b480884e1", "date" : "2008-07-22T13:14:03Z" }, { "body" : "Molecular understanding has led to practical, clinical outcomes; however, use of whole tumor tissue lacks sensitivity -&gt; so, look at microenvironment", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/77655735151544f6a428e9d144be04b1", "date" : "2008-07-22T13:17:04Z" }, { "body" : "should really look at different cell types in tumor separately: tumor cells need to recruit blood vessels etc. Could target cells around the tumor (e.g. blood vessel formation).", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/02e186f1438c4aff927c9a19f44941a5", "date" : "2008-07-22T13:17:32Z" }, { "body" : "Laser capture microdissection - can isolate individual cell types", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/f40b9d3dbb094182ad36c6bb0417fb99", "date" : "2008-07-22T13:18:42Z" }, { "body" : "&quot;laser capture micro dissection&quot; to remove wanted cell types. Have different stages of the disease right next to each other (hyperplastic stage, invasive ductal carcinoma - the earlier stage of the disease, normal tissue)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/67284b622bd341fda89ca032a41d8b40", "date" : "2008-07-22T13:19:47Z" }, { "body" : "need to use linear amplification to get enough DNA, this leads to 3' bias. so, need to use probes that are closer to the 3' end. need to learn which probes to discard as they give only noise anyway", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/a09f6936d3734684b6a9183871d4452d", "date" : "2008-07-22T13:22:15Z" }, { "body" : "across &gt;50 patients, cell types cluster together with blocks of differentially expressed genes", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/cd908d1061ef42ef872fb5ba9f924c36", "date" : "2008-07-22T13:22:57Z" }, { "body" : "Can now see distinct gene expression profiles for tumor, normal stroma, normal epithelium", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/885a540cb9714656a8b37c981181451a", "date" : "2008-07-22T13:23:34Z" }, { "body" : "Class discovery:  subtypes of tumor-associated stroma", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/561937b96a1e4d6ba4b8efc8a81ff5ef", "date" : "2008-07-22T13:25:24Z" }, { "body" : "tumor stroma identifies more subtypes (five or six different subtypes) of patients", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/1e9a3c3ea3424d4ebc5057c7af21193f", "date" : "2008-07-22T13:25:47Z" }, { "body" : "there is little overlap i nthe overexpressed genes between the different stroma subtypes", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/60010c8287a340c4bd7b5cf400fff4df", "date" : "2008-07-22T13:28:12Z" }, { "body" : "Take-home message seems to be that cell subtype, as identified by expression profiles, does correlate to clinical differences", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/94ad8350f85645ee991218074b31b699", "date" : "2008-07-22T13:30:14Z" }, { "body" : "stroma subtypes are associated with different clinical outcomes", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/8b04b6ac15074b9083560d32123785e8", "date" : "2008-07-22T13:30:34Z" }, { "body" : "Able to identify same signature via meta-analysis (had been obscured by heterogeneity / epithelial mixture etc)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/d657bcba2d1f4dd1a6d80fd3f19e423a", "date" : "2008-07-22T13:31:04Z" }, { "body" : "53 breast cancer tumors (stroma) able to correlate clusters from expression with clinical outcome (rather clustering by other factors such as ER status as with whole tissue).", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/f1f34ca96c6241c7b3c95c05909bcc80", "date" : "2008-07-22T13:32:57Z" }, { "body" : "Clinical outcomes relate to different pathways", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/3fdd199283944afba57829764f55078c", "date" : "2008-07-22T13:33:25Z" }, { "body" : "poor outcome -hypoxic and angiogenic characterization in signature", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/2b3543e3901a4332b07f5d7b2ed8d619", "date" : "2008-07-22T13:33:34Z" }, { "body" : "good outcome: express genes associated with immunosuppression. poor outcome: express genes realted to angiogenensis, hypoxia, type II macrophage markers. she speculates that these changes reflect the recruitment of new cell types to the cancer", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/5eeb716e0bad47fba1e3f6c823cfe02c", "date" : "2008-07-22T13:34:19Z" }, { "body" : "Key reference: 2008 Nature Medicine (<a rel=\"nofollow\" href=\"http://www.nature.com/nm/journal/v14/n5/abs/nm1764.html\" title=\"http://www.nature.com/nm/journal/v14/n5/abs/nm1764.html\">http://www.nature.com/nm...</a>) which highlights development of new stroma-derived prognostic predictor she describes in talk", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/ae5170f6bdbf4109aaca24d44494589a", "date" : "2008-07-22T13:34:56Z" }, { "body" : "Moving now to stroma-derived predictor of prognosis (SDPP)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/f7efbe174aaa42cbbcb66a2ccfa6c7de", "date" : "2008-07-22T13:36:03Z" }, { "body" : "Very cool point re loss of frizzled and implication re loss of inhibitor of WNT", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/8edd2f1a3b2f48469023e2e6bf415f6d", "date" : "2008-07-22T13:36:39Z" }, { "body" : "Experimental validation - immunohistochemistry, RT-PCR", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/6a5d70f770cb4a879042983fa410117f", "date" : "2008-07-22T13:37:59Z" }, { "body" : "SDPP works well and is provides new evidence in comparison with previous predictors", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/8e082a69c1d84021afda938bb7ee243e", "date" : "2008-07-22T13:44:28Z" }, { "body" : "integration of epithelial and stromal subtypes, not all combinations do occur", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/b20914f9cca74785be7e52bcb36159e9", "date" : "2008-07-22T13:45:27Z" }, { "body" : "different stroma/epithelial  combinations go along with different otucomes (with lots of variation, though)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/15a94c80c7ba425299b3bb798085c6b5", "date" : "2008-07-22T13:46:20Z" }, { "body" : "Key of identifying appropriate entities for cross-talk. From this, we can ask questions like How does basal cell type in epithelial define stromal subtype? These represent some of the open challenges in this area", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/119a29bd928e4b62b33210321b11c225", "date" : "2008-07-22T13:49:08Z" }, { "body" : "computational tools to allow identification of best way to utilize available mouse models - also to allow design of needed mouse models", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/04150591adf34e16a6ed7fbeaf7d5ac9/c/e51c4b8a8978432a9b7ff0be245f1b22", "date" : "2008-07-22T13:50:46Z" } ], "body" : "Keynote 5:  Morag Park - &quot;profiling the breast tumor microenvironment&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/04150591/keynote-5-morag-park-profiling-breast-tumor", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T13:00:25Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "date" : "2008-07-22T23:54:46Z" } ] }
{ "_id" : "e/096c4250050c466b8c0cb96953d4cc68", "feed_id" : "ismb-2008", "comments" : [ { "body" : "What I heard is that the number of paper submissions was down by 30%.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/7bc0909971b148f3bad7c7627946e36c", "date" : "2008-07-20T14:46:25Z" }, { "body" : "can anyone tell me why the espresso machine at the convention center breaks down every moment precisely when i need it most?", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/0fdd87f22fb9495ca0dd603144ece8b5", "date" : "2008-07-20T14:52:30Z" }, { "body" : "Paulo: So is the amount of free t-shirts. Conincidence ? ;)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/dd2b116ba19f47c985740b514cfd5672", "date" : "2008-07-20T14:56:02Z" }, { "body" : "we paid $435/head for food and coffee, the conference center+AV+MCC related costs amounted to another about $180/head. you do the math how much of your money went into food. totally with you on your surprise, but it is actually the same for most places in the world we went to; some were much worse than toronto, others much better (e.g. vienna).  - espresso machine: another one of those things: i for one need good espresso: you guys have no clue what the MCC would have charged for 'second cup' quality ..", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/40345d71cb394941aa46435c107c76f6", "date" : "2008-07-27T01:37:44Z" }, { "body" : "In Detroit there was no included food and in some days there was almost no place close to the GM Centre with good food (if you call Detroit's greektown a place that you can get decent food ...) and the registration price was adequate. Why include food in the registration when some people cannot afford it? Like me, unsupported post-doc living in Toronto. No way I am shelling 775 (700 reg + annual fee) plus whatever the BOSC costed and eat moderately bad food.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/5aad0041ae174b18957cca715e2a4659", "date" : "2008-07-27T02:06:51Z" }, { "body" : "The ISMB is a community effort and the organizers thereby responsible to the community to organize a financially viable meeting. I am glad that Burkhard is as bold as to discuss this issues in public. Organizing a conference is a multi-optimization problem that should have higher weights on scientific content, adequate conference rooms and WLAN (in that order) than food quality, which were met at this years' ISMB for sure.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/9925bd44968949edb66ad0191f86a8cf", "date" : "2008-07-27T12:36:20Z" }, { "body" : "Some conferences do not provide lunch at all (e.g. the genetics congress in Berlin in July), but for Stockholm, this is probably not an option (fair ground).", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/cea3cabfdc5242bd9be546c4f27ee3f1", "date" : "2008-07-27T12:42:57Z" }, { "body" : "IMO, good conferences do make a profit, always tough for scientific ones.  But the logistics and experience better be worth it then.", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/9c4b0b80e11f4ded92120615b0cd064d", "date" : "2008-07-27T18:46:08Z" }, { "body" : "no lunch is what i have been proposing since years; will become stronger on this! for Stockholm: too late (and yes too difficult); for Boston 2010: we already signed the contract including food, however, we will try our best to get out of it; for 2011 in vienna: difficult - upside: that's perceived as &quot;good food&quot;", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/a764bc3acfc04b85ab4ebb2375b3ba8e", "date" : "2008-07-28T16:19:18Z" }, { "body" : "profit: half of the ISCB annual budget originates from the ISMB profit, we need $180K from ISMB to survive; we now run ISMB at an incredibly ambitious low budget saving wherever we can, this is one reason why Toronto will create high profit/participant - mostly due to the fact that we cut on organizing costs. still the major issue remains that we pay for the facilities that could welcome 1000 more participants and with every new participant we would profit more. put differently: we have to grow or to shrink", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/b7b04f3664b54f4d8f1fc548d5fb86da", "date" : "2008-07-28T16:22:47Z" }, { "body" : "Was that &quot;paper submissions down by 30%&quot; true? $550 - 900 per person. 1000 attendee. Let's say... 30% on foods: $300 X 1000 = $300,000 for lunch and matrix party. Foods must be delivered to the wrong place.", "from" : { "name" : "Kuan-Ting Lin", "id" : "woodydon", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/02f1a7b925494289bb6643e3178f59f5", "date" : "2008-08-04T07:53:58Z" }, { "body" : "see our paper in PLoS CB on ISMB 2008 about numbers, although the following may not be in there: vienna proceedings submission=492, toronto: 292; ok; NOW please realize that this has absolutely NOTHING to do with costs! One issue: we had over 180 talks at ISMB 2008; 48 were from proceedings=less than 1/3. now the money: food/head was over $400 NOT 30%!!! there were over 1400 participants and the food was way more than 2* your estimate; matrix party was cheap! food &amp; rent for Liberty Grand was a lot.", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/675e528204114b43955b10af5fe6fd6e", "date" : "2008-08-06T01:50:07Z" }, { "body" : "Hey folks, ISCB almost died from less profitable meetings in Brazil and Australia...give Burkhard a break. I like his openness. Yes, the food could have been better (the box lunches at the Member's meeting during lunchtime were really good!), but I didn't see enough affordable restaurants on Front Street or near the CN Tower to handle us all. I do agree that when possible, letting us fend for ourselves is a better option. Sounds like that not possible in Stockholm, definitely possible at the Hynes in Boston.", "from" : { "name" : "John Greene", "id" : "jmgreene", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/666daf94bcbc4ec5808e56e0abb9830d", "date" : "2008-08-09T04:02:41Z" }, { "body" : "In Vienna (that is if it is again at the Vienna International Center) it is not that easy to get to food. I mean there is nothing in the immediate vicinity. Additionally as Burkhard already mentioned the food there was actually quite fine. Anyway, i appreciate the openness of the discussion here.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/096c4250050c466b8c0cb96953d4cc68/c/556b1f63a53c430d84a5ba343d917ef8", "date" : "2008-08-11T14:29:48Z" } ], "body" : "ISMB 2008 = highest profit/participant, as mentioned proudly by the chairman. He assures it's not because of the food, that they are actually spending quite a bit on the food. Maybe it's being delivered to the wrong place.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/096c4250/ismb-2008-highest-profit-participant-as", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T14:34:20Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Kuan-Ting Lin", "id" : "woodydon", "type" : "user" }, "date" : "2008-08-04T07:50:58Z" }, { "from" : { "name" : "Antonis", "id" : "antonis47", "type" : "user" }, "date" : "2008-07-28T16:04:48Z" }, { "from" : { "name" : "Jason Stajich", "id" : "stajich", "type" : "user" }, "date" : "2008-07-21T03:47:13Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-20T14:52:12Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-20T14:52:08Z" }, { "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "date" : "2008-07-20T14:51:04Z" } ] }
{ "_id" : "e/0eb92f6c80b5430b94e3e85b4e483955", "feed_id" : "ismb-2008", "comments" : [ { "body" : "and not at all expensive they say, oh no", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/db8cdcbece6b4b61b8da84914951aeb7", "date" : "2008-07-21T13:03:49Z" }, { "body" : "Yeah, not sure whether that went as intended.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/e4863b39caf248adaebb84b4d61925d7", "date" : "2008-07-21T13:04:36Z" }, { "body" : "Stockholm? Cool - almost bike-driving distance ;)", "from" : { "name" : "Pawel Szczesny", "id" : "freesci", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/4fa3ecd4d0274c9fa4c844218c8448b2", "date" : "2008-07-21T13:05:57Z" }, { "body" : "Well, if you don't need anything to eat or - God forbid it - a beer to drink then Stockholm is not that expensive ;-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/c534736b479c4355a9956af849d8bcda", "date" : "2008-07-21T13:08:30Z" }, { "body" : "Cool, that saves about 2500 dollar :)", "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/b981479a3e854feab08a0d2d2959cfdc", "date" : "2008-07-21T13:08:37Z" }, { "body" : "Fine with me, I will start my M.Sc. study this fall in Sweden ;-)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/0eb92f6c80b5430b94e3e85b4e483955/c/7776a8234c4346bca8a35de38a76ae86", "date" : "2008-07-21T13:36:43Z" } ], "body" : "Stockholm next year - &quot;trendy&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/0eb92f6c/stockholm-next-year-trendy", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T13:01:57Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-21T13:36:21Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T13:03:30Z" } ] }
{ "_id" : "e/0ed08e2255da40878c725b4af877dcbe", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Seems to be more preview than review?  Anyway, useful for us so we can avoid too much similarity in our report.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/0ed08e2255da40878c725b4af877dcbe/c/c0c6e59ff3924ad8a38fa370392ea675", "date" : "2008-08-06T07:45:58Z" }, { "body" : "Aye.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/0ed08e2255da40878c725b4af877dcbe/c/c5fd3f5dd1a94702873148c9db3a95d8", "date" : "2008-08-06T10:44:24Z" }, { "body" : "note the date: was written BEFORE ISMB, i for one am not good enough to devine &quot;reviews&quot; - we invite you guys to write reports about the meeting and send them to BJ to coordinate where they will go", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/0ed08e2255da40878c725b4af877dcbe/c/0ea46f232e79451b9ad10908728d16a9", "date" : "2008-08-08T14:36:34Z" } ], "body" : "ISMB 2008 report by the organizers (PLoS Computational Biology) - <a rel=\"nofollow\" href=\"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000094\" title=\"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000094\">http://www.ploscompbiol.org/article...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/0ed08e22/ismb-2008-report-by-organizers-plos", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-08-06T07:37:54Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-08-06T07:45:14Z" } ] }
{ "_id" : "e/0fecf37a5a9145e6b3986ad0ca3344e0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Not sure if this is my thing, but have to do one ontology talk :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/0fecf37a5a9145e6b3986ad0ca3344e0/c/a309857042c2457eacc5417f71141f8c", "date" : "2008-07-21T16:19:57Z" }, { "body" : "How to describe variation from a canonical ideal in qualitative ways; focus is on biomedical images", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/0fecf37a5a9145e6b3986ad0ca3344e0/c/e04a547bf93a407dac11eb558c0f897e", "date" : "2008-07-21T16:20:38Z" }, { "body" : "No, this is not my thing.  Going to take a break.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/0fecf37a5a9145e6b3986ad0ca3344e0/c/1b78791541b04f82b54a9ea78d012c19", "date" : "2008-07-21T16:23:53Z" } ], "body" : "HL23:  qualitative biological ontologies", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/0fecf37a/hl23-qualitative-biological-ontologies", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T16:19:21Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/14977abc5b86429ca23e943d878a63e3", "feed_id" : "ismb-2008", "comments" : [ { "body" : "SLIF pipeline:  processes pairs of captions and figures", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/35648174e93646338a2fc10bdf9a73db", "date" : "2008-07-21T14:49:32Z" }, { "body" : "Image processing:  (1), locate panel boundaries; (2), detect text annotation; (3), classify each panel image (is it micrograph?); (4), find scale bars", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/4359f63861d94d2b895f4bbd9662cc41", "date" : "2008-07-21T14:55:44Z" }, { "body" : "Next, process text in captions and relate to image", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/712dd48136974a7bb0e420e551a79184", "date" : "2008-07-21T14:56:01Z" }, { "body" : "SLIF used to spider PM Central; also uses a 15000 article PNAS corpus", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/1aacf7008e6644a39be83d265698bb67", "date" : "2008-07-21T14:56:46Z" }, { "body" : "Web interface allows search of the processed figures", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/207fca241f8940288b44c03ded762854", "date" : "2008-07-21T14:58:07Z" }, { "body" : "Of course, all this could be avoided using structured data/metadata", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/d5249d9dde9b469fbf3ed8cb1e8ffc3c", "date" : "2008-07-21T15:00:00Z" }, { "body" : "Having done all of this processing, I wonder why people don't then provide structured data rather than providing just a basic search interface?  Ah - they do, kind of; will return XML via SOAP.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/68e757dd5c0e40039181587b6f321d72", "date" : "2008-07-21T15:02:48Z" }, { "body" : "SLIF URL:  <a rel=\"nofollow\" href=\"http://murphylab.web.cmu.edu/services/SLIF/\" title=\"http://murphylab.web.cmu.edu/services/SLIF/\">http://murphylab.web.cmu.edu/service...</a>", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/e481d33b524c4e87a8f9ceb6854cde8a", "date" : "2008-07-21T15:04:44Z" }, { "body" : "Can use URL params (e.g. pixel size); also a SOAP service", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/cafbaa48e2e84a1289afc6be01fe9955", "date" : "2008-07-21T15:08:21Z" }, { "body" : "Aiming for full semantic representation of journal figures/captions (topic modelling)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/3aba27cb456041a8a49291030fdc946a", "date" : "2008-07-21T15:11:26Z" }, { "body" : "Not a bad talk, actually.  Time to run to another room.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/14977abc5b86429ca23e943d878a63e3/c/bf6744ddfe3d4b4c93e6cb1701c67787", "date" : "2008-07-21T15:11:53Z" } ], "body" : "TT09:  subcellular localisation from journal images + text", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/14977abc/tt09-subcellular-localisation-from-journal", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T14:46:34Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/1781f64132a046458a06246763d2d175", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Hmm, won't just one day be better to concentrate attendance and attention? Guess later is better to think more about it, earlier is better to have an impact on this conference.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1781f64132a046458a06246763d2d175/c/795b2dd7df3b437281ee2556b02d075b", "date" : "2008-07-20T20:50:17Z" }, { "body" : "I was thinking that it would be nice to have a place to gather for lunch and socialize both days, but given that it may force people to eat lunch here, maybe that's not attractive to most people...", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/1781f64132a046458a06246763d2d175/c/f40ff6f103014a9aa1ba8e0926882a6c", "date" : "2008-07-20T20:52:33Z" } ], "body" : "&quot;Science blogging and Web 2.0&quot; Birds of a Feather session submitted - for both Monday and Tuesday, not sure if they'll approve in time for Monday but we'll see.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/1781f641/science-blogging-and-web-2-0-birds-of-feather", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T20:46:59Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-21T12:21:37Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T00:40:06Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-20T20:52:45Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-20T20:49:21Z" } ] }
{ "_id" : "e/19484acbbf1d425f84de5c0189e908db", "feed_id" : "ismb-2008", "body" : "Ontology of Biomedical Investigations (OBI) general factsheet - <a rel=\"nofollow\" href=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/OBI_ISMB_Handout.doc\" title=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/OBI_ISMB_Handout.doc\">http://obi.svn.sourceforge.net/svnroot...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/19484acb/ontology-of-biomedical-investigations-obi", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T13:29:09Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-21T13:45:42Z" } ] }
{ "_id" : "e/1a4a089377e247a49f9e6bfd21919a99", "feed_id" : "ismb-2008", "comments" : [ { "body" : "why is there no equivalent to BLAST for small molecules? is there a fundamental difference between small molecule similarity and sequence similarity? (PB think that seq. alignment even works for non-evolved seq., I tend to disagree --&gt; site-directed mutagenesis!)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/99584257b45a4ae8983326b6e0a24b11", "date" : "2008-07-22T19:51:23Z" }, { "body" : "It's a good question.  I guess small molecules are defined by structure, rather than linear chains of letters.  They should still be searchable though.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/c3183187e3824151afa626142c226c9d", "date" : "2008-07-22T19:53:49Z" }, { "body" : "reviews fingerprint method; standard approach: Tanimoto", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/4a747125323d4ce1bdfab070c22f95f0", "date" : "2008-07-22T19:53:57Z" }, { "body" : "can come up with different chance models for fingerprint matches", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/78ed3b3e28ba4ea99c879af2a246b65f", "date" : "2008-07-22T19:56:44Z" }, { "body" : "Given the diversity in tautomers, conformers, the variety in R-groups, etc, it's a different problem, IMO", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/1e1271ee8d9c43768c52b7c80800fd22", "date" : "2008-07-22T20:03:41Z" }, { "body" : "[Huh, can't liveblog if the battery is empty]", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/654f12c5d73d4566b272c7e060f51945", "date" : "2008-07-22T20:38:27Z" }, { "body" : "based on the ratio between two Gaussian distributions (one for the union and one for the intersection), can get p-values / Z-scores / e-values for a particular database", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/91dbbca682a04b30ae3880e9e89c805b", "date" : "2008-07-22T20:39:32Z" }, { "body" : "evaluation: 55 known estrogen receptor binders x 100,000 random (presumably negative) compounds from ChemDB do leave-one-out tests on probability to get a false positive. Can fine-tune this to fingerprint size.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/d816985e4b7146099fb2b0ce8fdffafe", "date" : "2008-07-22T20:40:53Z" }, { "body" : "[Editorial remark: I think this is very important work. However, I'm skeptical that it is a good idea to use biased chemical libraries for such analyses. For sequence BLAST, your standard is the genome which is under evolutionary pressure. Chemical libraries are not under such pressures, and therefore you can get &quot;significant&quot; hits in your database that are due to uneven sampling of the chemical space. On the importance of library composition, see Martin et al. Do structurally similar molecules have similar biological activity?. J Med Chem (2002) vol. 45 (19) pp. 4350-4358", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/8a3c9c7834d242df8c2edec5d3e93c3d", "date" : "2008-07-22T20:45:19Z" }, { "body" : "Blast is acting on only a 1D string... There are many, *many* ways to define the similarity between molecules (see a review I wrote <a rel=\"nofollow\" href=\"http://dx.doi.org/10.1080/10408340600969601\" title=\"http://dx.doi.org/10.1080/10408340600969601\">http://dx.doi.org/10...</a>, but much more literature around). There is so much more complexity in small molecules than a amino acid sequence. Think if it as loop modeling for protein, but then without the luck of pinpointing the loop start and end to some homology modeled tertiary structure.", "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/70ab5fe44944429dac4a99f3b2a1a893", "date" : "2008-07-23T06:53:24Z" }, { "body" : "Still, sounds an interesting read. Did Baldi mention a paper, maybe?", "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/c855f88f87a4494ca5098bda61965f0b", "date" : "2008-07-23T06:55:17Z" }, { "body" : "yes, this is in the ISMB proceedings: <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/18586735\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/18586735\">http://www.ncbi.nlm.nih.gov/pubmed...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/cb045ef5a3b240f584a2bd0ee2d7e768", "date" : "2008-07-23T11:44:49Z" }, { "body" : "Michael, thanx!", "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "id" : "e/1a4a089377e247a49f9e6bfd21919a99/c/59f007af5593467cb4e766fe2516f52d", "date" : "2008-07-23T12:26:02Z" } ], "body" : "PT47: BLASTing Small Molecules - Statistics and Extreme Statistics of Chemical Similarity Scores. Pierre Baldi", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/1a4a0893/pt47-blasting-small-molecules-statistics-and", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T19:51:11Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-22T20:03:43Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-22T19:51:49Z" } ] }
{ "_id" : "e/1c8e6c33391840999b054b8c1a2bb9ab", "feed_id" : "ismb-2008", "comments" : [ { "body" : "aside: scatter density plot is a nice way to show a dense scatterplot", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "id" : "e/1c8e6c33391840999b054b8c1a2bb9ab/c/9e842b8eb8044ed080d3d3faa1ab3f03", "date" : "2008-07-23T16:05:31Z" }, { "body" : "I remember this guy from a blog post on SVMs at Flags and Lollipops", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/1c8e6c33391840999b054b8c1a2bb9ab/c/149d3a3e2976449a87ebfb686041e0a7", "date" : "2008-07-23T16:29:14Z" }, { "body" : "Noble is probably the most important advocates of SVMs in bioinformatics. The middle initial stands for SVM I think (in times like this)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/1c8e6c33391840999b054b8c1a2bb9ab/c/be5e0b44f3174223933d24ed8f1ec2d3", "date" : "2008-07-23T16:41:18Z" } ], "body" : "Nucleosome Positioning Signals in Yeast and Human Genomic DNA. - William S Noble", "feed_name" : "ISMB 2008", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/1c8e6c33/nucleosome-positioning-signals-in-yeast-and", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T16:04:27Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-23T19:22:53Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-23T17:25:10Z" } ] }
{ "_id" : "e/1e27f723910f490aab462322178c5114", "feed_id" : "ismb-2008", "comments" : [ { "body" : "If the weather is fine, I'd like to take a break after the keynote and go kayaking in the harbor in the direction of the islands... if someone else is interested, tell me. :)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1e27f723910f490aab462322178c5114/c/16e0dfa50c2447db9dab977069798048", "date" : "2008-07-20T20:55:43Z" }, { "body" : "I was planning to do that, not sure about the time though", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/1e27f723910f490aab462322178c5114/c/f58a18096e72477ba8cbb5f0864b70fb", "date" : "2008-07-20T21:11:21Z" }, { "body" : "The other possibility is of course Wednesday afternoon. I didn't find so many talks for Tue morning, but these are just my interests.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1e27f723910f490aab462322178c5114/c/660969817a3c4e858533c8a2c038a76c", "date" : "2008-07-20T21:29:40Z" }, { "body" : "If you want to come along: meet Tuesday at 10 am at the MTCC south exit (just above the ISMB registration desk). The kayak rental place is less than 500 m away.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/1e27f723910f490aab462322178c5114/c/7bea26d24b4e4c48b38bc07bc3c4f301", "date" : "2008-07-21T20:42:16Z" } ], "body" : "OT: Kayaking on Tuesday morning? - <a rel=\"nofollow\" href=\"http://www.paddletoronto.com/\">http://www.paddletoronto.com/</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/1e27f723/ot-kayaking-on-tuesday-morning", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T20:54:39Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/24d78690257849869b6f6dd3289378ec", "feed_id" : "ismb-2008", "comments" : [ { "body" : "nice", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/24d78690257849869b6f6dd3289378ec/c/ed5e4a95d8d34494a25539f708e1fa43", "date" : "2008-07-22T15:12:44Z" }, { "body" : "session chair rushed in. looks like he was at the SS05 session with everyone else", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/24d78690257849869b6f6dd3289378ec/c/35b59431aa3b4910b3a9c4af2da940cc", "date" : "2008-07-22T15:18:47Z" } ], "body" : "HL33: Session Chair MIA - if anyone sees Yanay Ofran they may want to point him to the session. The speaker, Giorgio Favrin took it in stride and went forward with his talk.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/24d78690/hl33-session-chair-mia-if-anyone-sees-yanay", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T15:02:06Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/27358b13946f4f57bf596017a4111cf8", "feed_id" : "ismb-2008", "body" : "PT 16: Protein Complex Identification by Supervisd Graph Local Clustering was cancelled at very short notice. No need to make the journey to 801 A.", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/27358b13/pt-16-protein-complex-identification-by", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:43:51Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/29b67aac38f24dd58c19b8596895d36e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Short bio on Aviv: <a rel=\"nofollow\" href=\"http://www.broad.mit.edu/about/bios/bio-regev.html\" title=\"http://www.broad.mit.edu/about/bios/bio-regev.html\">http://www.broad.mit.edu/about...</a>. (Much longer bio by the introductory speaker)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/ffc79f264f9d4499b3db1917a5230202", "date" : "2008-07-21T20:56:47Z" }, { "body" : "talking about TF network reconstruction network. outcome is still a network with not functional annotation. Important to reach a map that explains the biology", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/dff0363af7b64001998f82320b7c6cc6", "date" : "2008-07-21T20:59:28Z" }, { "body" : "want to reconstruct biological function, but get something that we can comprehend (complex networks vs. &quot;nice&quot; pathway representations).", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/600d87db1d4c480c96d3187181e02844", "date" : "2008-07-21T20:59:33Z" }, { "body" : "unifying concept: functional models, sets of entities that perform together to perform an identifiable and distinct function", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/57da450f5fea408094d93b8b346fa8ad", "date" : "2008-07-21T21:00:10Z" }, { "body" : "Idea is to reconstruct how signals are processed and processes carried out so we can understand what is happening at every level of the pathway. But this often leads to nasty hairball diagrams (she shows example). Rather, we'd prefer a detailed diagram of the inputs, outputs, dynamics of processes that allow hypotheses to be made and tested (shows example) but these are painstakingly created by hand by biologists", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/490bb315f0514627a0d3023b75e17a2d", "date" : "2008-07-21T21:00:16Z" }, { "body" : "caveat: modules we find from genetics/molecular interactions are not necessarily functional modules", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/c62512190dc048b5a2ee5c76af347dae", "date" : "2008-07-21T21:01:10Z" }, { "body" : "So, regulatory networks only today", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/3d458eac64f9446c9c00dd4f119f4281", "date" : "2008-07-21T21:01:37Z" }, { "body" : "are modules true bio units ? are modules a useful concept ? can we identify the pathways controlling the modules ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/b29722e1949f4f35b7a9a0ffb115adbc", "date" : "2008-07-21T21:02:23Z" }, { "body" : "3 questions: 1) are modules true bio entities?, 2) is modularity useful for representing biology? 3) can we identify pathways controlling these modules?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/9644b539312d46959ef6ad42011bacbd", "date" : "2008-07-21T21:02:40Z" }, { "body" : "Are modules true biological entities. ref: tanay, regev, shamir, PNAS 2005", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/9b7b9a7e1a344cc0820c28c26f9d7e59", "date" : "2008-07-21T21:02:44Z" }, { "body" : "Certain orthologous gene groups are co-expressed across different species. Not surprising. But are the regulatory mxns also conserved? Yes - in many cases, the TF binding motifs are conserved, as well as the TFs. BUT, in some cases, the proteins binding these sites are different across species.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/6205ec7c9e9f4f8c9dfd6cdfaacb4b4e", "date" : "2008-07-21T21:04:50Z" }, { "body" : "examples of conserved and divergent transcription regulation of modules", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/a8115b7571fd431295e281878f2b503f", "date" : "2008-07-21T21:05:54Z" }, { "body" : "Identify phylogenetic profile of cis-regulatory elements using sequence from many different species. Don't have expression data for all of them but assume that the orthologous genes are co-expressed bc they are co-exp in more distant species.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/b6dd6b4181584b57afa25fbf3765c02b", "date" : "2008-07-21T21:08:18Z" }, { "body" : "by mapping gene sets across different ascomycota between s. pombe and s. cerevisiae they could find the conservation or divergence of over-represented motifs across those species.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/9c1277f49d6d4378954b0cb644677760", "date" : "2008-07-21T21:08:29Z" }, { "body" : "a very neat example of evolution of TF binding sites by a redundant intermediate with two binding sites.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/8d3aef54bc59483f9010d40d168d7950", "date" : "2008-07-21T21:10:18Z" }, { "body" : "Trying to determine whether changes in regulatory sites result from gradual evolution or &quot;switching&quot;? Use phylogenetic analysis of site sequences to examine evolution of site", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/075540a6ce8a48eb959dcd002684ce64", "date" : "2008-07-21T21:11:27Z" }, { "body" : "Yep, this is great work even though the ribosome is probably one of the &quot;easy&quot; modules", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/1a948b203d6d4df5a14a58e9126000a2", "date" : "2008-07-21T21:11:36Z" }, { "body" : "New regulatory sites &quot;invading&quot; the promoters of an ancestral site. Regulatory redundancy --&gt; new site may push out ancestral site.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/095d429432d14ca7b21513da78673885", "date" : "2008-07-21T21:14:03Z" }, { "body" : "Open questions: Where do all the new binding sites come from?", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/89d2b569369b47c68de44417db819af5", "date" : "2008-07-21T21:14:53Z" }, { "body" : "How do new sites are created ? is it positive selection or neutral drift ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/50fc7a4da0dd4e36a992bc3f325c5c6f", "date" : "2008-07-21T21:15:16Z" }, { "body" : "Dawn Thompson lead authors phylogeny of modules", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/3dd2c76f0a6c423c9f045ca9c89279b0", "date" : "2008-07-21T21:16:28Z" }, { "body" : "13 species probed in carbon sources, data gathered: expression and LC-MS.MS metabolic data.... I would really like to have that data to use :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/12ff899403464648a179b9d757575e1f", "date" : "2008-07-21T21:17:49Z" }, { "body" : "Algorithm to infer a module phylogeny: MoPhy", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/7958e1f77ead4fa894a131bfbbc7f103", "date" : "2008-07-21T21:18:11Z" }, { "body" : "Great, a keynote with novel data on parallel profiling of fermentation in 13  yeast species", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/357b08dff2fb48349ed3d97c8180ce60", "date" : "2008-07-21T21:19:50Z" }, { "body" : "comparative expression in glucose depletion. divergence along evolutionary time occurs first for the dynamics of response", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/d2f0026e9f03460ebad63438a73d24b2", "date" : "2008-07-21T21:19:53Z" }, { "body" : "Moving on to second question: is modularity a useful perspective on system fxn? - using cancer as an example (lots and lots of data available, results already kind of modular - gene lists)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/51a0e72accc841abaaa92a24d4d86922", "date" : "2008-07-21T21:22:06Z" }, { "body" : "Building a module map of cancer (as opposed to just compiling gene lists). Have expression data and gene sets (Go categories, clusters, pathways)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/409ceff817794209a4f168d092970ad6", "date" : "2008-07-21T21:24:14Z" }, { "body" : "take gene sets and find repressed/induced gene sets", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/4872e24d656a4fa58f699e0d5fa732a4", "date" : "2008-07-21T21:24:36Z" }, { "body" : "Modules: core genes of (merged) gene sets. Can test modules vs. arrays", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/57f675f7e7b84806b417cb03c2d236e2", "date" : "2008-07-21T21:25:53Z" }, { "body" : "Arranged gene sets with significant changes against arrays in a matrix. Clustered the gene sets. Then threw out genes that did not contribute to clustering. Merged the genes remaining in gene sets in each cluster to get modules. Picture of a Cancer Module Map", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/d3f0c079e1164ee997be8d88ea69adb2", "date" : "2008-07-21T21:26:14Z" }, { "body" : "491 modules vs 94 conditions", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/4f689829d29945dcab93973b4f83e775", "date" : "2008-07-21T21:26:35Z" }, { "body" : "Example result - bone proliferation pathways showing up in primary breast cancer expression. Why? Pubmed search shows that many cancers, inc breast cancer, like to metastasize to bone. But this is primary, not metastatic tissue. Maybe, bone proliferation module turning on may foretell metastasis of the tumor?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/fafcac39c32046158b4d9686e3cbb085", "date" : "2008-07-21T21:29:08Z" }, { "body" : "Cancer and ES modules similarity", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/c1b4f9a7e64645fab97f6b88951ceef1", "date" : "2008-07-21T21:31:26Z" }, { "body" : "ES signature could be used a signal for prognostic. what is the mechanism ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/e520de79f25b40ada2aef523596b5c2e", "date" : "2008-07-21T21:32:41Z" }, { "body" : "Last part of talk: can we identify the pathways controlling modules?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/669bb9b9241443da8a2eda4e0fc35f60", "date" : "2008-07-21T21:34:40Z" }, { "body" : "From gene expression - assign genes to modules according to expression, infer regulatory pathway between modules that explains the expression patterns, throw away the gene assignments and re-assign, iterate until convergence.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/7fd01396fece4cd49e7cbaac2785bebf", "date" : "2008-07-21T21:38:34Z" }, { "body" : "It works! But why should it work? Many regulators are controlled post-transcriptionally. Turns out many of them are regulated post-transcriptionally by the targets they themselves control.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/155d4036cb234fda8017611a6addb2c7", "date" : "2008-07-21T21:40:23Z" }, { "body" : "gene sets are important and useful. from my view it has to do with selection pressure. selection for function not for how the function is accomplished", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/4612361ae59241a08c36ac1e0fa558fa", "date" : "2008-07-21T21:46:28Z" }, { "body" : "Models don't take into account Time (also not space:) , at different time scales (from environmental time to evolution time)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/99c00d7b245f4ec5926d9e9d46768d24", "date" : "2008-07-21T21:47:45Z" }, { "body" : "future outlook: look for principles and tools to look at time at different scales.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/47cd8b011a9148e1b92e3101d6a9512e", "date" : "2008-07-21T21:49:12Z" }, { "body" : "Four nice keynotes so far but this was probably the best", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/c42a96b2f3f74891b81cd7c7bfe59c50", "date" : "2008-07-21T21:50:23Z" }, { "body" : "yes, very cool talk", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/cb416a0c63d44212b4be7e3015860d15", "date" : "2008-07-21T21:54:52Z" }, { "body" : "Go women in science! So far Claire and Aviv's talks have been my favorites.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/612c9ce1f18249b6ad553caec115285c", "date" : "2008-07-21T21:55:34Z" }, { "body" : "It was very impressive; almost overwhelming, in fact.  Good work with the coverage.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29b67aac38f24dd58c19b8596895d36e/c/f962b6a4493d4d8e838003d6b4155131", "date" : "2008-07-21T22:33:06Z" } ], "body" : "Keynote: Aviv Regev on Modular Biology", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/29b67aac/keynote-aviv-regev-on-modular-biology", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T20:52:35Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Hsuan-Cheng Huang", "private" : true, "id" : "hchuang", "type" : "user" }, "date" : "2008-08-13T08:54:29Z" }, { "from" : { "name" : "Sutee Dee", "id" : "thaiyoshi", "type" : "user" }, "date" : "2008-07-22T03:49:57Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-21T23:14:55Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-21T20:59:46Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T20:55:48Z" }, { "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "date" : "2008-07-21T20:54:21Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T20:52:59Z" } ] }
{ "_id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Focusing on post-transcriptional regulation of expression by small RNA", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/16bd955163be4e6f871d599dfc295ed2", "date" : "2008-07-23T13:01:15Z" }, { "body" : "~ 85 sRNA known from E.coli; targets and function often unknown, but often conserved", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/196c2eaa5b284176988b8cc78fc4536f", "date" : "2008-07-23T13:02:27Z" }, { "body" : "miRNA regulators in eukaryotes: mechanism still unclear (inhibition/degradation/both)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/63fa1a51ce3e4e50a3429af2589be2a6", "date" : "2008-07-23T13:04:00Z" }, { "body" : "&gt; 500 miRNA in humans; also conserved; also few targets or functions known", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/c4db449fda1b42bead21efbd729df607", "date" : "2008-07-23T13:04:18Z" }, { "body" : "Comparing sRNA regulation to other types; transcriptional, PPI", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/40ef113ba54d4201ac720cb712d41831", "date" : "2008-07-23T13:07:58Z" }, { "body" : "Modelling and simulation of regulation:  regulator may be (1) always expressed, (2) switched on by external signal", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/c5792ec68e8145788ba0214d366f1c78", "date" : "2008-07-23T13:10:09Z" }, { "body" : "sRNA regulation advantageous where fast response required", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/c05dccb326424b1db6da7438782144e5", "date" : "2008-07-23T13:12:38Z" }, { "body" : "Next:  how does this integrate with transcriptional regulation?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/e391b09015364f3ca0f40fb371dfaea2", "date" : "2008-07-23T13:13:52Z" }, { "body" : "Finally, someone provides a clear, succinct summary of what a network interaction graph is", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/a198b4a86a554ebcabe9238d946897cf", "date" : "2008-07-23T13:14:47Z" }, { "body" : "Where 2 TFs required, feed-forward loop = AND gate", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/096881d1ea00469588d38eba1266ebf8", "date" : "2008-07-23T13:17:08Z" }, { "body" : "May be mixed loops:  combination of ncRNA and protein factors", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/836003f7861a417e99d5f51ff159d113", "date" : "2008-07-23T13:18:24Z" }, { "body" : "Example mixed feed-forward loop:  OmpR + MicF (sRNA) -&gt; ompF", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/28bc00b9ea0f44c09edc7ad9e9648f5e", "date" : "2008-07-23T13:20:03Z" }, { "body" : "Other examples known in bacteria and human", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/94d6472397534516a581468aa93d256d", "date" : "2008-07-23T13:21:37Z" }, { "body" : "Mixed negative feedback loops:  e.g. RyhB -&gt; Fur, E. coli; stochastic simulation.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/26c2d0d2a3284d75a379339bbfe1d49e", "date" : "2008-07-23T13:23:02Z" }, { "body" : "Summary:  mixed regulation extends possible regulation dynamics", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/e473673f21974e2f89701ce3c4e3cfbc", "date" : "2008-07-23T13:23:34Z" }, { "body" : "Moving onto predicting miRNA targets in genomes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/9cf3fab231e44236ad11d63afc7f972f", "date" : "2008-07-23T13:24:45Z" }, { "body" : "Use known targets to narrow the solution space; miRNA &quot;seed region&quot;; conservation at target site; repeat binding sites", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/db838fae24af4f3d988a7e1c89e58ec8", "date" : "2008-07-23T13:26:39Z" }, { "body" : "RepTar algorithm:  starts with 3'-UTR, HMM profiles repetitive signals, matches to miRNAs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/425c4fe4d633400b872f7b8dabe4d1ab", "date" : "2008-07-23T13:29:38Z" }, { "body" : "Validation using shuffled sequences and experimental data; not over-selling the method", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/5b926081b431473e911d36fe5d941a10", "date" : "2008-07-23T13:32:13Z" }, { "body" : "Predicted miRNAs:  seed match (84%), 3'-compensatory (11%), nearly-full match (5%)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/8d10c1f46f5049c4b72df6b5881f1657", "date" : "2008-07-23T13:33:05Z" }, { "body" : "Moving on to applications of RepTar:  viral miRNAs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/b65d376f2e8844508a5eff24078e07b0", "date" : "2008-07-23T13:34:17Z" }, { "body" : "Significant overlap of predicted targets for different viruses:  GO annotations make sense", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/33aad2a743ca4c52a0b18f7c2299eddb", "date" : "2008-07-23T13:37:39Z" }, { "body" : "Second set of targets are immune system-related; do viruses use miRNA to down-regulate immune system?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/4035186e4121410bb3060012cbf830eb", "date" : "2008-07-23T13:38:15Z" }, { "body" : "HCMV:  evades NK cells by mimicking MHC-I to make cell appear &quot;self&quot;", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/8c8c6a5140f94a898c40b565465c362d", "date" : "2008-07-23T13:42:01Z" }, { "body" : "MICB - top target for HCMV miRNA UL112; experimental validation by over-expressing UL112 in cell lines; MICB down-regulated, controls are not.  Also use luciferase reporter assay with 3'-UTR and mutagenesis of binding site.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/4bdf0875be8c4ebe9e9a5212a985b430", "date" : "2008-07-23T13:43:08Z" }, { "body" : "Viral infection of UL112 deletion mutant confirms results", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/cf7168baeea64c45983159585b5396a3", "date" : "2008-07-23T13:51:10Z" }, { "body" : "Describing further experimental confirmation.  Obviously quite excited about her results :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/5cea27262dbc4d85abf6756cde09ee70", "date" : "2008-07-23T13:52:45Z" }, { "body" : "Viral miRNAs may therefore be therapeutic targets; e.g. for antisense RNA, or mimic miRNA effect for immunosuppression", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/849b301116694a4e8509f12dd1c7b2bf", "date" : "2008-07-23T13:54:50Z" }, { "body" : "Great talk.  Wrapping up now - running through almost to 10 am.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/53ad9bcbec4e4ec7b6c41cf67db6511b", "date" : "2008-07-23T13:55:27Z" }, { "body" : "Good coverage too, Neil", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/e0c55e9271654388861cdead9ef8eb66", "date" : "2008-07-23T13:58:20Z" }, { "body" : "Wow, the Neil Saunders one-man show :)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/29ec0f3d5a1c4f2d807a5f42e959bf50/c/1bf92e746ca446939bc4b8f58fbc7333", "date" : "2008-07-23T14:06:19Z" } ], "body" : "Keynote 7: Hana Margalit - &quot;intriguing roles for small ncRNAs in cellular regulatory networks&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/29ec0f3d/keynote-7-hana-margalit-intriguing-roles-for", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T12:57:32Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Hsuan-Cheng Huang", "private" : true, "id" : "hchuang", "type" : "user" }, "date" : "2008-08-13T08:54:34Z" }, { "from" : { "name" : "Ricardo Almeida", "id" : "ricardoalmeida", "type" : "user" }, "date" : "2008-07-24T13:35:49Z" }, { "from" : { "name" : "Samuli Eldfors", "id" : "eldfors", "type" : "user" }, "date" : "2008-07-23T17:38:31Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-23T14:06:02Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-23T13:54:20Z" } ] }
{ "_id" : "e/2a35b367266a42d3adca96e724389462", "feed_id" : "ismb-2008", "comments" : [ { "body" : "introduction about network directionality in signaling networks, kinases, SH2, etc, In vitro binding affinity and specificity is not enough to specify in vivo binding (docking, co-expression, etc). Plug for STRING (<a rel=\"nofollow\" href=\"http://string.embl.de/\">http://string.embl.de/</a>). Kinase specificity models from Netphorest (<a rel=\"nofollow\" href=\"http://netphorest.info/\">http://netphorest.info/</a>) and functional interactions networks from STRING. All published work already.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/2a35b367266a42d3adca96e724389462/c/b81f3c496cf5410e914e5d0d150c8940", "date" : "2008-07-18T17:53:02Z" }, { "body" : "Lars: Introduction to Netphorest, building a resource of binding models.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/2a35b367266a42d3adca96e724389462/c/29e5caa0b87643e8bc81206820a01622", "date" : "2008-07-18T18:04:57Z" } ], "body" : "joint talk - Rune Linding and Lars Juhl Jensen on in vivo phosphorylation networks - <a rel=\"nofollow\" href=\"http://networkin.info/search.php\" title=\"http://networkin.info/search.php\">http://networkin.info/search...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/2a35b367/joint-talk-rune-linding-and-lars-juhl-jensen-on", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T17:50:36Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-18T18:37:58Z" } ] }
{ "_id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Lunch! &lt;:-/", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/e8d6a3474c0a4c9499bcc6bbbfd77d34", "date" : "2008-07-20T17:22:47Z" }, { "body" : "I don't understand the smiley - the food was terrible. Oh, and they had run out of noodles before I got served :(", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/50511888780f4994a4387d392b417165", "date" : "2008-07-20T17:40:01Z" }, { "body" : "That was before I went to lunch. I was hungry ;). Specially for the amount of money it cost to come here they could do a better job with the food.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/00f2715924914ae590f8e4846cae40bc", "date" : "2008-07-20T17:42:50Z" }, { "body" : "Not sure how it was for the omnivores, but with the vegetarian noodles, i had one piece of tofu on the entire plate. Oh yes and a plate full of paper sprirals masquerading as noodles", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/d044e9a547754517aabed50201c107a6", "date" : "2008-07-20T17:44:42Z" }, { "body" : "I'm not one to complain - but lunch sucked :)  The food court across Front Street (Simcoe Place I think?) is an OK alternative.  I got a pile of chow mein there yesterday for 5 bucks.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/f9bb140d97184cd18369b77ff226d054", "date" : "2008-07-20T17:48:16Z" }, { "body" : "I thought it was much better than Friday. Which isn't to say much, but it was mostly edible.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/fad059aa567e44ecb48e82e089d381f5", "date" : "2008-07-20T17:49:04Z" }, { "body" : "Absolutely horrible food in addition to a rather unpleasant service I might say", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/e701c1dd2bbd499b97423511ac0542c8", "date" : "2008-07-20T17:50:51Z" }, { "body" : "i agree! worst food ive ever had at a conference -- maybe this is why their profits/attendee is so high!", "from" : { "name" : "sourav", "id" : "sourav", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/ab8875f2c74c480fa9f9f6ff6410ff4b", "date" : "2008-07-20T17:51:47Z" }, { "body" : "Rubbish, they ran out before I even got there - hotdog in from of the CN tower for me", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/e9eea6f7158940d8926c1d37313aa80f", "date" : "2008-07-20T18:23:07Z" }, { "body" : "It could be much worse - think ISMB 2004 in Glasgow!", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/2b7500ab24084c9dbcac0e2fb3a2c69e/c/4626e7bd18494e3d8f49e160f947c81e", "date" : "2008-07-20T18:26:42Z" } ], "body" : "Lunch ! :)", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/2b7500ab/lunch", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T16:36:11Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/30803ec0593c46baa93e9abf83af2091", "feed_id" : "ismb-2008", "comments" : [ { "body" : "So the &quot;pan-genome&quot; = core genome (essential genes shared by all strains/members), then the non-essential genes, and then the &quot;genomic halo&quot; of genes that may be found in only one or a few strains.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/30803ec0593c46baa93e9abf83af2091/c/70e95a9e3e044ac4b5adee5a88a84e36", "date" : "2008-07-20T14:30:16Z" }, { "body" : "She also mentioned the idea that lateral gene transfer may ensure the survival of genetic material beyond the death of the individual organism.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/30803ec0593c46baa93e9abf83af2091/c/cb4c67a9dd8d48398847da8afc195431", "date" : "2008-07-20T14:30:54Z" } ], "body" : "Claire mentioned the fact that even within a species such as e.coli, different strains can be composed of very different genes - in 3 strains (non-pathogenic, pathogenic, and uropathogenic) of e.coli, there was less than 40% overlap in the genes.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/30803ec0/claire-mentioned-fact-that-even-within-species", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T14:29:11Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/3094712fe3d5483f8173472e990fda9a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Protein networks can represent the relevant contextual data.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/f1bb1db6a72d49938f44181032ecf323", "date" : "2008-07-21T15:21:10Z" }, { "body" : "Guessing this is largely about NetworKIN which I know of, but never seen presented so worth the effort.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/51a3db10a833486db5881417ceed74a5", "date" : "2008-07-21T15:21:53Z" }, { "body" : "NetPhorest - phosphorylation motifs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/82b7527f449246b39fbf1d9abc88ca31", "date" : "2008-07-21T15:22:33Z" }, { "body" : "STRING supplies network information", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/4af5bb6304c24b679f4ba555d11a4a50", "date" : "2008-07-21T15:22:56Z" }, { "body" : "60-80% of specificity comes from network, for 4 kinase families", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/79965a035e2b42c4942bac20497a49ac", "date" : "2008-07-21T15:24:33Z" }, { "body" : "Have done some experimental validation of predictions, e.g. RAD50", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/7992f28e13a44fb7901575476388f612", "date" : "2008-07-21T15:26:10Z" }, { "body" : "MS MRM method (multiple reaction monitoring); specific and sensitive phosphosite detection", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/72d2d2ca6583489599a49fc3d7b26322", "date" : "2008-07-21T15:28:52Z" }, { "body" : "URL:  netphorest.info", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/f357701e863e4d6e944cd4d30cf26fce", "date" : "2008-07-21T15:30:18Z" }, { "body" : "Oncogenic Tyr kinases = lower specificity; interesting", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/25856e24426b433ebfd1fb5a4c9b8f78", "date" : "2008-07-21T15:32:21Z" }, { "body" : "Note to self:  stop wasting my time on kinases back in Brissie, these guys have it covered :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/5fb0a907b6f44a09847d8c7db336e035", "date" : "2008-07-21T15:34:05Z" }, { "body" : "And nicely finished well on time.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/3094712fe3d5483f8173472e990fda9a/c/edc67db49d7443799711e663b89364c9", "date" : "2008-07-21T15:36:10Z" } ], "body" : "HL20:  Rune Linding - phosphorylation networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/3094712f/hl20-rune-linding-phosphorylation-networks", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T15:20:20Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T15:45:06Z" } ] }
{ "_id" : "e/315fb1989a7744f5b862bd7992723ffe", "feed_id" : "ismb-2008", "comments" : [ { "body" : "it has been a while since I learned about tree search algorithms.  re-reading Norvig would be good for my soul", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "id" : "e/315fb1989a7744f5b862bd7992723ffe/c/3cc0f7cd63f34aaa85ed988272d2f5c6", "date" : "2008-07-22T18:29:56Z" }, { "body" : "use a set of compounds as a basis to generate feature vectors; use any similarity measure you want", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "id" : "e/315fb1989a7744f5b862bd7992723ffe/c/3cfb7a9a5b614c05aa8792582012fb38", "date" : "2008-07-22T18:34:24Z" }, { "body" : "<a rel=\"nofollow\" href=\"http://bioweb.ucr.edu/ChemMineV2/mcs\" title=\"http://bioweb.ucr.edu/ChemMineV2/mcs\">http://bioweb.ucr.edu/ChemMin...</a> - open, and C source available with python bindings", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "id" : "e/315fb1989a7744f5b862bd7992723ffe/c/483eb5f7306a4915becc5a46e683daaf", "date" : "2008-07-22T18:40:48Z" } ], "body" : "Searching &amp; Predicting Drug-Like Compounds Using Max Common Substructure (Yiqun Cao)", "feed_name" : "ISMB 2008", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/315fb198/searching-predicting-drug-like-compounds", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T18:20:07Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-22T18:32:51Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-22T18:26:00Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-22T18:21:58Z" } ] }
{ "_id" : "e/320913693ab745938789e838b061eda7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Integrating chemical genomics and target proteins", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/a8e04d411bf44c32b9f065846013ac88", "date" : "2008-07-20T18:47:48Z" }, { "body" : "Sources for &quot;gold standard&quot; KEGG Brite, Brenda, Super Target and DrugBank", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/5dd8b2bdb5f94b8e849b408f9b492ed4", "date" : "2008-07-20T18:49:15Z" }, { "body" : "Gold standards in drug-protein interaction data:  doesn't seem to be much", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/4d95069723f34454bd9419b5ca30bd5d", "date" : "2008-07-20T18:49:20Z" }, { "body" : "And we're off into graph theory again.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/bb013b0ca88940999ba0b6d81dcc86a4", "date" : "2008-07-20T18:49:38Z" }, { "body" : "most drugs and proteins have small number of interactions - is this an annotation / knowlegebase issue?", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/dbd5bc7f1a0c48308ed708a62640112a", "date" : "2008-07-20T18:51:16Z" }, { "body" : "SIMCOMP - graph matching algorithm", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/9ba422a686494ee5bb39510d31c4faf8", "date" : "2008-07-20T18:51:24Z" }, { "body" : "Now comparing drug structures with network distance from target; correlation, as you might expect", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/a5fd54b5677845539753cc2dc51e750f", "date" : "2008-07-20T18:53:02Z" }, { "body" : "Comparison of drug structure similarity and network distance. would be nice to have confidence measure or stratification approach for network distances", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/5783607e72364c3b84a50cc8739578f8", "date" : "2008-07-20T18:53:05Z" }, { "body" : "Having a few sound problems, just as we get to the prediction part", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/dbd5109764374b078ab59d1687839d49", "date" : "2008-07-20T18:55:08Z" }, { "body" : "Pharmacological space:  cf chemical and genomic spaces; from this, predict new interactions for new compounds/proteins", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/4a617a8fedab49959166c0445b52b8f8", "date" : "2008-07-20T18:56:29Z" }, { "body" : "Nearest neighbor approach for prediction - slide is not very clear about details. I s this just similarity of new entity to existing nodes?", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/e4eb549484df48ad9a596a7d319b8dd7", "date" : "2008-07-20T18:56:41Z" }, { "body" : "Looks interesting but a little hard to follow - should follow this one up later.  Ah, here come the ROC curves :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/33990daf703243cca1c96db52dbc5e6e", "date" : "2008-07-20T19:02:54Z" }, { "body" : "Hmmm .... most companies I know use IPA or other commercial", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/029087b52ec1449cbda16eab6840fa0f", "date" : "2008-07-20T19:05:04Z" }, { "body" : "Like the idea of an all v. all KEGG genes v. KEGG molecules", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/320913693ab745938789e838b061eda7/c/6cfe4315179446e9a4140f82e8cad4df", "date" : "2008-07-20T19:25:40Z" } ], "body" : "PT12:  prediction of drug target interaction networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/32091369/pt12-prediction-of-drug-target-interaction", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:47:18Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/33a974d0310e47d9a382edba1a1dd9a3", "feed_id" : "ismb-2008", "comments" : [ { "body" : "You're flying out today?", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/766134ba5f7c4a5b8d75264507e8e5b3", "date" : "2008-07-23T18:59:25Z" }, { "body" : "yeap, around 6pm today", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/e0af636ee57543eda95d57c548c87ef3", "date" : "2008-07-23T19:00:15Z" }, { "body" : "Too soon, we barely talked. Have a safe trip back to California.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/4fdecd8aa37f489da778276b1e2b9461", "date" : "2008-07-23T19:01:13Z" }, { "body" : "I am also on my way to Pearson, it was nice meeting you all (Pedro, Shirley, Neil, Roland..).", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/51d093615e0a43f5a78c905d952737c7", "date" : "2008-07-23T19:22:19Z" }, { "body" : "Nice to meet you all as well, it looks like I missed some good sessions/keynotes, but the FF coverage was great!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/36f2ce6ca2b8487aaf5c3887487fa0fd", "date" : "2008-07-23T19:56:35Z" }, { "body" : "It was great to meet you all! I missed all the talks, but thanks to the FF coverage, I at least have a pretty good idea of what I missed ;-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/030c838458854be4b2fb99af44d63f74", "date" : "2008-07-23T20:40:52Z" }, { "body" : "Great to see everyone, finally.  Safe trips home to you all; I'll be back in Brisbane (and online) August 5.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/33a974d0310e47d9a382edba1a1dd9a3/c/6983469e3fb34d5e8ae52317fe92889a", "date" : "2008-07-23T21:12:31Z" } ], "body" : "I am leaving soon, thanks to everyone that participated. It was a fun and interesting experiment. See you &quot;around&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/33a974d0/i-am-leaving-soon-thanks-to-everyone-that", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T18:56:58Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-23T19:19:38Z" }, { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-23T18:57:14Z" } ] }
{ "_id" : "e/3783f5d7a0cd48a3a70c7cfee43b8da9", "feed_id" : "ismb-2008", "comments" : [ { "body" : "great: let ISCB know, we'll link to it!", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/3783f5d7a0cd48a3a70c7cfee43b8da9/c/c7d23308201541d89e58e96cca9bfeb7", "date" : "2008-07-27T01:24:51Z" } ], "body" : "We're putting together a conference report but would like to include the more &quot;human&quot; side of things. If you have funny stories, anecdotes, speaker quotes, reflections, or would like to contribute, just encapsulate it in 1 para or less and we'll fit in as many as we can. Paste here or link to it.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/3783f5d7/we-re-putting-together-conference-report-but", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T18:30:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-24T22:35:30Z" } ] }
{ "_id" : "e/379a2f95c54149bf9c6ad98520d62b7c", "feed_id" : "ismb-2008", "body" : "FYI: proposed to FF to place a comment link at the bottom, and other things we missed at ISMB - <a rel=\"nofollow\" href=\"http://groups.google.com/group/friendfeed/browse_thread/thread/0f76bbfcfe2b8d71/2a453d8ced169b20#2a453d8ced169b20\" title=\"http://groups.google.com/group/friendfeed/browse_thread/thread/0f76bbfcfe2b8d71/2a453d8ced169b20#2a453d8ced169b20\">http://groups.google.com/group...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/379a2f95/fyi-proposed-to-ff-place-comment-link-at-bottom", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-28T18:53:58Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-08-03T13:17:34Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-28T19:41:55Z" }, { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-28T19:37:27Z" }, { "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "date" : "2008-07-28T19:23:26Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-28T19:13:02Z" } ] }
{ "_id" : "e/3d71d080a97742039bfda0fa76b1f2d4", "feed_id" : "ismb-2008", "comments" : [ { "body" : "the images are rather noisy, so only low-res versions :(", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/3d71d080a97742039bfda0fa76b1f2d4/c/0d987e0a7c024673a5aaf0bb1b7a30b8", "date" : "2008-07-27T12:16:05Z" } ], "body" : "Tuesday's circle of laptops - <a href=\"http://friendfeed.com/e/48c4da44-bb16-5784-3dab-6f022e9575fb\" title=\"http://friendfeed.com/e/48c4da44-bb16-5784-3dab-6f022e9575fb\">http://friendfeed.com/e...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/3d71d080/tuesday-circle-of-laptops", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-27T12:16:05Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "thumbnails" : [ { "url" : "http://farm4.static.flickr.com/3094/2706588290_7427bc81bf_s.jpg", "height" : 75, "link" : "http://friendfeed.com/e/48c4da44-bb16-5784-3dab-6f022e9575fb", "width" : 75 }, { "url" : "http://farm3.static.flickr.com/2091/2705751913_b9ca4867b1_s.jpg", "height" : 75, "link" : "http://www.flickr.com/photos/micha2305/2705751913/", "width" : 75 } ], "likes" : [ { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-08-02T06:47:50Z" }, { "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "date" : "2008-07-27T15:35:42Z" } ] }
{ "_id" : "e/3ee26a9e113e43b4b493f8b1a811c57e", "feed_id" : "ismb-2008", "body" : "After talking with Reinhard Schneider, one of the ISMB09 organizers, I opened a new room to try to begin the discussion how to integrate the ISMB homepage with FF/microblogging in general. I hope we can find some low-tech solutions with the help of the FF API and widgets. - <a href=\"http://friendfeed.com/rooms/ismb-microblogging-coordination\" title=\"http://friendfeed.com/rooms/ismb-microblogging-coordination\">http://friendfeed.com/rooms...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/3ee26a9e/after-talking-with-reinhard-schneider-one-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2009-02-12T11:05:48Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2009-02-12T13:03:07Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2009-02-12T12:21:19Z" }, { "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "date" : "2009-02-12T11:43:00Z" } ] }
{ "_id" : "e/426e2bddc03742d79156925bc1770c9f", "feed_id" : "ismb-2008", "body" : "Ontology of Biomedical Investigations (OBI) poster presented during the Bio-ontologies SIG - <a rel=\"nofollow\" href=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/OBI-BioOntologySIG-ISMB08-Poster.pdf\" title=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/OBI-BioOntologySIG-ISMB08-Poster.pdf\">http://obi.svn.sourceforge.net/svnroot...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/426e2bdd/ontology-of-biomedical-investigations-obi", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T13:27:49Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T13:52:53Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-21T13:45:40Z" } ] }
{ "_id" : "e/43114187c92f4cce931f6e71dc8fd95e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Came in ~ 10 min late", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/c456dfaa6120415b9f89e2cfc585ebaf", "date" : "2008-07-22T16:00:13Z" }, { "body" : "Goal is to find candidate genes likely to be involved in complex disorders by integrating data from the many genome-wide functional studies already run. Two relevant questions - how to find _all_ gene variants relevant to a disease? How to find _novel_ genes/variants?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/9c568d792bb649139832ffe5da2be268", "date" : "2008-07-22T16:01:37Z" }, { "body" : "Using progeria as an example. Progeria = premature aging of children, very very rare, on average death occurs at age 15, 90% from artherosclerosis. But patients show loss of fat starting around age 2. Gene identified but obviously something very complex going on", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/ad38133ff09349e69b53263428870a26", "date" : "2008-07-22T16:03:09Z" }, { "body" : "RNAi study in worms - inactivating 112 genes increases fat content, inactivating another 305 decreases fat content - but worms don't even have fat cells.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/c9ec19c3ca1a40cc91051a0b3de3fa6d", "date" : "2008-07-22T16:04:09Z" }, { "body" : "compared 49 studies/data sets in a variety of organisms and modalities (mouse microarrays, proteomics, linkage studies, whole genome knockouts, worms, human) investigating fat cell or obesity to a knowledge gold standard (273 genes with variants known to be associated with obesity). Interested in quantifying the sensitivity of each individual study", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/30a7cde8e35e4760b37d8da46a9f5606", "date" : "2008-07-22T16:06:37Z" }, { "body" : "Shows ROC curves for models based on individual studies evaluated against gold standard, then shows ROC for a simple model that just integrates all of the individual studies. Integrated model significantly beats the performance of all of the individual models.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/aefc7401f2cb437a82349f330d1feb39", "date" : "2008-07-22T16:08:19Z" }, { "body" : "Big take home point - all of these data were publicly available. Did not have to do any additional experimental work to produce a much better model for predicting disease genes. The real point is that combining experiments does better than single studies. This is the power of &quot;integromics&quot;", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/856bbdc95ced4a7692a5ca80d3f52931", "date" : "2008-07-22T16:09:31Z" }, { "body" : "Ok, so we can predict known variants. What about discovering novel variants?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/5b96c46a5f694c7e942ce7076e8dc95b", "date" : "2008-07-22T16:10:09Z" }, { "body" : "Talking about positive predictive value now. He likes PPV &lt; 100% bc means the remaining % not in the gold standard positive set might be novel positives", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/26e84d88c69648a48a66e11fde41e5a7", "date" : "2008-07-22T16:12:49Z" }, { "body" : "Audience question: how does this method compare to traditional meta-analysis? Answer: still cutting edge, integrating different types of data across different species, so do need much more development. But naive methods so far are showing a ton of promise.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/37d8677459d844dc9b25d69da787c9ca", "date" : "2008-07-22T16:15:55Z" }, { "body" : "Audience question: how many genes do you think _are_ involved in obesity? Answer: if there's a long tail, well, there's a long tail! It's quite possible half the genome may be associated with obesity, with type 2 diabetes, aging, etc. These are very complex biological phenomena.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/43114187c92f4cce931f6e71dc8fd95e/c/dbea623ea2d7470e82d5b95d858def77", "date" : "2008-07-22T16:16:51Z" } ], "body" : "HL37: Atul Butte - Integration of genome-wide experiments to find genes associated with complex polygenic disorders: fighting back against the limitations of GWAS", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/43114187/hl37-atul-butte-integration-of-genome-wide", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T15:59:20Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Technical difficulties - blank screen, worried looking podium; oh right, here we go", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/25e0129bdae645de9a4f19b10b0902b8", "date" : "2008-07-20T15:17:42Z" }, { "body" : "PredictProtein aimed at experimentalists, not experienced bioinfo people", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/50abb78c884e4d5b8b38fc1291b904a6", "date" : "2008-07-20T15:21:16Z" }, { "body" : "Meta-disorder = MD = acronym confusion :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/3a20d374fc344411bc3f73d165fc5223", "date" : "2008-07-20T15:25:33Z" }, { "body" : "OK, not getting much joy from this.  Going to take a break and return for InterPro.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/e81a568e43674a8ebef37463f8e6007f", "date" : "2008-07-20T15:27:13Z" }, { "body" : "Things are picking up:  jBio, a javascript library inspired by BioPerl", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/c51d7250f0554920bcc9b20406ec0393", "date" : "2008-07-20T15:40:11Z" }, { "body" : "jBio documentation &quot;to do&quot;; how familiar", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/4c83b9ba98ff4836b9c49f9b52ad3a1e/c/7bf3b9b2020f4803965841e1abb6a9b1", "date" : "2008-07-20T15:40:34Z" } ], "body" : "TT02:  PredictProtein", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/4c83b9ba/tt02-predictprotein", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T15:17:07Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/4e55542be5204045a34eb36b0c5ead95", "feed_id" : "ismb-2008", "body" : "Metagene - prokaryotic gene finding in metagenomics samples - <a rel=\"nofollow\" href=\"http://nar.oxfordjournals.org/cgi/content/abstract/34/19/5623\" title=\"http://nar.oxfordjournals.org/cgi/content/abstract/34/19/5623\">http://nar.oxfordjournals.org/cgi...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/4e55542b/metagene-prokaryotic-gene-finding-in", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T13:42:41Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/518c020408fc42e6a44cf87d925f77c8", "feed_id" : "ismb-2008", "comments" : [ { "body" : "his website is <a rel=\"nofollow\" href=\"http://www.cs.toronto.edu/~gvwilson\" title=\"http://www.cs.toronto.edu/~gvwilson\">http://www.cs.toronto.edu/~gvwils...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/34ea366825bb482fa8c57289d9e03d85", "date" : "2008-07-17T16:57:09Z" }, { "body" : "Shirley - I'd be interested in coming along.  I'll be up in Toronto tomorrow (Friday).", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/b62a6efff50b4287992789934425d6c5", "date" : "2008-07-18T03:37:57Z" }, { "body" : "We will be there.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/3c61dae5531b4fb9a2cdfa9e00c8720a", "date" : "2008-07-18T03:55:09Z" }, { "body" : "I am arriving on Saturday. To bad. Wish I could've been these", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/2d9ed951b4ec4162a2142c01e842d983", "date" : "2008-07-18T07:33:47Z" }, { "body" : "I'm interested, but I'm attending the BOSC SIG which will still be going on then.  Have you settled on a location to meet?  If it's at or near the conference site maybe I can duck out quickly.", "from" : { "name" : "D. Joe Anderson", "id" : "deejoe", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/783803ea80244abf9789c1a4cc448836", "date" : "2008-07-18T14:50:43Z" }, { "body" : "It will be around ISMB's registration area.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/9d2df64bdf654236b1a0366a293ac8d2", "date" : "2008-07-18T15:24:27Z" }, { "body" : "I might come as well.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/5aeeca40047e45cc84dd8cbf1383ab13", "date" : "2008-07-18T15:31:28Z" }, { "body" : "There don't seem to be many options for coffee close enough to the meeting area so I think we'll just be hanging around where there are couches/chairs.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/518c020408fc42e6a44cf87d925f77c8/c/b2a3f19cdcc1483593a1456f31658e9f", "date" : "2008-07-18T18:20:53Z" } ], "body" : "Greg Wilson is a prof at U Toronto who has &quot;been teaching software development to scientists and engineers for about ten years now, and am interested in open source/open science issues&quot;. We're meeting for coffee around 3 on Friday- can anyone else make it?", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/518c0204/greg-wilson-is-prof-at-u-toronto-who-has-been", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-17T16:56:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/5228b4a2d76c4ede812535a883dae357", "feed_id" : "ismb-2008", "comments" : [ { "body" : "From the seminal PLoS CB paper :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/b14ce3dcce9947ffa9578869e4ebca79", "date" : "2008-07-21T19:47:54Z" }, { "body" : "I think Pedro has the support of all FriendFeed room members. Shirley, me, Roland in a row. :) Lars in front..., and now we're covered. Aah! Recursion!", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/4b8435fcd007498e9cde0533811abe95", "date" : "2008-07-21T19:48:17Z" }, { "body" : "Whoa, paraphrasing Dobhansky", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/9547c7125fa74dbdb8a80652a931ac57", "date" : "2008-07-21T19:50:47Z" }, { "body" : "Pedro's working the crowd and uniting us all in our geekiness", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/8d9af1d1ed6e4af391b75263862dd665", "date" : "2008-07-21T19:50:52Z" }, { "body" : "A presentation including a xkcd comic strip is automatically awesome ;-)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/3706459f1c4c43fc9f561081815c2419", "date" : "2008-07-21T19:52:15Z" }, { "body" : "Difficult to study evolution of protein interactions - mostly indirect methods only", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/728271c272b1474191cfab56576b0cb9", "date" : "2008-07-21T19:52:58Z" }, { "body" : "The original  <a rel=\"nofollow\" href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030025\" title=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030025\">http://www.ploscompbiol.org/article...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/bf2b204d5e674ad692c6632e3c298bb0", "date" : "2008-07-21T19:53:27Z" }, { "body" : "Assign age of protein by looking at phylogenetic dist of orthologs. If can't find ortholog in other species then probably a very recently duplicated protein", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/1492bf04344e428282c4ed9c33f2ab93", "date" : "2008-07-21T19:53:36Z" }, { "body" : "Interaction might be inherited with the duplication, or the interaction might be created or lost after the duplication in one of the duplicated proteins.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/70c844189aa547b6831e6e4fac9b4f3c", "date" : "2008-07-21T19:54:41Z" }, { "body" : "100 to 1000 interactions change every million years?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/66a367a31a32478bb047bb2e6610e64b", "date" : "2008-07-21T19:56:27Z" }, { "body" : "What protein domains are associated with fast rates of interaction evolution? - those that have more potential interaction surfaces, faster more transient interaction types (like phosphorylation)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/c3cab115db1e4a64b914bc6221a5cff6", "date" : "2008-07-21T19:57:49Z" }, { "body" : "Fast link dynamics = optimal network solutions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/9604e9be136c4f7fad7408d1e708cb2a", "date" : "2008-07-21T19:57:59Z" }, { "body" : "preliminary results: for fungal genomes of 4-10K proteins, 1-10 phosphoproteins gained/lost per million yrs", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/0a9d75050da645a7bd3cd12822293af9", "date" : "2008-07-21T20:00:23Z" }, { "body" : "New results not in the paper: Phosphorylation data in pombe, candida, cerevisiae. Rate of change 10e-05 kinase interactions", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/28018c46267c4a2d9c54321554bfa18f", "date" : "2008-07-21T20:00:23Z" }, { "body" : "showed examples of protein phosphorylation complexes that have diverged", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/24390ac8cab54d91ba7d590a7bba7cbf", "date" : "2008-07-21T20:02:30Z" }, { "body" : "Example replication (ORC?) complex proteins conserved, phospho patterns change significantly.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/67bacdb3e6a44766a95fff91fa121d0e", "date" : "2008-07-21T20:02:48Z" }, { "body" : "IIRC, Yck1 has Ser-rich motifs where pSer may be recognised", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/b542c69755f04ef8a832755591218164", "date" : "2008-07-21T20:07:00Z" }, { "body" : "And he wraps up with a Wordle summary.  What a hero.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/9db9da32ac5741f298ce29b09db17bc8", "date" : "2008-07-21T20:07:21Z" }, { "body" : "Can you share the slides Pedro?", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/b503926e95974a378006f14c8e0027ff", "date" : "2008-07-21T21:20:26Z" }, { "body" : "I would also like a copy of your presentation, Pedro", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/a97cf6c2befc42a390f0dbcdf65b5a4e", "date" : "2008-07-21T21:26:55Z" }, { "body" : "Sure, I will put it up on Slideshare or submit to Nature Precedings and I will add a link here.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/78164edd9239466c8280ca4b712e5edf", "date" : "2008-07-21T21:30:16Z" }, { "body" : "sorry I missed this one, looking forward to the slides", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/269b0665dedb4345a95a40860f48f5c0", "date" : "2008-07-21T21:41:21Z" }, { "body" : "Looks like I missed something quite wonderful.  Darn!!!", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/5228b4a2d76c4ede812535a883dae357/c/c8a6013597504f29b40ae40d52e88b9e", "date" : "2008-07-22T00:12:53Z" } ], "body" : "HL31:  Cellular Interaction Networks, by one Dr Beltrao", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/5228b4a2/hl31-cellular-interaction-networks-by-one-dr", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T19:41:35Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "date" : "2008-07-21T21:20:11Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T20:07:15Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-21T19:51:06Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-21T19:50:12Z" }, { "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "date" : "2008-07-21T19:49:25Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-21T19:47:07Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T19:46:46Z" } ] }
{ "_id" : "e/573ee62ce2224831b4f25c446d86eb1a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Want to get location prediction for uncharacterized proteins by looking at the literature (even though it's very easy in the lab and for truly uncharacterized proteins you don't have lit. data). To find authoritative papers, take PubMed links from SwissProt. In these abstracts, extract and stem non-common words. Identify bi-grams that correlate well with just one subcellular localization (e.g. chaperon with ER). \n\nVery thorough comparison to previous studies. Try to address problem with unstudied proteins by looking at homologs (HomoLoc) and allowing the user to describe the protein in her own words (DiaLoc). Works on pasted wikipedia entry.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/573ee62ce2224831b4f25c446d86eb1a/c/54a8e39ad2084dd5837eb7775c70f595", "date" : "2008-07-21T15:27:17Z" }, { "body" : "oops, Shirley live-blogged this while I just jotted down some nodes on paper. <a href=\"http://friendfeed.com/e/f57985d8-8b66-49b2-ac0f-7f5d6405e615/HL16-SherLoc-Predicting-protein-subcellular/\" title=\"http://friendfeed.com/e/f57985d8-8b66-49b2-ac0f-7f5d6405e615/HL16-SherLoc-Predicting-protein-subcellular/\">http://friendfeed.com/e...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/573ee62ce2224831b4f25c446d86eb1a/c/ba1bac21618540dda5b3514f621cc850", "date" : "2008-07-21T16:11:15Z" } ], "body" : "HL16: SherLoc: High-accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data. Hagit Shatkay", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/573ee62c/hl16-sherloc-high-accuracy-prediction-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T15:26:48Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "date" : "2008-07-21T15:50:58Z" } ] }
{ "_id" : "e/59027dcd051d46dfbb94fb084a1e7de3", "feed_id" : "ismb-2008", "comments" : [ { "body" : "&quot;Theory: Genetic redundancies should disappear&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/e7df3ceee5bc4328a28e42fd14582359", "date" : "2008-07-21T14:50:10Z" }, { "body" : "Opening question: Are redundant pairs co-regulated ?&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/e8b2d819030642edb81f16236a25eae2", "date" : "2008-07-21T14:51:43Z" }, { "body" : "CCR (Conditional Co-Regulation): predicts knockout phenotype", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/7858b01b115b4e7b9d2810ac3ed686d4", "date" : "2008-07-21T14:52:47Z" }, { "body" : "Ran Kafri talks now about two publications that challenge their results", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/93a3c21a85d148308d9415236c79c95a", "date" : "2008-07-21T14:53:47Z" }, { "body" : "Talking about S. cerevisiae: Due to 3 studies about 200 redundant pairs are known.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/29653b26238349b0a732a15530100155", "date" : "2008-07-21T15:00:13Z" }, { "body" : "Majority of redundant genes fall into the category of signal transduction.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/a69abbac52314a40aea25303ed9fb916", "date" : "2008-07-21T15:02:58Z" }, { "body" : "&quot;Biggest question, for what we don't have an answer for: What is the advantage of redundant duplicates ?&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/a1f6c379ee8d4009a16ce43f9db13ee5", "date" : "2008-07-21T15:04:52Z" }, { "body" : "Hypothesis: &quot;Redundancy serves the system for more robust control&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/3a27f8f003d54226a962d26b7d74c64e", "date" : "2008-07-21T15:06:23Z" }, { "body" : "Hopefully something concrete at ISMB 2009", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59027dcd051d46dfbb94fb084a1e7de3/c/7d099a760be04a9eb666ab6df8b4cd98", "date" : "2008-07-21T15:07:29Z" } ], "body" : "HL18: The Utilization of Redudancy by Genetic Networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/59027dcd/hl18-utilization-of-redudancy-by-genetic", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T14:49:40Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/59d311d040f145208c80a36ffe130b72", "feed_id" : "ismb-2008", "comments" : [ { "body" : "&quot;The answer to deal with the data growth is not in more and more hardware. Everything I show you today is independent of hardware.&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/f2b785561132415ca9637f5db7e0ddac", "date" : "2008-07-20T18:45:55Z" }, { "body" : "Gives a broad introduction. Talks now about paired-end reads used to classify mutations.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/c6a909856d714d988dd0b627965fcc1a", "date" : "2008-07-20T18:53:55Z" }, { "body" : "Take home message according to Arif Anwar about the genomics part he talked about is: &quot;Being able to do large scale genomics and reliably find structural variations and InDels is critical.&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/08c84f910d984b75a485e1bfdb7f6f30", "date" : "2008-07-20T18:58:35Z" }, { "body" : "Now he is sharing a few words about transcriptome sequencing.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/8ae48a6c28644cf8a7863a98a3cb0913", "date" : "2008-07-20T19:00:37Z" }, { "body" : "Coming to one of Synamatix's tools: SXOligoSearch. &quot;Hundreds of times faster on eukaryote-sized genomes&quot;. Well, faster than what ?", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/842fe894489f4fcfa78203fe2ae42b6a", "date" : "2008-07-20T19:02:41Z" }, { "body" : "Love that statement", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/346de6db922248e884f9707653868f16", "date" : "2008-07-20T19:03:56Z" }, { "body" : "Sales jargon, let's see the the stats to back it up.", "from" : { "name" : "Nube", "id" : "abbazeeba", "type" : "user" }, "id" : "e/59d311d040f145208c80a36ffe130b72/c/4538169ce1474f2ebb4ba276838373b1", "date" : "2008-07-21T09:03:09Z" } ], "body" : "IT06: Beyond Next Generation Sequencing", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/59d311d0/it06-beyond-next-generation-sequencing", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:43:40Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T19:03:52Z" } ] }
{ "_id" : "e/59d83c39d634488cb0acc329233038eb", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Lymphochip - mapping lymphocyte microarray data to interaction networks", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/8f6a3152d3fc40429a49e26bc6350289", "date" : "2008-07-20T18:20:09Z" }, { "body" : "Not clear to me how it works, but there are scores and p-values so it must be good", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/4f3ee98c72134fad9c363eb96c999458", "date" : "2008-07-20T18:23:46Z" }, { "body" : "Moving onto graph theory of course; looking for maximally-connected subgraphs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/85bbe5d36798466faedd17734272336a", "date" : "2008-07-20T18:26:17Z" }, { "body" : "Getting into some complex graph solving algorithms now; losing me a little", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/efa2026988c3452da52cd5e0068f92b9", "date" : "2008-07-20T18:29:42Z" }, { "body" : "They want to go open source but are tied to a commercial library", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/2398745d9c4044f2a9c0b73b03ee5299", "date" : "2008-07-20T18:37:11Z" }, { "body" : "Hmm, find it always odd to use a novel, general algorithm for a very particular data set", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/cf40b22f60f24f159d2cee791b5d527b", "date" : "2008-07-20T18:39:22Z" }, { "body" : "the only way they can do this solution to an NP-hard problem is to use very sparse graphs", "from" : { "name" : "sourav", "id" : "sourav", "type" : "user" }, "id" : "e/59d83c39d634488cb0acc329233038eb/c/9cc0acd73b514d24827425b2c396d7dc", "date" : "2008-07-20T19:37:07Z" } ], "body" : "PT10:  functional modules in protein-protein interaction networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/59d83c39/pt10-functional-modules-in-protein", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:19:20Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Sutee Dee", "id" : "thaiyoshi", "type" : "user" }, "date" : "2008-07-20T19:31:23Z" } ] }
{ "_id" : "e/5db414453ab040f7bf4b83e773989257", "feed_id" : "ismb-2008", "comments" : [ { "body" : "mm, no it does not. Works if you &quot;save as&quot; rather then click it", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/5db414453ab040f7bf4b83e773989257/c/03dc700a73bc49b29e157c4ef830ac4b", "date" : "2008-07-21T14:39:18Z" } ], "body" : "Ontology of Biomedical Investigations (OBI) poster presented during the main ISMB conference - <a rel=\"nofollow\" href=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/obi_ismb_poster_main.pdf\" title=\"http://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/developer/posters/obi_ismb_poster_main.pdf\">http://obi.svn.sourceforge.net/svnroot...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/5db41445/ontology-of-biomedical-investigations-obi", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T13:28:31Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-21T13:45:39Z" } ] }
{ "_id" : "e/60f95dea7f5d454da296abddbeb69cab", "feed_id" : "ismb-2008", "comments" : [ { "body" : "&quot;system genetics&quot; e.g. GFP-tag all proteins, knock-down all genes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/23eb325e4b8f4b28ab65c8fd575122ba", "date" : "2008-07-21T13:07:39Z" }, { "body" : "Technological development that drive bioiinformatics again", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/f1f35a2e755e4a79b01e0d2ff73eb122", "date" : "2008-07-21T13:10:06Z" }, { "body" : "Imaging:  advances in microscopy, lots of data to store and process; imaging analysis is difficult", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/0dc3390a4d284425810c2aa30d1b3d2e", "date" : "2008-07-21T13:10:34Z" }, { "body" : "low signal to nose, strong priors", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/3b8fd7f11fea4a4798f31f2257e54e4c", "date" : "2008-07-21T13:11:47Z" }, { "body" : "visual analysis of e.g. video not good for quantitation of variables", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/3fb02da109b4474b8a71ae8e809b7cb7", "date" : "2008-07-21T13:15:56Z" }, { "body" : "example computational analysis:  tracking of tubulin in mitosis", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/fa739dcc128e4718bd6b0b04d4a2c7ce", "date" : "2008-07-21T13:17:58Z" }, { "body" : "next example:  worm atlas cell expression; first, straighten your worm", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/ebb4564afddf4e1fbbd465f5c2c2bfbc", "date" : "2008-07-21T13:19:30Z" }, { "body" : "WANO:  tool for manual annotation of labelled worm nuclei images; attempt to make manual work efficient and provides training data", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/24dc0ae7d3804efc854e97a01804197f", "date" : "2008-07-21T13:21:09Z" }, { "body" : "Semi-automated, get the human in the loop at some point", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/335d1553e4ae4709a2795ffd76b8fff0", "date" : "2008-07-21T13:21:13Z" }, { "body" : "95% accuracy in automated recognition of worm cell type", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/c51a6d2ea26e4fdcafb10dfc033b2f51", "date" : "2008-07-21T13:23:10Z" }, { "body" : "Stereotypy in early development", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/1e025b18e6d74749a285262723dc89b7", "date" : "2008-07-21T13:24:22Z" }, { "body" : "Stereotypy - cell position is quite invariant in developmental stages", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/1468245b593e4d80997134c3db325a5e", "date" : "2008-07-21T13:24:39Z" }, { "body" : "Tracking mouse whiskers - cool but what's the application?", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/7539aefc3e4f4587867f7de116f64ab8", "date" : "2008-07-21T13:27:12Z" }, { "body" : "Moving on to &quot;tracking mouse whiskers&quot;: it is just what it sounds like", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/fe2f8fe09a7349399f74fe51e1e8e9a8", "date" : "2008-07-21T13:27:32Z" }, { "body" : "Next example:  fly brain digital atlas", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/533c18c14f8c4b48b5aeabe4c8526249", "date" : "2008-07-21T13:32:42Z" }, { "body" : "&quot;Imaging much more interesting than sequences. My life is very colorful these days&quot;. EW Myers", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/a595634cdfbb4f92a0ff50ad0101452f", "date" : "2008-07-21T13:33:41Z" }, { "body" : "Current efforts are annotation and models; but ultimate goal is mining data", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/03b33a77b79b4c5fa770c6cd6bfa6a9c", "date" : "2008-07-21T13:35:24Z" }, { "body" : "Fly brains:  20 000 neurons/hemibrain; largely hard-wired in the genome; 104 neural progenitor cells", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/6bd7575fa98548288cb01195ceffdb05", "date" : "2008-07-21T13:37:19Z" }, { "body" : "No epigenetics in brain development, should all be encoded in the genome seq only", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/d72a6388e37b40b7b92cd9fc17a31c5c", "date" : "2008-07-21T13:38:26Z" }, { "body" : "CS types in the audience get restless as Eugene waxes lyrical about fly brains", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/fc89ad1ce49941daaad837a4f5f80592", "date" : "2008-07-21T13:38:54Z" }, { "body" : "MARCM:  heat shock technique to &quot;light up&quot; cell lineages; stochastic", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/0f7904d65d8b44dfae2584be1d309e79", "date" : "2008-07-21T13:40:29Z" }, { "body" : "promoter-GFP fusions complement MARCM; aim is a complete brain cell space map", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/1b655930fd974c2c8b6a17b5a13a755b", "date" : "2008-07-21T13:43:34Z" }, { "body" : "mosaic analysis with a repressible cell marker (MARCM)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/69fcf835ea154af291b1323e25fb973a", "date" : "2008-07-21T13:43:36Z" }, { "body" : "Last part:  a stochastic mouse brain atlas; rather more complex than fly (100s of millions of neurons)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/6db3e3af21e04e718e4018a3fe04bb7a", "date" : "2008-07-21T13:48:42Z" }, { "body" : "Quite a fun talk.  Over-running a little now.  Main point:  microscopy is becoming high-throughput.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/60f95dea7f5d454da296abddbeb69cab/c/35e8b61fc4c84d9c9132d3b8cfb4a36f", "date" : "2008-07-21T13:55:27Z" } ], "body" : "Keynote 3:  Eugene Myers - &quot;imaging bioinformatics&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/60f95dea/keynote-3-eugene-myers-imaging-bioinformatics", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T13:02:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-21T13:36:16Z" }, { "from" : { "name" : "Thomas Lemberger", "id" : "thomaslemberger", "type" : "user" }, "date" : "2008-07-21T13:30:04Z" } ] }
{ "_id" : "e/622afc3c2d874878b2755ac61a28f5ef", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Lyfe style factors in disease. Ex - Smoking and lung cancer. There is a long delay between decay of smoking on the mortality of lung cancer. Conducted genome wide association study w(GWS), found 2 loci associated with lung cancer.  1 of the locus - genotype found in 10-15% of cases. Interesting problem of separating association with cancer from predisposition for addiction. If there is no association with other cancers that correlate with smoking then it is less likely to be do to dependence.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/e901241439334dbb9aa3cbaa25f44fba", "date" : "2008-07-20T14:59:09Z" }, { "body" : "Lung cancer samples: Pre-disposition to cancer? (In addition to pre-disposition to tobacco dependence). Identified two relevant loci.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/87a98694448b405b90132b17bcf7c109", "date" : "2008-07-20T14:59:25Z" }, { "body" : "Effect of one locus: 10-15% of risk of lung cancer can be attributed to the locus. (?)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/73b0921c54284d66a3c51d227ec7ee4c", "date" : "2008-07-20T15:01:41Z" }, { "body" : "Locus is close to nicotinic acetylcholine receptor... makes sense I guess. But, these receptors are also expressed in lung tissue. (Bind to nicotine and to lung carcinogens). Interestingly, this locus is only very weakly correlated with tobacco dependence (&lt;= 1 cigarette per day).", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/4d8d9355795e47dca347a0386fed08f3", "date" : "2008-07-20T15:03:18Z" }, { "body" : "Gene-environment association to asthma. Found a region with 30 genes associated to child asthma. 736 individuals GWA with additional gene expression. Combining eQTL with the region associated to disease, allowed them to focus in 2 genes.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/2045ba7862ea4f57b91b9798b746c3b0", "date" : "2008-07-20T15:08:23Z" }, { "body" : "Previous speaker was Mark Lathrop (France), now Mark Daly (Harvard)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/804767a0f15640c48a33d65208b68be4", "date" : "2008-07-20T15:15:27Z" }, { "body" : "Talk starting by Mark Daly <a rel=\"nofollow\" href=\"http://massgeneral.org/chgr/faculty_daly.htm\" title=\"http://massgeneral.org/chgr/faculty_daly.htm\">http://massgeneral.org/chgr...</a> about the HapMap project <a rel=\"nofollow\" href=\"http://www.hapmap.org/\">http://www.hapmap.org/</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/6ebf91b1200542c1be92e80955062898", "date" : "2008-07-20T15:16:57Z" }, { "body" : "If I understood this correctly they are using probes from genome wide association studies to look for copy number variations.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/d7b27ad28d04483487a0fa3dc4b822ca", "date" : "2008-07-20T15:26:53Z" }, { "body" : "Can use HapMap reference panel to map and combine previous SNP studies", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/73f3b2bcdb5e488dad4c671ce2d931d0", "date" : "2008-07-20T15:33:34Z" }, { "body" : "Meta-analysis of 3 or 4 studies on Crohn's disease yields &quot;striking excess of positive assocations&quot;", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/d51c439e51d74021b4bc09a5b6e740ad", "date" : "2008-07-20T15:34:20Z" }, { "body" : "However, the variants discovered with the meta-analysis have only weak associations with the disease, so they don't have much diagnostic value", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/bed8ce4b81194f31953ad35c28fea21f", "date" : "2008-07-20T15:36:12Z" }, { "body" : "3 recent studies for Chohn's disease. Meta analysis of the 3 studies shows that the power to identify association is limited to sample size. Many more associations found in the combined meta-analysis and used a replication study did not say directly how many were replicated. Caveat, no single variant explains well. combined association might explain 10% of disease propensity .", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/93d0fd4d2a6f4994a332a18488a51dbd", "date" : "2008-07-20T15:37:02Z" }, { "body" : "&quot;Getting to the Biology&quot; ... I wonder if he will live up to this title :). Showed a few experimental examples of how the variations implicated disrupt function but not how they might be related to cancer", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/934892b4b74a41058910dc99e37f86fb", "date" : "2008-07-20T15:38:10Z" }, { "body" : "Computational method: identify genes implicated by SNP of CNV, score pair wise similarity between genes using functional data. score genes by the number of related genes in other association studies, assign significance. Showing text mining approach for (?) functional association (I think). Using the text mining to look for words associated to loci (that are associated to disease). Nice example with height study.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/efa40451092e40709cc3c6b16e6a1393", "date" : "2008-07-20T15:46:11Z" }, { "body" : "Lead on scoring approach is soumya raychaudhuri", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/b3a20aff161546d3a0cf714816e278bb", "date" : "2008-07-20T15:47:15Z" }, { "body" : "General comment: There are plenty of genes to analyze now. Need more tools to look for the functional changes and look for treatment.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/50130a3690a248579a174989236e0906", "date" : "2008-07-20T15:50:00Z" }, { "body" : "For prediction, only had 40% success rate  (30/74)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/853c81389b3b4971b26cce58feacff55", "date" : "2008-07-20T15:50:01Z" }, { "body" : "Last speaker: David Balding (Imperial College London, UK)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/9825a7767f6846c5bf43c03c6b4be648", "date" : "2008-07-20T15:50:37Z" }, { "body" : "Great point - given that variants from GWAS explain little of the genetic contribution to disease, is the rest complexity (CNV, epistasis) or are the studies just so poorly designed (too much heterogeneity, still underpowered) etc", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/93a3eaba72b2490caaf473589d58956e", "date" : "2008-07-20T15:53:08Z" }, { "body" : "will focus on statistical issues: e.g. relatedness is important in linkage studies, but unknown and a hindrance in association studies", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/fcba728ddc584b8d848dc2d8b051e1f4", "date" : "2008-07-20T15:54:34Z" }, { "body" : "He is talking about the differences in concept between linkage and association. Thinking about how to find kinship to use in association studies.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/4efc06c333ab44d1bb342c64270fa811", "date" : "2008-07-20T15:56:28Z" }, { "body" : "Idea of approaches for intermediate relatedness and cryptic kinship", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/eaf09a581b44425386e3632f71b2be18", "date" : "2008-07-20T15:57:24Z" }, { "body" : "Approaches for evaluation of all snps - both work here and from matthew stephens", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/a5389c4a84b947b58435069b17a5512a", "date" : "2008-07-20T16:00:33Z" }, { "body" : "Haplotype associations - most recent work see <a rel=\"nofollow\" href=\"http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/7/972\" title=\"http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/7/972\">http://bioinformatics.oxfordjournals.org/cgi...</a>", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/e13373becde044bea03389e001c1ad01", "date" : "2008-07-20T16:09:17Z" }, { "body" : "use of time scaling to accelerate genetic simulations. Application to human history and selected sites reaching fixation. Can use to simulate GWA data. Have sequence level simulated data so will have whole genome and can take on issue of correlation head-on. Software is Fregene . Link is <a rel=\"nofollow\" href=\"http://www.ebi.ac.uk/projects/BARGEN/download/FREGEN/node1.html\" title=\"http://www.ebi.ac.uk/projects/BARGEN/download/FREGEN/node1.html\">http://www.ebi.ac.uk/project...</a>", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/622afc3c2d874878b2755ac61a28f5ef/c/5d0770e2703740e19521a01926b4fbe1", "date" : "2008-07-20T16:15:26Z" } ], "body" : "Genomes: Mining Genetic Variations", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/622afc3c/genomes-mining-genetic-variations", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T14:56:25Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Sutee Dee", "id" : "thaiyoshi", "type" : "user" }, "date" : "2008-07-20T19:38:51Z" } ] }
{ "_id" : "e/62a722baec2a4b0e87d74859d4a07f6b", "feed_id" : "ismb-2008", "body" : "Concept of &quot;species&quot; in flux w/regard to metagenomics/microbiome. Microbiome community composition may be considered a set of phylotypes, a set of genes, or maybe even just a set of functional capabilities.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/62a722ba/concept-of-species-in-flux-w-regard-to", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T14:23:42Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/64a9359b665d4788863f35773613d44f", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Full text and data are not online but not integrate. A role for bio-ontolgies here", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/000cc73257d1427e842838098ff082e5", "date" : "2008-07-20T15:50:53Z" }, { "body" : "Seamliss integration between data and the publication upon which the data are based. Seamless integration of the authoring and publishing process. New mediums for publications i.e podcasts and video. Professional networks", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/a683184cecb4480691b726c34374d0a1", "date" : "2008-07-20T15:52:51Z" }, { "body" : "Open access is key - emerging gneeration of digital scientists", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/9fe8ba6816474fac8e2f134af752d4b0", "date" : "2008-07-20T15:53:49Z" }, { "body" : "Improving semantic consistency in the literautre - best done at the point of authoring. Post processing to establish semantic content. Alot of effort goes into ascribing semantics to data submission, i.e strucuture to PDB - no semantic ascription on the literature", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/70a6ecd1410f4634a370d0f6e1315b31", "date" : "2008-07-20T16:01:36Z" }, { "body" : "Biolit - Integrating Open Literature and Databases <a rel=\"nofollow\" href=\"http://biolit.ucsd.edu\">http://biolit.ucsd.edu</a>", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/e8b10203e84a4beabf265748adf62a1d", "date" : "2008-07-20T16:06:06Z" }, { "body" : "BioLit mashes up data and paper and ontology terms and repurposes a new paper - with call outs and mouse overs. Why do we not do this at the time of authoring. The publisher is a warehouse for the workflow of scientific endeavor not just the result of the end product", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/70dfb2dc6d744259913412201ea2bc15", "date" : "2008-07-20T16:15:04Z" }, { "body" : "Biolit Plug-in exists for word - to enable this semantic annotation at the authoring time - ugh where is the Open office and latex plugings....", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/b7d6f35cf818417c9186eb51dfebb5d2", "date" : "2008-07-20T16:16:48Z" }, { "body" : "Scivee tv plug <a rel=\"nofollow\" href=\"http://www.scivee.tv/\">http://www.scivee.tv/</a>", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/1abf71b395974dac95c51277ed7a605a", "date" : "2008-07-20T16:28:17Z" }, { "body" : "Postercasts - go round taking videos and interview people at poster presentation session. The poster then exists longer than the 20 minutes of the session.", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/f5ba2cf598004c51adf31a48b7ba5f30", "date" : "2008-07-20T16:30:49Z" }, { "body" : "I like that idea about the posters :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/aae7e77de5fd47eba562d6c2fbc02005", "date" : "2008-07-20T16:35:26Z" }, { "body" : "The postercast idea is cool.  Get everyone a flip camera and record away", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/928f1310570b4a4b939a05223d6c0136", "date" : "2008-07-20T16:36:49Z" }, { "body" : "Needs more integration with semantic rich ontologies as opposes to tags. Need to disseminate the information.", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/1457fe4236654982858fe2329bd4dd0a", "date" : "2008-07-20T16:42:02Z" }, { "body" : "But what about authoring tools.  The barrier to entry is the tools for people to integrate their content with existing vocabularies.", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/2c2a55d3482a48999627830534dcf218", "date" : "2008-07-20T16:44:48Z" }, { "body" : "Of course even better would be a version of Calais or Zemanta dedicated to life science content", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/5ad6d2bab39e4a16ae919c494f7ade1e", "date" : "2008-07-20T16:45:08Z" }, { "body" : "Something linke Zemanta for life science would be perfect - via Google docs....when it gets a reference manager facility", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/64a9359b665d4788863f35773613d44f/c/dcfe19002ea049b08142ec24acd0671e", "date" : "2008-07-20T18:24:47Z" } ], "body" : "Bio-ontologies Keynote. Phil E. Bourne. Some Thoughts on Scholary Communication and the Role of Bio-ontologies.", "feed_name" : "ISMB 2008", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/64a9359b/bio-ontologies-keynote-phil-e-bourne-some", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T15:47:17Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Matt Wood", "id" : "themza", "type" : "user" }, "date" : "2008-07-20T18:27:18Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-20T17:58:08Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T16:36:26Z" } ] }
{ "_id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029", "feed_id" : "ismb-2008", "comments" : [ { "body" : "can we definea  protein ligad binding site from structure ? Maybe we could find alternative binding sites (off targets)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/6f37b64e42fc4eeab6fa4832cddf985b", "date" : "2008-07-18T14:55:56Z" }, { "body" : "off targets are important for side-effects but also to reposition drugs to treat other diseases.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/a084c14d8bc14989b6fe2251a91cba4e", "date" : "2008-07-18T14:57:42Z" }, { "body" : "Method: 1)start with known targer-ligand complex; 2)characterize primary site in a geometrical potential 3) search for off targets ; 4) dock ligand variants on primary and off targets 5) statistical analysis of docked ligands to find off targets", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/7ba1d52dd78a4da6a03fc4619527520e", "date" : "2008-07-18T15:01:06Z" }, { "body" : "reference on geometric potential: Xie and Bourne BMC Bioinformatics 2007", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/bf700564c1b549cfbd23a2e60b6f255c", "date" : "2008-07-18T15:02:08Z" }, { "body" : "Second reference: Xie and Bourne PNAS 2008 (I think) about geometric alignments.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/a4b46cbc8f924d07926fac8c24d79c9a", "date" : "2008-07-18T15:05:41Z" }, { "body" : "Damn, should have sneaked in. But I guess he's giving a similar talk on Monday at 3:15 pm.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/4eeb54e98522437483bac7e5da184223", "date" : "2008-07-18T15:11:17Z" }, { "body" : "Example of use: Reposition of existing TB drug. Found ligand binding link between NAD binding fold and SAM binding domain. Parkinson drugs binding SAM domains  could be use to bind a TB NAD domain. Drugs do inhibit growth of TB but at high doses. Ongoing work.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/e6074862f42a41f9a2e51185980b57ff", "date" : "2008-07-18T15:11:24Z" }, { "body" : "Example of side effects: Tamoxifen story: PLoS Comp Bio 2007 3(11)e217", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/65a339bd7e864230a613302a08ff80c7", "date" : "2008-07-18T15:12:33Z" }, { "body" : "Torcetrapib story. (nice plug to In the pipeline blog) Cholesterol pathway introduction. CETP probably target but multiple off-targets possible. Too many off targets to understand effects by single protein analysis. Pathway analysis of perturbed off targets is going to be important", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/6e041cd044484684ae76506a888f4978", "date" : "2008-07-18T15:20:44Z" }, { "body" : "Here's a link to the Tamoxifen paper: <a rel=\"nofollow\" href=\"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030217\" title=\"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030217\">http://www.ploscompbiol.org/article...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/2ba8fef0f3374de58bd9ff221f173ad6", "date" : "2008-07-18T15:24:58Z" }, { "body" : "Hmm, Pedro, I think we are in the same room... if only I knew what you looked like!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/2c4bb59afd744838a08dfca5e5537b1b", "date" : "2008-07-18T18:17:40Z" }, { "body" : "Yes you can.  If you can define a descriptor that encapsulates geometry, chemistry and biology. Non-trivial, but not impossible.  Also there are things like allosteric sites and predicting those from structure (<a rel=\"nofollow\" href=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=34332\" title=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=34332\">http://www.pubmedcentral.nih.gov/article...</a>)", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/668a560add4149d09aaf8da7d6594ca4", "date" : "2008-07-18T18:33:02Z" }, { "body" : "Audience member asked whether designing drugs to be deliberately promiscuous would become desirable, potentially for synergistic effects. Phil seemed to respond affirmatively, I'm a little more skeptical that drug companies would want to move in this direction. It seems to me that the more targets you have, the less you'll know about the actual potential outcomes and the harder it will be to design studies.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/71839e041c4b464bb68e19ceaed5224d", "date" : "2008-07-18T18:39:05Z" }, { "body" : "@Shirley: Industry is certainly thinking about it since a few years, cf. e.g. this paper: <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/16442279\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/16442279\">http://www.ncbi.nlm.nih.gov/pubmed...</a> (Hopkins, Can we rationally design promiscuous drugs?)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/9ae4bef7133d4dbe9e6a2db13d6c48e3", "date" : "2008-07-18T18:45:37Z" }, { "body" : "Multiple target families or multiple targets in a family?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/37e7958e96b24c78bb10f6a47c12dd79", "date" : "2008-07-18T18:47:15Z" }, { "body" : "Definitely an approach companies doing high throughput xtallography are taking", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/ba85aab547d3408fa4e304eae1923afa", "date" : "2008-07-18T18:48:32Z" }, { "body" : "Phil has a talk this evening titled: &quot;I'm not a PDBid I'm a biological macromolecule&quot;.  It sounds entertaining :)", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/6610d3ac07ea47a4b7d9302ba7ed4029/c/250fb52da6eb4011a81689bf4b8ff1de", "date" : "2008-07-18T18:56:49Z" } ], "body" : "Philip E. Bourne talking on drug targets", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/6610d3ac/philip-e-bourne-talking-on-drug-targets", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T14:55:15Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-21T19:15:28Z" }, { "from" : { "name" : "tim", "id" : "behindtherabbit", "type" : "user" }, "date" : "2008-07-19T17:07:56Z" } ] }
{ "_id" : "e/66300cc9cf254653a7531ff328607b93", "feed_id" : "ismb-2008", "comments" : [ { "body" : "some pictures from ISMB2008 (sorry for the duplication)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/66300cc9cf254653a7531ff328607b93/c/ebd868c4a24e4867a3ecb70d4ebef37e", "date" : "2008-07-25T00:38:45Z" }, { "body" : "want to put up a web site with many photos from ISMB 2008: anyone to help?", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/66300cc9cf254653a7531ff328607b93/c/49786a1ca7374ea7a3319b1ff2ff10bb", "date" : "2008-07-27T01:25:41Z" } ], "body" : "Flickr: &quot;ismb2008&quot; - <a rel=\"nofollow\" href=\"http://flickr.com/photos/tags/ismb2008/\" title=\"http://flickr.com/photos/tags/ismb2008/\">http://flickr.com/photos...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/66300cc9/flickr-ismb2008", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-25T00:38:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "date" : "2008-07-27T09:54:50Z" } ] }
{ "_id" : "e/685a365c9ef64ec1b5b748e2619a0790", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This is David Jaffe from Broad Institute", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/b2bf4b4bd8204de9856cbd5a4fd24798", "date" : "2008-07-20T20:55:54Z" }, { "body" : "ChipSeq - maps chromatin state to the genome", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/00c8a1b8a15246d68f9ac9f5971f2eec", "date" : "2008-07-20T20:56:50Z" }, { "body" : "David: ChipSeq &gt;&gt; ChIP-chip", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/935dc0f6aaf04b70a0a74d94bfc905ef", "date" : "2008-07-20T20:58:37Z" }, { "body" : "Epigenomics - looks at chromatin modification; identify gene switches", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/dce964b81ac34fce834966bb17ddfe75", "date" : "2008-07-20T20:59:20Z" }, { "body" : "model system is ES cell differentiation to neural types in vitro", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/2a5443b5c0804b659bf53604f7da7065", "date" : "2008-07-20T21:00:54Z" }, { "body" : "Looking at C methylation; use restriction digest to see 90% of CpG islands from analysis of 1% of genome", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/80bc6960ef1d459e8c7941358f06e2cf", "date" : "2008-07-20T21:04:48Z" }, { "body" : "in vitro differentiation causes different C-met than in vivo. This C-Met increases with the time in culture. maybe something similar going on in cancer ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/b639bbc4fdfc4803a9e550960e7e319e", "date" : "2008-07-20T21:07:26Z" }, { "body" : "Next up:  high throughput polymorphism discovery; bacterial and human examples", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/e839f893088c4429bda42f5713b85e45", "date" : "2008-07-20T21:07:28Z" }, { "body" : "SNP finding in M. tuberculosis strains; 3% not covered (high GC) but finds all the rest", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/eaf21f87f0984426bfd0639e0e35718c", "date" : "2008-07-20T21:09:12Z" }, { "body" : "Oh no, I am not in the session and have a poster on this...", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/94ef6e193f6b4abbaa763fdf0e497d88", "date" : "2008-07-20T21:10:22Z" }, { "body" : "V cholerae drug resistance example for SNP polymorphism mapping. (work by Jim Gomez and Deborah Hung) culture with and without rifampicin. sequenced both and only one difference found. repeated 5 times and only 2 mutations found. I am surprised that so few were found.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/8f51ff9f04d2402aa6655cc49003b78c", "date" : "2008-07-20T21:10:41Z" }, { "body" : "Wonder whether airline will reimburse me for that", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/fb6e3a2b68124dc2a2cc8cb168612112", "date" : "2008-07-20T21:10:53Z" }, { "body" : "Next example: looking for a single SNP determining antibiotic resistance mutation in V. cholerae (rif/rpoB)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/c087bf876d55499ba2bfa771e1869435", "date" : "2008-07-20T21:10:55Z" }, { "body" : "checking differences in Methylobacterium extorquans, growing for 600 generations in MeOH.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/911c7474e93e483782eab042f81d5598", "date" : "2008-07-20T21:11:34Z" }, { "body" : "And another:  directed evolution of MeOH utilisation; major genomic change on repeated subculturing", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/a3fce214d5654de5ad54c04340850af2", "date" : "2008-07-20T21:12:25Z" }, { "body" : "half of second chromosome deleted in strains cultured in MeOH for those 600 generations.Did not mention if change was observed often", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/d43fe7c124604acd804f95e1c3be8968", "date" : "2008-07-20T21:13:24Z" }, { "body" : "Moving on to human polymorphism discovery", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/e9db38cef95b43d5a73a1c33d5588f90", "date" : "2008-07-20T21:13:27Z" }, { "body" : "On to the humans; looking for somatic mutations that lead to tumours; sanger technology sensitive to stromal contamination; so, go to single molecule", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/09f63d83ad58493c834037595c98ca8e", "date" : "2008-07-20T21:13:31Z" }, { "body" : "Target genes -100 genes samples - 24 tumor normal pairs; new mutations not seen in previous technology", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/986e5f96bd4a45fd8069e53e9453a12c", "date" : "2008-07-20T21:15:22Z" }, { "body" : "Last example:  de novo genome assembly; trade off coverage, read length, cost (Illumina, 454)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/107acd37cc874ce4bc10ef968b8793f2", "date" : "2008-07-20T21:16:41Z" }, { "body" : "and we're at the final part: de novo sequence assembly", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/f70727c84b364ae987c0aa7aeda1fdfd", "date" : "2008-07-20T21:16:45Z" }, { "body" : "current technology trades read length with cost. what combination of tech to get better coverage at low cost", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/604a9a019a8c40cfb2be3429110b4ef4", "date" : "2008-07-20T21:17:47Z" }, { "body" : "tiny reads make it very hard to align sequences, new tools needed.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/06b829bbfd0343dc8b205904313c8f41", "date" : "2008-07-20T21:20:26Z" }, { "body" : "ALLPATHS:  algorithm for very short read assembly; test with simulated 30bp reads gives perfect e. coli assembly; pretty good with real data too", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/3ce817d8932d4f319f1e43411b8242e2", "date" : "2008-07-20T21:20:57Z" }, { "body" : "The ALLPATHS paper: <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/18340039\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/18340039\">http://www.ncbi.nlm.nih.gov/pubmed...</a>", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/4ebd9d057e7b4ae6a8a8c2e3f54ff309", "date" : "2008-07-20T21:22:54Z" }, { "body" : "comparing E. coli assembly with Illumina 454 and 3730. cost between illumina nd 454 similar as well as final assembly quality.Base quality 54-60.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/6a1918e62b274ec7b7c8bb16be15786b", "date" : "2008-07-20T21:25:56Z" }, { "body" : "99% of an E.coli assembly are in regions &gt;10kb and 90% in &gt;90kb", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/e851bee91ee54885b83607e450245086", "date" : "2008-07-20T21:27:51Z" }, { "body" : "Lots of assembly statistics now:  bottom line - it's pretty good; also for high GC; 36 bp reads good up to at least 40 Mbp genomes (fungi)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/1b7c5d3a56d64bdf82f56ded6dfeae1f", "date" : "2008-07-20T21:27:54Z" }, { "body" : "GC content is not the problem, repeats are a bigger issue imho", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/124ec0a7bcd942c6bc02c78d4003ddde", "date" : "2008-07-20T21:28:27Z" }, { "body" : "or the combination of repeat and high GC as in Mtb", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/9417e632fddc4e99a6531760fb12a5c2", "date" : "2008-07-20T21:29:04Z" }, { "body" : "&quot;Short reads sequencing can be used as THE general-purpose tool&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/45c0dcae01d44a2587777cb493cbb467", "date" : "2008-07-20T21:32:29Z" }, { "body" : "Is that one group ? scary slide", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/f3300104e13d423d8fa15940aba2a670", "date" : "2008-07-20T21:33:06Z" }, { "body" : "Acknowledgements - about a gazillion people.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/950b38b1211c44c1b40e398c4d9cf716", "date" : "2008-07-20T21:33:27Z" }, { "body" : "And this is a wrap, unbelievable 12 minutes left for questions. Very disciplined presenters until now.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/685a365c9ef64ec1b5b748e2619a0790/c/7452bb72d10a4d3b8475a78cabc9ea01", "date" : "2008-07-20T21:34:04Z" } ], "body" : "Keynote 2:  enormous amounts of sequencing", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/685a365c/keynote-2-enormous-amounts-of-sequencing", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T20:54:58Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/69fcc83932744d3d8a1f9db621862448", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Carlos P. Sosa started with an outline of the evolution of supercomputers.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/b5db271eb23d4105a13de5aeb76f3538", "date" : "2008-07-20T18:18:47Z" }, { "body" : "Explains the process of parallelization by the example of BLAST.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/e5220a72f99443afbc29a6e27ae27cfe", "date" : "2008-07-20T18:21:38Z" }, { "body" : "Now this is a talk I would have loved to attend.  What about high availability systems?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/e12d573755e44a5d8ba2837a28255140", "date" : "2008-07-20T18:25:41Z" }, { "body" : "Mentions mpiBlast and how it achieves parallelization", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/39e4ea99653e43d3bf614048649da7d5", "date" : "2008-07-20T18:27:49Z" }, { "body" : "Are we still limited to MPI?  There are so many clever ways of achieving distribution now, especially with something like BLAST", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/a119d86025cf44af96200eedd18323c3", "date" : "2008-07-20T18:28:49Z" }, { "body" : "Identified problems mit mpiBlast: &quot;scales only to 64 nodes, afterwards no improvement in parallelization&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/9ea15663ab0d45438f4b64b1b1fa9ad2", "date" : "2008-07-20T18:31:54Z" }, { "body" : "Carlos shows a nice animation of their implementation of mpiBlast on a massively parallel system: &quot;blue gene&quot;. Scales to ten of thousands of nodes.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/664b97c1695a48fbb975600a2c36d525", "date" : "2008-07-20T18:36:17Z" }, { "body" : "&quot;Complete genome to genome comparison (16 million sequences vs. 16 million sequences) in about 12h.&quot;", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/015c6d1e9f584567b485e6bf647bb13d", "date" : "2008-07-20T18:37:38Z" }, { "body" : "mpiblast works great provided the database fragments fit into node memory; even I managed &quot;supralinear increases&quot; a few years ago on a crappy cluster.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/26368b3e70754c208b327cea8b9086f5", "date" : "2008-07-20T18:38:43Z" }, { "body" : "Wraps up by talking about HMMer but only skips through the slides due to time. One would think that those slides would be more interesting than a 5 min introduction to supercomputing..", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/eed524e2c3f64b05a2ffaecefa3b098a", "date" : "2008-07-20T18:39:32Z" }, { "body" : "Wonder how he defines supercomputing.  Using a Blue Gene for BLAST is overkill.  Smart caching (memcache, etc) would be interesting to see", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/9e902332035d4a9695419c3b9783e7d3", "date" : "2008-07-20T18:47:27Z" }, { "body" : "Did the talk touch upon parallel computing with graphics cards? Current implementations provide upwards of 800 processors in a single GPU (ATI Radeon™ HD 4800, NVidia GeForce) for $300. How about a supercomputer at everyone's desk", "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/309c20e1fb8844b2b29709223f6b5e7e", "date" : "2008-07-20T18:54:57Z" }, { "body" : "Accelerated computing.  Programmatic models are still hard.  Too much (although CUDA is changing that a bit).  For most tasks, just massive distribution should work and that's cheap)", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/2aeaf811dece40c7a86d9f993086f693", "date" : "2008-07-20T19:06:07Z" }, { "body" : "Burke: Nope, no sighting of a GPU reference at all", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/bc754180ce2849b1b36cbee01dd57fd0", "date" : "2008-07-20T19:10:59Z" }, { "body" : "What about the Open Compute Language (OpenCL) initiative?", "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/6992ed365a90491a94377750d4704a49", "date" : "2008-07-20T19:11:08Z" }, { "body" : "That's a double no.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/69fcc83932744d3d8a1f9db621862448/c/ed453d00f2be400dbf5abf37243dc88a", "date" : "2008-07-20T19:14:31Z" } ], "body" : "IT05: Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers.", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/69fcc839/it05-next-generation-of-selected", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:18:00Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T18:25:07Z" } ] }
{ "_id" : "e/6a2e75a0ba4045c4847500aa1d665948", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The lady who picked up my tray appeared a little bit offended when I didn't finish my &quot;lasagna&quot;. :-/", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/6a2e75a0ba4045c4847500aa1d665948/c/56eefdc36b4e4ccaac992956868d71a0", "date" : "2008-07-18T18:34:49Z" }, { "body" : "Not asking for much. Water at lunch would be nice, and maybe something to snack on during the breaks. They also take away the coffee when breaks are over, which doesn't seem necessary. Throw us a bone, here!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6a2e75a0ba4045c4847500aa1d665948/c/815c6b37ed494de3b2d54f07bf020f6d", "date" : "2008-07-18T18:50:30Z" }, { "body" : "agreed, the lunch was really bad.  I think tomorrow I'll go outside the conference.", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/6a2e75a0ba4045c4847500aa1d665948/c/9c3f4142d9454f0c917934d1fd7871dc", "date" : "2008-07-18T18:52:37Z" } ], "body" : "On the non-science side, food and beverage offerings thus far leave something to be desired", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/6a2e75a0/on-non-science-side-food-and-beverage-offerings", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T18:23:49Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-18T18:40:28Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-18T18:34:05Z" } ] }
{ "_id" : "e/6e7969ceef4546178972e9e8171358ed", "feed_id" : "ismb-2008", "body" : "Wow, the coverage so far is very interesting. May be I stay here and remain an illusory persona.", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/6e7969ce/wow-coverage-so-far-is-very-interesting-may-be-i", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T15:30:26Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/6f99d0c20900455ca70355214629b8aa", "feed_id" : "ismb-2008", "body" : "Mark Wilkinson just gave a great talk on the future of BioMoby. I like the idea of Connotea-like tagging of the services to improve service discovery.", "feed_name" : "ISMB 2008", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/6f99d0c2/mark-wilkinson-just-gave-great-talk-on-future-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T13:41:04Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pierre Lindenbaum", "id" : "yokofakun", "type" : "user" }, "date" : "2008-07-19T20:48:15Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-19T16:41:54Z" } ] }
{ "_id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Nah - bloggers don't need icebreaker events ;-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/883e6c6ab75d4caf8a75cdc026c801f5", "date" : "2008-07-19T14:56:54Z" }, { "body" : "Hmm, perhaps as a newbie blogger, I still feel like I need them!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/50b182dce9994069aa7561aa9b625974", "date" : "2008-07-19T17:50:15Z" }, { "body" : "I think that you have been blogging longer than I ...", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/ca78cee78d6f46ca9315526b23fb3e2d", "date" : "2008-07-19T20:50:46Z" }, { "body" : "Unfortunately there was no way in hell to put it on the schedule *Edit* Given the weather, I am rather happy that scheduling made it impossible to attend", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/fff50fcef5984d949fc166290f139eb2", "date" : "2008-07-19T21:44:19Z" }, { "body" : "You all missed out on a good rain shower!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/202e9086c25b45e095da9a849b35dc81", "date" : "2008-07-20T01:19:33Z" }, { "body" : "Hmm, the opening reception was pretty deserted. Well, with only tidbits and a cash bar, I guess you didn't miss much..", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/1250fbea8e92460381cc0681329fffd7", "date" : "2008-07-20T11:39:12Z" }, { "body" : "I was at the reception as well, but left soon after to get real food.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/6fadeb8e69054f8fb2dfb28d57a53cc6/c/184a79fa23f847a9b8e675603fb25f32", "date" : "2008-07-20T14:19:49Z" } ], "body" : "Anyone else signed up for the &quot;orienteering&quot; event today?", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/6fadeb8e/anyone-else-signed-up-for-orienteering-event", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T14:51:07Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/718a151103214fef822ba2f944cfa1c7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "NMPDR - National Microbial Pathogen Data Resource", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/d561eada55024c15befac7a92c2aba2c", "date" : "2008-07-22T15:46:37Z" }, { "body" : "Genome upload:  fasta or genbank format; for GBK, can preserve original gene calls and reannotate functions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/bc82ea2d041d411da2ccd5068ebd5e21", "date" : "2008-07-22T15:47:41Z" }, { "body" : "Only handles prokaryotic genomes so far", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/88892b6261cb4e029dd0768d3c159434", "date" : "2008-07-22T15:49:31Z" }, { "body" : "Initial job processing 12-24 hours", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/175027a5b7d840d5b6c49cd3ac42f070", "date" : "2008-07-22T15:50:55Z" }, { "body" : "System for assigning functional roles:  requires sequence match to all components of a pathway", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/20e683ac01d442448f28c3ff6369ec7e", "date" : "2008-07-22T15:54:44Z" }, { "body" : "SEED viewer; shows your genome in context of other public genomes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/751a01ba39ad411388414d1ebe978ea1", "date" : "2008-07-22T15:57:18Z" }, { "body" : "Summary:  it looks like a nice tool for annotation and comparative analysis", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/29b604ef68af46babcf6c9814decdac2", "date" : "2008-07-22T16:01:58Z" }, { "body" : "You know, a lot of these technology track talks would work better as screencasts", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/c3dc8522ea2740c6996f24e86d5be3ff", "date" : "2008-07-22T16:02:47Z" }, { "body" : "hnn new ... record screencast in advance, add live soundtrack", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "via" : { "name" : "fftogo", "url" : "http://www.fftogo.com/" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/d16add20acc044a8919336679460ac50", "date" : "2008-07-22T16:14:24Z" }, { "body" : "Deepak - exactly; live website demos never seem to work well", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/718a151103214fef822ba2f944cfa1c7/c/15b4b210971146728e96226bc1953c81", "date" : "2008-07-22T16:22:58Z" } ], "body" : "TT26:  Leslie McNeil - &quot;RAST; rapid automated microbial genome annotation server&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/718a1511/tt26-leslie-mcneil-rast-rapid-automated", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T15:45:53Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/71e7d792e6554f34855ae9cfc4c23084", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Lars is also micro-blogging on Tumblr", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/71e7d792e6554f34855ae9cfc4c23084/c/bac3816881be428eb7380a31129885fe", "date" : "2008-07-18T15:43:04Z" } ], "body" : "Live: ISMB 2008 coverage - <a rel=\"nofollow\" href=\"http://larsjuhljensen.wordpress.com/2008/07/18/live-ismb-2008-coverage/\" title=\"http://larsjuhljensen.wordpress.com/2008/07/18/live-ismb-2008-coverage/\">http://larsjuhljensen.wordpress.com/2008...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/71e7d792/live-ismb-2008-coverage", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T15:43:04Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Robert Murphy: Mining images and caption from the scientific literature", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/bdb04defd4be40cc88d6efc2ffd8bb32", "date" : "2008-07-23T14:50:49Z" }, { "body" : "Images should be understandable without the text", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/62df120027f64ba0aedcd6ea8ab603a8", "date" : "2008-07-23T14:51:25Z" }, { "body" : "Examples: different colours, blank fields (information!), non-regular grids, graphs and images in the same grid", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/bd7f805747ae48f2ae96bcf30a3153cb", "date" : "2008-07-23T14:55:29Z" }, { "body" : "(missing due to slow connection)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/2ccfa495db124982a6e9584e2eeee56d", "date" : "2008-07-23T14:55:42Z" }, { "body" : "Hand label, supported by machine learning, store in data base. Recognize scale bars,  type of image, find the references between caption and figure.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/8042b834f90544898de68c31e226ee5d", "date" : "2008-07-23T14:57:35Z" }, { "body" : "SLIF: Subcellular location image finder <a rel=\"nofollow\" href=\"http://murphylab.web.cmu.edu/services/SLIF/\" title=\"http://murphylab.web.cmu.edu/services/SLIF/\">http://murphylab.web.cmu.edu/service...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/fd7132461c214c828417bf610f66bde9", "date" : "2008-07-23T14:58:03Z" }, { "body" : "Interrogate the database by protein, location, cell type, resolution, GO terms, etc.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/6b588a9994b74cc39f12e8e8592a5173", "date" : "2008-07-23T15:01:43Z" }, { "body" : "Future: more automated system, improve practices for defining figure contents in papers.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/0584a7e12cd042a2baae129910c2686d", "date" : "2008-07-23T15:03:53Z" }, { "body" : "Mentions the Elsevier journal contest", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/f52b3d1c6a3f49efb615e107d73ec9e8", "date" : "2008-07-23T15:04:47Z" }, { "body" : "Future: Structured digital caption - hidden XML tags, includes coordinates, panel label, panel type, annotations, scale and length units", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/e69d8407c1924299add950dbf7040532", "date" : "2008-07-23T15:06:00Z" }, { "body" : "Use of multilayer figures should be included with archival XML", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/ac84c14f05b848fca3729ed0ed7746e7", "date" : "2008-07-23T15:07:27Z" }, { "body" : "Very interesting work creating value, certainly underused", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/04e19687400048aea4173b63faa4e602", "date" : "2008-07-23T15:08:18Z" }, { "body" : "The presentation is available too <a rel=\"nofollow\" href=\"http://murphylab.web.cmu.edu/presentations/20080721ISMBtechtrackSLIF.pdf\" title=\"http://murphylab.web.cmu.edu/presentations/20080721ISMBtechtrackSLIF.pdf\">http://murphylab.web.cmu.edu/present...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7204f7e08e9443ffa5fe1fe8f1b4d4e3/c/569186089be4442f9374408922a803a7", "date" : "2008-07-23T15:12:32Z" } ], "body" : "SS07: The future of scientific publishing", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7204f7e0/ss07-future-of-scientific-publishing", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T14:48:50Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Thomas Lemberger", "id" : "thomaslemberger", "type" : "user" }, "date" : "2008-07-23T15:54:24Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-23T15:12:33Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-23T14:53:29Z" } ] }
{ "_id" : "e/7319e8dfc3384bb1be96c09738e28811", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Starts with overview of RNAi knockdowns", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/eb162ea2950347ac93cadc552ef2acc1", "date" : "2008-07-22T16:17:46Z" }, { "body" : "Introduction to genetic interaction mapping in C.elegans and S. cerevisiae Charlie Boon Joal Bader, Roth , Trey Ideker etc", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/3a8093f7b3ff44c693a63053eeca50d2", "date" : "2008-07-22T16:18:02Z" }, { "body" : "double RNAi perturbations to get genetic interactions in C.elegans. Quantified the interaction by progeny numbers", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/1288ec844c014af0927aba6b2cacdd87", "date" : "2008-07-22T16:20:05Z" }, { "body" : "Quite interesting experimental design; worms in plates fed RNAi-inducing bacteria", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/b7468a195641469cb276924bbd342d0f", "date" : "2008-07-22T16:20:08Z" }, { "body" : "Reference paper: <a rel=\"nofollow\" href=\"http://jbiol.com/content/6/3/8\">http://jbiol.com/content/6/3/8</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/77b31c7e801640669757dc10fe37d1cc", "date" : "2008-07-22T16:21:21Z" }, { "body" : "Method acronym is SGI :)  similar precision, better recall than other HT studies", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/2fc4f0d9e5dc4d1aba54ac0efa65bddc", "date" : "2008-07-22T16:24:12Z" }, { "body" : "clustering of genetic interactions to determine functional cohesive groups (calls them congruency groups/networks)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/741a2e632e574bf29921d9acc76f451a", "date" : "2008-07-22T16:26:15Z" }, { "body" : "They cluster &quot;congruent SGIs&quot; in a heatmap; can also construct network graphs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/ad35e6c8e1f84617a346741b70a5d1d9", "date" : "2008-07-22T16:26:17Z" }, { "body" : "Superimposed network uses SGIs and other data sources", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/afe84418ec004ac09655476318051bdd", "date" : "2008-07-22T16:27:27Z" }, { "body" : "He is following the structure of the JB paper linked above.Right .. this is a highlight session :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/d6aa2d70095a447c9731e8a74cf6da22", "date" : "2008-07-22T16:27:50Z" }, { "body" : "That phrase &quot;highly connected subnetworks&quot; crops up again", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/6f9955a6010e4ebebb606a1932fca174", "date" : "2008-07-22T16:28:22Z" }, { "body" : "Identification of gene modules; example given is bar-1", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/999aafae066a4abbacdbe4212fca831b", "date" : "2008-07-22T16:29:35Z" }, { "body" : "Red Nile dye accumulation - a simple assay for fat storage", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/20814f69bec84a58b4a63f2bbe16bd11", "date" : "2008-07-22T16:30:23Z" }, { "body" : "Negative interactions tend to fall across pathways in worm", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/c514017c9612428bb9ab04e59c2ae8ee", "date" : "2008-07-22T16:31:51Z" }, { "body" : "Bridging analysis - do SGIs connect subnetworks or are they contained within them?  Find significant bridging of SGIs between pathways.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/b6f23c92704b4161a942c7a7af5a0ffe", "date" : "2008-07-22T16:31:58Z" }, { "body" : "Are SGIs conserved across species C. elegans to S. cerevisiae. Not very conserved. Caveat mentioned that the interactions were targeted for metazoan pathways. Other possible caveats not mentioned (RNAi is knockdown not KO as in S. cerevisiae). Bridging between modules more conserved than individual interactions (hard to decouple between statistics and biological significance)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/3953f8d587a749a2b22b51f2daadcf89", "date" : "2008-07-22T16:35:37Z" }, { "body" : "Summary:  largest metazoan gene network dataset to date.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7319e8dfc3384bb1be96c09738e28811/c/9f8a9fda7a4d40039e5cc850a150b5b4", "date" : "2008-07-22T16:35:39Z" } ], "body" : "HL40: A global analysis of genetic interactions in C.elegans (Matthew Weirauch)", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7319e8df/hl40-global-analysis-of-genetic-interactions", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T16:17:03Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/767ff69a3c004e61bc58e673fc53de12", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Guess this is already old news: <a rel=\"nofollow\" href=\"http://www.molmovdb.org/\">http://www.molmovdb.org/</a> – &quot;Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis&quot;", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/767ff69a3c004e61bc58e673fc53de12/c/9c0a155445554030ad608e9eb1d0c95e", "date" : "2008-07-18T17:44:15Z" } ], "body" : "Mark Gerstein: Computational Proteomics: Studying Protein Motions from a Database Perspective", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/767ff69a/mark-gerstein-computational-proteomics", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T17:43:46Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/7b6c2b76f01a41508f9a621c417a3336", "feed_id" : "ismb-2008", "comments" : [ { "body" : "A method to automatically detect subgraphs within networks", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7b6c2b76f01a41508f9a621c417a3336/c/99616a4f36a540c4b8663f464b24ad1a", "date" : "2008-07-20T19:23:08Z" }, { "body" : "Color coding approach in general: assign random colors to nodes in the graph, repeat the assignment many times --&gt; should be able to detect query subgraph with high probability", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7b6c2b76f01a41508f9a621c417a3336/c/066610869df9473fbf552851abc73973", "date" : "2008-07-20T19:24:08Z" }, { "body" : "To clarify, you actually assign one of k colors at random to each node in the graph independently", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7b6c2b76f01a41508f9a621c417a3336/c/72ae0b44d0f74b05a3a971b3130a5d1d", "date" : "2008-07-20T19:25:27Z" }, { "body" : "I admit I'm not fully following this algorithm... anyone else here feel free to elucidate", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7b6c2b76f01a41508f9a621c417a3336/c/ccf586c2ef8a4147ba4e836bb90d9737", "date" : "2008-07-20T19:26:15Z" } ], "body" : "PT14: Biomolecular network motif counting and discovery by color coding - <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/papers.php#Protein_Interactions_and_Molecular_Networks\" title=\"http://www.iscb.org/ismb2008/papers.php#Protein_Interactions_and_Molecular_Networks\">http://www.iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7b6c2b76/pt14-biomolecular-network-motif-counting-and", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:22:37Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/7df7c23a51f94c5f82dc38695ff909cd", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Introduction: the rapid growth of databases and publications", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/54b2e6e4261e4ce6928e8fa2ff37311c", "date" : "2008-07-23T15:16:37Z" }, { "body" : "Blurring the distinction of databases and journals, particular in biology as a fact based science", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/d1eb1e57218a4c318657127363b6e733", "date" : "2008-07-23T15:17:30Z" }, { "body" : "distinctions between databases and journals are blurring", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/14ee500d4892450f9cabfd8b70eec752", "date" : "2008-07-23T15:17:49Z" }, { "body" : "New Vision: Science 2.0: studying the structure of publishing", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/2c91f07163fd4f09806f4a642137f5de", "date" : "2008-07-23T15:18:21Z" }, { "body" : "science 2.0 == science about science (??? wouldn't that be meta-science ???)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/c222ffb6659d4bd18146500c381d88f7", "date" : "2008-07-23T15:18:21Z" }, { "body" : "Science 2.0 as the science of science ( I don't think I agree with this definition)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/5dcfd4ee6c09425db7427dcb719b256c", "date" : "2008-07-23T15:18:44Z" }, { "body" : "Seeking a New Biology through Text Mining, Andrey Rzhetsky; <a rel=\"nofollow\" href=\"http://www.cell.com/content/article/abstract?uid=PIIS0092867408008167\" title=\"http://www.cell.com/content/article/abstract?uid=PIIS0092867408008167\">http://www.cell.com/content...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/238087b1633347a28e589cb6940420c1", "date" : "2008-07-23T15:19:20Z" }, { "body" : "Web mining: extract simple statements, find new information.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/6919d92b597e446da06ee5742e0b099a", "date" : "2008-07-23T15:19:55Z" }, { "body" : "Structure of science: Co-authorships, subjects", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/765f997896c649039bbd1eb4bc3e4458", "date" : "2008-07-23T15:20:20Z" }, { "body" : "Seringhaus et al., Chemistry Nobel Rich in Structure,  <a rel=\"nofollow\" href=\"http://www.sciencemag.org/cgi/content/full/315/5808/40\" title=\"http://www.sciencemag.org/cgi/content/full/315/5808/40\">http://www.sciencemag.org/cgi...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/6998f4421c1542f6a9e274ff1fc6d73e", "date" : "2008-07-23T15:22:09Z" }, { "body" : "Mashups: Search for nobel prize by subject <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/17204626\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/17204626\">http://www.ncbi.nlm.nih.gov/pubmed...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/322f20e9f83f4c1da26b9be348b1a142", "date" : "2008-07-23T15:22:14Z" }, { "body" : "using text mining to understand the structure of science, how ideas evolve, etc (the net is not great here). highly studied genes, knowledge bias. I think Valencia has been one of the first to show this.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/35f2fdec68834033a5e884d64ea689fe", "date" : "2008-07-23T15:22:19Z" }, { "body" : "Would also be easier to follow a less productive scientist", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/97543205f45a42398959f814f4aed463", "date" : "2008-07-23T15:23:00Z" }, { "body" : "Uncovering trends in gene naming; Michael R Seringhaus et al; <a rel=\"nofollow\" href=\"http://genomebiology.com/2008/9/1/401\" title=\"http://genomebiology.com/2008/9/1/401\">http://genomebiology.com/2008...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/f241fe3dee6d45da8760cd5eb74043e3", "date" : "2008-07-23T15:24:03Z" }, { "body" : "comparing literature nane over-representation with something like google search rank for gene names. Not surprisingly the names that are more abundant in &quot;human discourse&quot; than in literature are &quot;funny&quot; names that already exist.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/bcf182966ce9485e8addf68e38861ca6", "date" : "2008-07-23T15:24:52Z" }, { "body" : "comparing name co-authorship graphs in different institutes (that is an interesting idea .. it would be interesting to do this for different science topics)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/7e20ca9fabee4f2c801ef655ed679eb9", "date" : "2008-07-23T15:30:34Z" }, { "body" : "Structure of co-authorship networks in relation to consortia to identify bias in selection of targets for structural genomics projects", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/b20f33758b6a43d8b24df6b68b477b14", "date" : "2008-07-23T15:31:46Z" }, { "body" : "mapping science topics as whole (I did not get the name of the authors for this)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/eaecf466cb844905b433b656ae880cf8", "date" : "2008-07-23T15:32:36Z" }, { "body" : "Giving the example of RNAi where the birth of the field is captured in the databases. Clusters of co-authorship graphs over time", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/ac771f3bae8f43739f70f15c415b23ac", "date" : "2008-07-23T15:35:03Z" }, { "body" : "The impediments to the vision of a connected way of scientific publishing", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/cbd2e4083b554948a19ba8b294350b03", "date" : "2008-07-23T15:38:09Z" }, { "body" : "Federation rather the centralization", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/0414e86726c543acb65cb37a30776bea", "date" : "2008-07-23T15:38:27Z" }, { "body" : "getting to the idea of structured abstract. Involving the authors in the production of a machine readable abstract for the work.Saying that even a small set of structured abstracts could be used as gold standard.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/b57334a455a747eab604b5039f7d5092", "date" : "2008-07-23T15:42:29Z" }, { "body" : "Notes the absence of a social framework for protecting data on the web", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/132371d9926a487aa8cd4baf6bcf9c55", "date" : "2008-07-23T15:43:06Z" }, { "body" : "social framework for the protection of papers and data on the web. We don't know how to regulate data sharing online. a legal problem that needs to be resolved.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/e44ebe33f11e4ee2ae0fafa466de5bea", "date" : "2008-07-23T15:43:28Z" }, { "body" : "Lots of interesting lectures on the subject at <a rel=\"nofollow\" href=\"http://lectures.gersteinlab.org/\" title=\"http://lectures.gersteinlab.org/\">http://lectures.gersteinlab.org/</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7df7c23a51f94c5f82dc38695ff909cd/c/fec3fbc171a7436b99b195ca270125aa", "date" : "2008-07-23T15:45:37Z" } ], "body" : "SS07: The future of scientific publishing - Mark Gerstein on text mining to study the structure of science", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7df7c23a/ss07-future-of-scientific-publishing-mark", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T15:15:05Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-23T18:09:02Z" }, { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-23T16:45:35Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-23T15:31:00Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-23T15:20:14Z" }, { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-23T15:18:16Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-23T15:15:47Z" } ] }
{ "_id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "And she finished in time to take questions. At my last conference, the ICG in Berlin, only one or two out of 12 spekers managed.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/8337432dfef548c1af0d0abdb201fa58", "date" : "2008-07-20T13:48:31Z" }, { "body" : "Queston: Challenges for bioinformatics. Answer: treatments incomplete data sets, metagene nice but needs continued efforts. Functional assignments. Contextual metadata for environments, undefined as of now, needs more data, statistical analysis, study design, time series analysis, power calculation, sequencing coverage, compare across data sets, particular on the singeltons and other rare data points. Comparisons.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/6a67e0668f2e46d791bc418e044570be", "date" : "2008-07-20T13:55:08Z" }, { "body" : "Role of natural variability due to phages and microbial interaction. the catastrophic action of tooth brushing", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/5d2290de51ce40a0b869a369d888bc6e", "date" : "2008-07-20T13:57:10Z" }, { "body" : "Also mentioned that standards for annotation and metadata will be crucial.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/dab42956f6094665bff2d2b6511051c1", "date" : "2008-07-20T14:25:09Z" }, { "body" : "In terms of metadata, she said &quot;more is more&quot;! :)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/69bf2d8c0ca24afa87be49e8ff895f83", "date" : "2008-07-20T14:25:57Z" }, { "body" : "Shirley: Well it is hard to argue with that ;-)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/7ec60c9bdc0f4711b6cc3d1da32d36b0/c/0b5e92c74be94c12a58d867369d5b5cc", "date" : "2008-07-20T14:53:27Z" } ], "body" : "Conclusion: need a proper definition of microbiome, do stable and similar is it between humans, resilience, deliberate manipulation feasible or useful? I found it a nice review of what is happening", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7ec60c9b/conclusion-need-proper-definition-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T13:47:13Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-20T15:41:30Z" } ] }
{ "_id" : "e/7f6c467b8d074bdcac2bde53492d5fdf", "feed_id" : "ismb-2008", "body" : "&quot;When it smells like a banana, it is done&quot; - Randy Rettberg from MIT speaking about one component from the Registry of Standard Biological Part - <a rel=\"nofollow\" href=\"http://partsregistry.org/IGEM:MIT/2006/Growth_dependent_banana_odor_generator\" title=\"http://partsregistry.org/IGEM:MIT/2006/Growth_dependent_banana_odor_generator\">http://partsregistry.org/IGEM:MI...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7f6c467b/when-it-smells-like-banana-is-done-randy", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T14:27:53Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-19T16:41:48Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-19T14:30:14Z" }, { "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "date" : "2008-07-19T14:29:59Z" } ] }
{ "_id" : "e/7f9de14a494e430a894d3826264e41b6", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Missed the start; now giving demo of CAMERA website", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/2a083be87d9a45498a696680b78f87ce", "date" : "2008-07-21T16:01:06Z" }, { "body" : "Live website demos are always precarious :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/ef9370d4abf344f2b57b4a81e915ed99", "date" : "2008-07-21T16:02:37Z" }, { "body" : "URL:  <a rel=\"nofollow\" href=\"http://camera.calit2.net/\">http://camera.calit2.net/</a>", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/cb071aede6414953b4276dd5a83ed9f8", "date" : "2008-07-21T16:04:49Z" }, { "body" : "The website looks quite nice; dashboard layout, FTP for raw data", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/3f6b50e25db64b3b9b2aead115b79e2f", "date" : "2008-07-21T16:05:14Z" }, { "body" : "It's not the slickest presentation, but does look like a good web resource", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/8dbb4aaa915148ebb2188cd8c5ed32e8", "date" : "2008-07-21T16:11:46Z" }, { "body" : "Also contains an annotation pipeline", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/7f9de14a494e430a894d3826264e41b6/c/28590b7c6659431e930a46b421abfdd5", "date" : "2008-07-21T16:12:01Z" } ], "body" : "TT13:  CAMERA - metagenomics tools + data", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/7f9de14a/tt13-camera-metagenomics-tools-data", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T16:00:16Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/80bfba0dbc8548c1b96910acf1217584", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I thought this panel discussion deserved more than micro-blogging, so I posted it on my blog with a few comments.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/a43ffcdd1ba94041916a428c69d21fbd", "date" : "2008-07-20T18:08:35Z" }, { "body" : "Nice blog post.  Many biology labs do have &quot;embedded&quot; bioinformaticians and you are right:  these are non-permanent postdocs.  I've been one for years!  I don't believe that academia knows how to employ computational biologists in a productive, career-enhancing way.  I've always argued that there should be permanent &quot;bio IT support&quot; roles, but if you're not a potential go-getting future group leader, they just don't know what to do with you.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/a48a53143e2745c1ae8f6fa93be49044", "date" : "2008-07-20T20:09:10Z" }, { "body" : "Thanks Michael", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/b622b83c62a646118895dd2225874418", "date" : "2008-07-20T20:14:37Z" }, { "body" : "Which is why some institutes have an IT core (hutch/ISB).  Not sure how well those work, but its clearly a non-academic track.  Plus your salaries need to be higher, since your competition pays more", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/5030eec9056c411481eb367262db26a0", "date" : "2008-07-20T20:15:32Z" }, { "body" : "I really should comment on this in more length as I am 'bio IT support' (a term I don't like because really it's data analysis support and not 'IT' support), although I confess there is a chunk of that.  Certain institutes do embrace this, and I believe that our unit is valued within the University.  Neil, your point is spot on though, we have to go out and repeatedly *tell* people how we might be useful to them, because it never occurs to *them* that you might be useful.", "from" : { "name" : "Daniel Swan", "id" : "dswan", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/f00536f699cd408dbe86dad731f3c6d2", "date" : "2008-07-20T20:30:16Z" }, { "body" : "What we end up with is with the people who already appreciate that bioinformatics is essential to their work or people who really have no idea what bioinformatics is about, but need a gently push in the right direction.  Then you get the people who think you are their local computing service and here to fix their wireless.  Oh well.  It's a great way to engage in a broad range of scientific questions and I love it :)", "from" : { "name" : "Daniel Swan", "id" : "dswan", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/b6ad110fecfc405a864909231ce3c22d", "date" : "2008-07-20T20:32:40Z" }, { "body" : "I am with Neil on this and even discussed it on Thursday night. WE get lost in a limbo and no one knows what to do with us. We are not IT and at the same time not PIs or don't want to be post-docs.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/80bfba0dbc8548c1b96910acf1217584/c/7d11799df2fe43a7bed18cd381ca0400", "date" : "2008-07-20T21:20:48Z" } ], "body" : "&quot;Career Paths in Bioinformatics and Computational Biology&quot; - <a rel=\"nofollow\" href=\"http://blog.mckuhn.de/2008/07/ismb-2008-career-paths-in.html\" title=\"http://blog.mckuhn.de/2008/07/ismb-2008-career-paths-in.html\">http://blog.mckuhn.de/2008...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/80bfba0d/career-paths-in-bioinformatics-and", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:07:48Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "date" : "2008-07-20T21:18:18Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-20T18:23:52Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T18:19:04Z" } ] }
{ "_id" : "e/82756e3309b4456084d6ed74f06ccc41", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Here are my movements folks.  Land Toronto July 16 17:35.  I'm free July 17, 18 and possibly 24; will catch up with Paulo on at least one of those days.  Unlikely to have cell phone access, but will check email, twitter and friendfeed as often as possible.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/82756e3309b4456084d6ed74f06ccc41/c/55ec889e2a324eb0999a7bf6e5e9bf66", "date" : "2008-07-15T02:19:44Z" } ], "body" : "Anyone coming to Toronto and interested in meeting me please send me a message at nuin AT genedrift DOT org and we can organize something", "feed_name" : "ISMB 2008", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/82756e33/anyone-coming-to-toronto-and-interested-in", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-12T00:39:41Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/855284348e084375a89928aafbd0b333", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Archive of twitter hash tag <a href=\"http://friendfeed.com/search?q=%23ismb2008\">#ismb2008</a> - you could try just &quot;ismb&quot; too", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "id" : "e/855284348e084375a89928aafbd0b333/c/1cdd5fa76be24d04aec4441a702c4f87", "date" : "2008-07-24T03:19:09Z" } ], "body" : "ismb2008 - Twitter Search - <a rel=\"nofollow\" href=\"http://search.twitter.com/search?q=ismb2008\" title=\"http://search.twitter.com/search?q=ismb2008\">http://search.twitter.com/search...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "url" : "http://friendfeed.com/ismb-2008/85528434/ismb2008-twitter-search", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-24T03:19:09Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/8b4457bd39b145fbb4fc8910f4ef3328", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The pub (Loose Moose Tap &amp; Grill) is located at 146 Front Street West\n<a rel=\"nofollow\" href=\"http://tinyurl.com/6qs4ku\">http://tinyurl.com/6qs4ku</a>.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/8a19e33aae194615993efcd58c67620e", "date" : "2008-07-17T02:51:39Z" }, { "body" : "Any place called the Loose Moose has to be good", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/5f94c4d1ae004deb9a168a01dfb04be8", "date" : "2008-07-17T02:58:34Z" }, { "body" : "I've never been there even though it is as downtown as it can be, right in front of the Union Station, close to the Rogers Centre (old Skydome), CN Tower and conference centre.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/33393cc832584fdb99a37faac607aaf3", "date" : "2008-07-17T03:06:51Z" }, { "body" : "When is this event?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/098f4a58f3d74957938c55aa2e5a6d91", "date" : "2008-07-17T18:45:56Z" }, { "body" : "July 21st, sorry my bad.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/0dce7f6c8ee8414ba07fa6b60a19e612", "date" : "2008-07-17T23:28:48Z" }, { "body" : "The venue has changed: from the Loose Moose to the Elephant and Castle, but the time remains the same. <a rel=\"nofollow\" href=\"http://tinyurl.com/5heg2s\">http://tinyurl.com/5heg2s</a>", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/1038d5eab2b046c3bf546d7216ed693a", "date" : "2008-07-19T12:42:32Z" }, { "body" : "Is there a specific time for this? Dinner time? after the poster session (8-ish)? Also would this be an appropriate place to brainstorm for the BoF - if most of us will be there then it might make sense, but don't want to impose on the hosts of course", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/cd1d719ddd774712983c08504c61e7dd", "date" : "2008-07-21T16:29:47Z" }, { "body" : "6:30 the invitation says.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/8b4457bd39b145fbb4fc8910f4ef3328/c/38b61daf96134dceb48b2b013d495d71", "date" : "2008-07-21T16:50:22Z" } ], "body" : "Michelle Brazas and Francis Oullette would like to invite those of you that will be (or are) in Toronto this coming week for the ISMB meeting to join us for a gathering of the friends of CBW for refreshments and munchies.", "feed_name" : "ISMB 2008", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/8b4457bd/michelle-brazas-and-francis-oullette-would", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-17T02:51:08Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/8c0140d8dd5e4e92b31dea8b25e19c61", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This was a talk at the Student Symposium. They first took a protein interaction network and weighted edges by common Gene Ontology (GO) terms. They then identified nodes of known function and &quot;flowed&quot; the probability through the network. In the end, they got nice, big modules. My concern is only that they probably just recovered the GO annotation through their algorithm... Of course it's important to take such previous info into account, but you shouldn't be surprised when you get good modules out in the end, as the Gene Ontology was likely partly built by looking at these modules.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/8c0140d8dd5e4e92b31dea8b25e19c61/c/0b6a96d7f0ca48dd854cf456203a1362", "date" : "2008-07-18T15:16:02Z" } ], "body" : "Cho Young-Rae: Functional module detection by functional flow pattern mining in protein interaction networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/8c0140d8/cho-young-rae-functional-module-detection-by", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T15:12:53Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "tim", "id" : "behindtherabbit", "type" : "user" }, "date" : "2008-07-19T17:09:55Z" } ] }
{ "_id" : "e/8d4e3ece0a2549718270d52c31f0751a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "lots of people trickling in for this one with the provocative title", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/61c13ec62010479883a168ff227aef59", "date" : "2008-07-21T15:12:42Z" }, { "body" : "highest scoring paradigm predominates in comp bio - sequence alignment, max parsimony, max likelihood, etc, but holds only asymptotically as data grows compared to unknowns. Many comp bio problems have high dimensionality unknowns compared to the data, so highest scoring paradigm no longer holds", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/69777807918347fbb88a70f59916f7ef", "date" : "2008-07-21T15:14:22Z" }, { "body" : "obviously max score is attractive, because how can you do better than the most likely, or highest scoring? Question posed: &quot;how good is a sample size of one, even if it's optimal?&quot;", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/778d37fd82ed4b15a1d95720e867ba2c", "date" : "2008-07-21T15:15:10Z" }, { "body" : "Using example of predicting optimal structure for RNA sequence - will you pick the one with lowest free energy? Would you be willing to bet? He'll take your bet and even give you odds.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/753d84019ba54568adb996c8bd471cb1", "date" : "2008-07-21T15:17:41Z" }, { "body" : "Essentially data gives weak recommendation to any one solution. But often people mean the optimal solution, _and others like it_.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/63a89a8c91e641fca6e0cd7604302806", "date" : "2008-07-21T15:18:45Z" }, { "body" : "For this example, suggest clusters of structures. In a published study, showed that min free energy one does not necessarily fall in the best clusters. Is often an outlier in a weighted ensemble of structures. Would you be willing to bet on an outlier?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/fa3667388dff4ea2ae50f3f24e68fa3d", "date" : "2008-07-21T15:20:35Z" }, { "body" : "Showed distance to mean and distance to mode on same plot. For both, the &quot;optimal&quot; score is far from where the vast majority of data lie", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/ddf32059f0b04ed3b8647c2d604a4647", "date" : "2008-07-21T15:23:43Z" }, { "body" : "Instead, use statistical decision theory. Would like functions that allow you to model probability of solutions, calculate minimum expected loss", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/7703b7cb1cd141e5926bd2dd79d72823", "date" : "2008-07-21T15:24:44Z" }, { "body" : "Examples of loss functions: 0/1 loss is what highest scoring methods have. Hamming distance loss is where you lose a point for every bit different you are from centroid", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/c846cf3bf75345d38a30829ea035ba03", "date" : "2008-07-21T15:26:39Z" }, { "body" : "Ensemble-based estimators: weight all members of ensemble. Increased loss with more differences (hamming). Find solution that maximizes the marginal probability over all components of the solution, based on centroid. --&gt; Marginal probabilities are sufficient statistics, find path through them that maximizes the sum. If no constraints, then solution is to select best of each component as max summing path", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/4222a0ebc585464d80bf441a7feb3986", "date" : "2008-07-21T15:29:26Z" }, { "body" : "Theorem 3: centroid also optimal under power law loss. Theorem 4: centroid is the feasible solution nearest to mean under squared error loss", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/d325f783a28741c4a60d2858b86b6126", "date" : "2008-07-21T15:31:52Z" }, { "body" : "Back to RNA structure prediction. Centroid approach improves 3.5% in sensitivity over max free energy, and 30% improvement in precision.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/87a831f52b6c4c75aae2466f65bd3f93", "date" : "2008-07-21T15:33:56Z" }, { "body" : "Another example using alignment of protein structure by homology. Compares rmsd to actual structure for probability (consensus) based alignments vs. maximum similarity alignments. RMSD almost always higher for max similarity.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/77863fd62d4948d0b33ff7042a27e8e7", "date" : "2008-07-21T15:35:50Z" }, { "body" : "Remaining issues: how to compare solutions without ground truth? --&gt; a good estimator will have much of the posterior space compactly around itself (narrow bayesian confidence limits). Also, multimodality - the posterior space will be multimodal, no single solution will be representative of the entire posterior.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/d2268c0358154d57962a9fd828cfa778", "date" : "2008-07-21T15:38:47Z" }, { "body" : "FIrst audience question: if we're still using discrete binary components, isn't this still like 0/1 loss? Answer: the components are 0/1 but we are summing over many components so it is a consensus/centroid approach.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/cc28a028e9564afc8deec0925b5898e1", "date" : "2008-07-21T15:51:02Z" }, { "body" : "Take away message - highest scoring paradigm not the best choice for many comp bio applications. Probability and consensus based methods are better for cases where you have high-dimensionality of unknowns, and they give you a much better idea of the confidence associated with predictions.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/49f670440f714dabb009e11bb9d1fdf9", "date" : "2008-07-21T15:52:46Z" }, { "body" : "Paper with much of the work presented in this talk: Ding et al 2005 - <a rel=\"nofollow\" href=\"http://www.rnajournal.org/cgi/content/full/12/3/323\" title=\"http://www.rnajournal.org/cgi/content/full/12/3/323\">http://www.rnajournal.org/cgi...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8d4e3ece0a2549718270d52c31f0751a/c/9b9dde2ef15940faa48b24d8551e63f8", "date" : "2008-07-21T15:53:24Z" } ], "body" : "HL18: Toward the demise of scoring procedures for discrete high-dimensional unknowns", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/8d4e3ece/hl18-toward-demise-of-scoring-procedures-for", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T15:12:19Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/8dbb58faea1c49aaa890a2e1a3fb161c", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Can cluster results and assign function to orphans strongly associated with genes or complexes of known function. The component networks produced a lot of predictions, not many of which overlapped with existing databases or studies, but they are going for coverage and focus on true orphans.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/8dbb58faea1c49aaa890a2e1a3fb161c/c/380787f8b7cd4aaea15a07fbe7f4875b", "date" : "2008-07-19T13:26:02Z" } ], "body" : "Andrew Emili giving a talk about assigning function to orphan genes in e.coli. Uses tandem MS and other exp'tl methods to generate PPI network, uses genomic information to create genome context network, then integrates the two with a propagated topological overlap measure.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/8dbb58fa/andrew-emili-giving-talk-about-assigning", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T13:24:16Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "tim", "id" : "behindtherabbit", "type" : "user" }, "date" : "2008-07-19T17:05:08Z" } ] }
{ "_id" : "e/8eef6aac8641460bbb365460eae8e88e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This is a pharmacogenetics type talk", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/343f127fd8534034b33e09aaee3812a2", "date" : "2008-07-20T15:00:40Z" }, { "body" : "Focusing on lung cancer at the moment", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/c76ad0f3c9e74a169befc57da891c7cf", "date" : "2008-07-20T15:01:45Z" }, { "body" : "Is a nicotine receptor really a lung cancer marker?  Apparently so.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/e26c221ec5b843feb8f3dbce7787966b", "date" : "2008-07-20T15:03:24Z" }, { "body" : "Neil - do you have a link to the final speaker list/order and abstracts? the link i had bookmarked is still vague: <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/special_session_details.php#session1\" title=\"http://www.iscb.org/ismb2008/special_session_details.php#session1\">http://www.iscb.org/ismb200...</a>", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/4923e555cb5844d9a24fb72246f7deef", "date" : "2008-07-20T15:03:56Z" }, { "body" : "Shannon - I'm relying on the conference program CD just now; not sure what's online", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/22484c4f6b574e4492d2c741f91a8c71", "date" : "2008-07-20T15:08:15Z" }, { "body" : "Moving on to asthma - markers on chr 17", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/fb235182d2be4a2dad42792a9a9fbec3", "date" : "2008-07-20T15:08:57Z" }, { "body" : "Web tool for linking gene expression and disease markers; didn't catch the URL", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/97758d64a796453085a3368a380fa91b", "date" : "2008-07-20T15:10:12Z" }, { "body" : "Paper from same study is Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KC, Taylor J, Burnett E, Gut I, Farrall M, Lathrop GM, Abecasis GR, Cookson WO, A genome-wide association study of global gene expression.\nNature genetics 39:1202-7 2006\nPubMed ID: 17873877", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/519444c44d014c71bc63f5eb78263ec9", "date" : "2008-07-20T15:12:08Z" }, { "body" : "Last example is a Crohn's disease marker; chr 5; a gene-poor region", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/c1cd2eccb68d4364bf5716f36e622333", "date" : "2008-07-20T15:13:39Z" }, { "body" : "Please repost the web tool for linking gene expression and disease markers, if you find it again, Neil.  It would be very useful.", "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/4753cc9638ae46f5a838799854118968", "date" : "2008-07-20T16:16:31Z" }, { "body" : "URl for browser is <a rel=\"nofollow\" href=\"http://www.sph.umich.edu/csg/liang/asthma/\" title=\"http://www.sph.umich.edu/csg/liang/asthma/\">http://www.sph.umich.edu/csg...</a>", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/4e06f027550346778e2d7cd0faf4d9b4", "date" : "2008-07-20T16:24:08Z" }, { "body" : "Shannon's on the ball - thanks!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/3b04e9b52df3403889546ead52489980", "date" : "2008-07-20T17:51:12Z" }, { "body" : "This is probably one area where the pharma industry has spent a considerable amount of time the past few years (look at work by GSK and Rosetta/Merck).  Any of those folks around?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/8eef6aac8641460bbb365460eae8e88e/c/5ee19ea248a74355b4dc8b99e4da85fe", "date" : "2008-07-20T17:53:01Z" } ], "body" : "SS01:  mining genetic variation", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/8eef6aac/ss01-mining-genetic-variation", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T15:00:20Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T17:51:30Z" }, { "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "date" : "2008-07-20T16:15:25Z" } ] }
{ "_id" : "e/940ea9a42a274d0c8168f69c707ce21a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Pardon me. I don't get it. Where's the proceeding?", "from" : { "name" : "Kuan-Ting Lin", "id" : "woodydon", "type" : "user" }, "id" : "e/940ea9a42a274d0c8168f69c707ce21a/c/756c9861de754f14a63c40c1090a881a", "date" : "2008-08-04T08:36:33Z" }, { "body" : "<a rel=\"nofollow\" href=\"http://bioinformatics.oxfordjournals.org/content/vol24/issue13/index.dtl\" title=\"http://bioinformatics.oxfordjournals.org/content/vol24/issue13/index.dtl\">http://bioinformatics.oxfordjo...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/940ea9a42a274d0c8168f69c707ce21a/c/99c4e6aacad44e589bb7033af1654d42", "date" : "2008-08-04T15:27:04Z" }, { "body" : "Thanks", "from" : { "name" : "Kuan-Ting Lin", "id" : "woodydon", "type" : "user" }, "id" : "e/940ea9a42a274d0c8168f69c707ce21a/c/2356dabf22634b709d02d68d6fba5ca1", "date" : "2008-08-05T07:40:36Z" } ], "body" : "ISMB 2008 Conference Proceedings now available on-line at: <a rel=\"nofollow\" href=\"http://bioinformatics.oxfordjournals.org/current.dtl\" title=\"http://bioinformatics.oxfordjournals.org/current.dtl\">http://bioinformatics.oxfordjo...</a> - <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/ismbnews.php\" title=\"http://www.iscb.org/ismb2008/ismbnews.php\">http://www.iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Kuan-Ting Lin", "id" : "woodydon", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/940ea9a4/ismb-2008-conference-proceedings-now", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-08-04T08:36:11Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/95138e78183a4045915f646b42fdcecb", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Initial Example Yeast QTL strains", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/45193f8993e44458b0816bfa7a139350", "date" : "2008-07-21T16:19:43Z" }, { "body" : "&quot;Genetical Genomics&quot; integration and analysis of genotyping and expression to identify regulators", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/2b9c2307408e4277a302faec400681ac", "date" : "2008-07-21T16:22:52Z" }, { "body" : "Reviews common problems: large genetic regions, multiple hypothesis testing, and that complex trait composition applies to regulators as well (multiple regulators potentially of small effect and with redundancy)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/d103d96351c94d4db5165b9602f9f45f", "date" : "2008-07-21T16:24:06Z" }, { "body" : "Integration of physical interaction data - with idea that it will give us true regulators. If we have 10 genes in locus, true regulator should be closer wrt network distance than others to target gene. random distribution of others (not sure if i agree with that- could be other types of correlation)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/c8dacc99ace64afb810086d901672ed6", "date" : "2008-07-21T16:26:08Z" }, { "body" : "Need scoring to rank interactions and identify true regulator", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/6c40399c18b34a8293bc8524d26d64d5", "date" : "2008-07-21T16:26:45Z" }, { "body" : "Simulation (based on idea of communication as electric current). weak confidence equivalent to high resistance etc.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/eaca1d310dba447a87d598e8c77eb3fb", "date" : "2008-07-21T16:30:48Z" }, { "body" : "Note: score all pathways not just most likely", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/4e4c41429e634c21b948b0ef4d4be843", "date" : "2008-07-21T16:31:38Z" }, { "body" : "Computational Fine mapping example. reference was knock out expression data in yeast. 550 associations between regulator and target gene. random accuracy =22%.  Tu et al random walk 48%, shortest path 64% eqed 72%", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/b53f146fbbee44b7b2a6987f5ea0688d", "date" : "2008-07-21T16:34:05Z" }, { "body" : "Integrating several e-qtl loci. Idea similar to epistasis that main effects may not be significant but joint effects are important. Inclusion of genes not significant but which connect loci", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/116507bfd0254f80a3e649eb91a380a9", "date" : "2008-07-21T16:35:58Z" }, { "body" : "Important point: several e-qtls that reinforce same part of the network. ability to mine integrated information", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/e286da52059b4783bfae74887ddc500f", "date" : "2008-07-21T16:37:57Z" }, { "body" : "<a rel=\"nofollow\" href=\"http://www.andreas-beyer.de/\">http://www.andreas-beyer.de/</a>", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/93868bf1e0ea4d82872eeda589c22707", "date" : "2008-07-21T16:38:36Z" }, { "body" : "Q: wouldn't bayesian networks be more natural approach rather than circuit with constraints", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/3f38a1ba87534ee98076ac483a8e2eaa", "date" : "2008-07-21T16:40:16Z" }, { "body" : "Q:how were weights define? Prob based on confidence of PPI. Also ability to exploit correlation in expression", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/95138e78183a4045915f646b42fdcecb/c/e1b82edcf4564c2a80e14a8cf6b17f43", "date" : "2008-07-21T16:42:58Z" } ], "body" : "HL 24: eQED", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/95138e78/hl-24-eqed", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T16:17:47Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-24T22:57:44Z" } ] }
{ "_id" : "e/970b2087488048e885d4d7286aee9b2f", "feed_id" : "ismb-2008", "comments" : [ { "body" : "the Start conference will have an ombudsman following twitter/IM/email to give the audience a voice. nice idea.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/970b2087488048e885d4d7286aee9b2f/c/11f87ed4765b42f69a4cae50629945e1", "date" : "2008-07-26T10:40:25Z" } ], "body" : "Conference hack: Embracing the backchannel at Start - <a rel=\"nofollow\" href=\"http://www.veen.com/jeff/archives/000996.html\" title=\"http://www.veen.com/jeff/archives/000996.html\">http://www.veen.com/jeff...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/970b2087/conference-hack-embracing-backchannel-at", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-26T10:39:23Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-26T22:12:22Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-26T16:03:46Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-26T13:19:01Z" } ] }
{ "_id" : "e/9873da2181704c3d905623fb871be624", "feed_id" : "ismb-2008", "comments" : [ { "body" : "a blog post about a tutorial on ncRNA", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "id" : "e/9873da2181704c3d905623fb871be624/c/de251037e1954080aa3ce9cd14d99832", "date" : "2008-07-21T04:16:55Z" } ], "body" : "Jacks of Science » Blog Archive » ISMB 2008 and What the Heck Are Non-Coding RNA - <a rel=\"nofollow\" href=\"http://www.jacksofscience.com/biology/ismb-2008-and-what-the-heck-are-non-coding-rna/\" title=\"http://www.jacksofscience.com/biology/ismb-2008-and-what-the-heck-are-non-coding-rna/\">http://www.jacksofscience.com/biology...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "via" : { "name" : "Bookmarklet", "url" : "http://friendfeed.com/share/bookmarklet" }, "url" : "http://friendfeed.com/ismb-2008/9873da21/jacks-of-science-blog-archive-ismb-2008-and-what", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T04:16:55Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pawel Szczesny", "id" : "freesci", "type" : "user" }, "date" : "2008-07-21T09:01:50Z" }, { "from" : { "name" : "Jason Stajich", "id" : "stajich", "type" : "user" }, "date" : "2008-07-21T04:21:30Z" } ] }
{ "_id" : "e/9c1cfad12248471fa6ae300d35c04402", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Missed the start; seems to have developed an SVM classifier for thermostability", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9c1cfad12248471fa6ae300d35c04402/c/359bc3b409d345d1927cbe086f197ebd", "date" : "2008-07-22T15:28:11Z" }, { "body" : "88% accuracy; 12/14 thermostable variants classified correctly.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9c1cfad12248471fa6ae300d35c04402/c/e19dbc2f29fb4b2c9d2bd24e5778a357", "date" : "2008-07-22T15:29:42Z" }, { "body" : "And finished way ahead of time", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9c1cfad12248471fa6ae300d35c04402/c/ffff9899631044cd879a05fbde511872", "date" : "2008-07-22T15:30:30Z" } ], "body" : "PT35:  predicting thermostability change from multiple sequence mutations", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/9c1cfad1/pt35-predicting-thermostability-change-from", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T15:27:39Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/9d11301616624b90b97722555d3c3027", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I know the conference is not quite over, but it'd be cool if we could connect in Dopplr to see when we can live-micro-blog the next conference :) <a rel=\"nofollow\" href=\"http://www.dopplr.com/traveller/mkuhn\" title=\"http://www.dopplr.com/traveller/mkuhn\">http://www.dopplr.com/travell...</a> (If you don't know Dopplr, it's a Web 2.0 service that lets you see if you happen to travel to the same town as someone you follow.)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/9d11301616624b90b97722555d3c3027/c/c14cbabedc284fe4a06ac4a91e67cec6", "date" : "2008-07-22T03:47:00Z" }, { "body" : "<a rel=\"nofollow\" href=\"http://www.dopplr.com/traveller/mndoci\" title=\"http://www.dopplr.com/traveller/mndoci\">http://www.dopplr.com/travell...</a>", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/9d11301616624b90b97722555d3c3027/c/114aa030bd80430bb0b15ca77112346f", "date" : "2008-07-22T04:23:21Z" } ], "body" : "Dopplr?", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/9d113016/dopplr", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T03:45:10Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "date" : "2008-07-22T12:38:55Z" } ] }
{ "_id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc", "feed_id" : "ismb-2008", "comments" : [ { "body" : "From a Plant Physiology paper (I think)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/527e561a6bbc47a5a2ddcb38e9ea8254", "date" : "2008-07-21T18:44:01Z" }, { "body" : "From a distance, Matt rather resembles J Eisen.  Or indeed, Peter Jackson.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/0bd538abc9bb4a0b869dd2dffc312eea", "date" : "2008-07-21T18:44:52Z" }, { "body" : "A quick primer on plant metabolism and the various relevant -omics", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/d742ba945bad401abe80a4c32a8fbb19", "date" : "2008-07-21T18:45:55Z" }, { "body" : "resembles Eisen's or Jackson's enthusiasm", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/9297fc6cfe9946c0ba6fee0abb8da4ce", "date" : "2008-07-21T18:48:59Z" }, { "body" : "Experimental high-throughput PPi still expensive; an issue for plant scientists?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/d797121799454ce695c212637b3cb5d0", "date" : "2008-07-21T18:49:00Z" }, { "body" : "guess that's what you mean", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/1221e726d93f4948a21f3ed24fe058a9", "date" : "2008-07-21T18:49:10Z" }, { "body" : "The dreaded phrase &quot;excel spreadsheet&quot; - we'll let that pass.  Oh, here it comes again.  138 000 rows.  Oh well.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/7cf972cef00c43f9ace600a536b20c43", "date" : "2008-07-21T18:49:34Z" }, { "body" : "Basic idea:  conserved orthologs = conserved interactions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/be57545587744aad93c2ea5b558009fd", "date" : "2008-07-21T18:51:37Z" }, { "body" : "This is all Arabidopsis, by the way.  Only 217 confirmed reactions from ~ 69 000 predictions.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/846ce8da4bbc4f17b88400e68722fd75", "date" : "2008-07-21T18:54:24Z" }, { "body" : "Spreadsheet again, at least they are using Office 2007, previous versions had to stop at 65000 rows", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/bd65468ba8d54f7eb249a82f09759315", "date" : "2008-07-21T18:54:41Z" }, { "body" : "One problem is that interactome data is lacking even from the non-plant model organisms.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/eb23d7b03c794438950b258110ed1a1d", "date" : "2008-07-21T18:55:34Z" }, { "body" : "Attempting to estimate total interactions from the known ones; also assigning confidence values from various criteria (largely based on degree of conservation)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/28b28099e2ab482f88c1c2e93070e353", "date" : "2008-07-21T18:57:39Z" }, { "body" : "Looking at the high confidence list:  see highly connected hubs, as in other species", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/2b42eb11089e4f09ae68dc80b9dd1e51", "date" : "2008-07-21T19:00:34Z" }, { "body" : "&quot;Giant hairy ball&quot; - your typical figure of a network :)  A plug for Cytoscape.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/af68e52b54334cfc9f19917e0b47c31f", "date" : "2008-07-21T19:01:25Z" }, { "body" : "Interaction correlates with SCL.  Who'd have thought?  Or is it that SCL and interaction predictions agree well?  Same for co-expression.  But then, you have to be co-expressed to interact, right?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/bd446b22e3e34e768dda9424074b3837", "date" : "2008-07-21T19:03:31Z" }, { "body" : "The original paper <a rel=\"nofollow\" href=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=17675552\" title=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=17675552\">http://www.pubmedcentral.nih.gov/article...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/9f3f798146764c4696392e31ee67d9de", "date" : "2008-07-21T19:03:44Z" }, { "body" : "Now trying to extend known pathways:  focusing on trafficking (syntaxin, snares, snaps)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/b6af1ad8b228409796fbe4300b51276b", "date" : "2008-07-21T19:06:08Z" }, { "body" : "URL:  bar.utoronto.ca", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/2de889be96994f4881f8a9d27282f3b5", "date" : "2008-07-21T19:07:04Z" }, { "body" : "He's fearsomely fearless.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/5226af56b0bd479da8db19b6673b9378", "date" : "2008-07-21T19:07:29Z" }, { "body" : "Final example:  new Calvin cycle proteins", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/9e93433d59ba4fdb96d1f54d1af6adcc/c/59cadd44167a4c0294e0f1b504b88584", "date" : "2008-07-21T19:08:41Z" } ], "body" : "HL27:  Matt Geisler - &quot;a predicted plant interactome using conserved eukaryotic interactions&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/9e93433d/hl27-matt-geisler-predicted-plant-interactome", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T18:40:05Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T18:45:21Z" } ] }
{ "_id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I arrived in question time. He is throwing stress balls as a prize to anyone asking questions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/1c7cd333c7c74fb6adaf427f1d3ddf93", "date" : "2008-07-20T17:29:08Z" }, { "body" : "Mentioning a plug-in that allows the export of a Cytoscape session to a webpage.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/0c5cf989abc84b8eb62a60b905d40ca1", "date" : "2008-07-20T17:35:22Z" }, { "body" : "Someone suggested that it would be useful to add images background to the nodes. Right now it is possible to do it as a programmer but not as user. Gary is showing a plugin called GenePro that lets users color nodes with different colors (pie shapes).", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/2b643f5a58444338bd4b75f2379ed57e", "date" : "2008-07-20T17:38:51Z" }, { "body" : "Someone asked about blinking nodes. general laugh from the audience :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/8ef1475a9c654f6a8b499c50c365c649", "date" : "2008-07-20T17:49:42Z" }, { "body" : "Re images to nodes: Guess they were looking at STRING/STITCH :-)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/89c4a14d9ef542998dc4859665ec25db", "date" : "2008-07-20T17:49:45Z" }, { "body" : "Roadmap: Web version of cytoscape that does not depend on Java, support for scripting, more modular design of the program to hopefully improve plugin lifetime (reducing changes on whole code). General focus on making it easier for developers to make new plugins.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/8a7d33067c084f8fb982e88328a625cf", "date" : "2008-07-20T17:54:01Z" }, { "body" : "Cytoscape announce at Google Groups <a rel=\"nofollow\" href=\"http://groups.google.com/group/cytoscape-announce\" title=\"http://groups.google.com/group/cytoscape-announce\">http://groups.google.com/group...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/b9856bb326a149e7bee9e8f0b5621723", "date" : "2008-07-20T18:01:05Z" }, { "body" : "Demo next Wednesday", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/7403e9571d6e43109006840c8c14e27c", "date" : "2008-07-20T18:02:43Z" }, { "body" : "Interesting.  I've always felt that Cytoscape was a platform waiting to be taken out of its cage.", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/a0eafb5d7fa64b0e87956b1c2ed40592/c/3546f01c5f7f4a8f8d101c8bbb69c74b", "date" : "2008-07-20T18:03:47Z" } ], "body" : "BOF: Gary Bader talking about Cytoscape - <a rel=\"nofollow\" href=\"http://www.cytoscape.org/\">http://www.cytoscape.org/</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/a0eafb5d/bof-gary-bader-talking-about-cytoscape", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T17:28:27Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T17:33:36Z" } ] }
{ "_id" : "e/a1d9b73ab86b4bfcb3a4c3c84e1636ff", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The same is often true for presentations, people just don't seem to realize that they will talk about the content anyway.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/a1d9b73ab86b4bfcb3a4c3c84e1636ff/c/dda0a24501cc400ba9e857cc5e97db01", "date" : "2008-07-20T13:45:28Z" }, { "body" : "The quick and lazy way to make a poster is to chop up your manuscript, blow it up, and lay it out on your poster. It's just laziness.", "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "id" : "e/a1d9b73ab86b4bfcb3a4c3c84e1636ff/c/cbffd9b6177a4f77974f0750d7c4ba8d", "date" : "2008-07-20T16:33:21Z" }, { "body" : "It's one reason I don't like scientific conferences as much as I should.  The quality of presentations is poor (not content per se, but the presentation itself)", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/a1d9b73ab86b4bfcb3a4c3c84e1636ff/c/c170b024a8794f30ba8b2af4c472fa4f", "date" : "2008-07-20T16:38:03Z" }, { "body" : "If only people saw it more as an opportunity to present your work in a creative way - often more effective than a paper because the format isn't as constrained and you can be there to discuss any fine points.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/a1d9b73ab86b4bfcb3a4c3c84e1636ff/c/0e3dde8c29f048309e447fa831908f1d", "date" : "2008-07-20T17:25:34Z" } ], "body" : "Took a quick look at the posters - why do people insist on putting so much text on them?", "feed_name" : "ISMB 2008", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/a1d9b73a/took-quick-look-at-posters-why-do-people-insist", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T13:22:32Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T16:37:09Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-20T14:21:09Z" } ] }
{ "_id" : "e/a4699e8b803d4652a65a89702ae56a92", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I don't think it is possible to force start collaborations but I suspect that we have plenty of common ground to work with. Maybe we could take one or two hours to explore possible collaborative projects. This could take any form from brainstorming over a glass of beer, writing up some possible projects or really hacking away at something. Possibly some of the current projects listed in the Biogang wik (<a rel=\"nofollow\" href=\"http://openwetware.org/wiki/Biogang\" title=\"http://openwetware.org/wiki/Biogang\">http://openwetware.org/wiki...</a>)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/d074bcf85e754f8582adf9340f0f3726", "date" : "2008-07-07T18:31:42Z" }, { "body" : "I can try to provide the space. I will see if there is any meeting room available at MaRS as soon as I get back there next week. Would be good to know the number of people.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/d340c22b350146c0a15e3cf2ddbe1aa4", "date" : "2008-07-07T18:53:47Z" }, { "body" : "Ah now this is what we're talking about ... good luck folks", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/d49d533d3a4244b693cbeeac79a55421", "date" : "2008-07-07T21:59:22Z" }, { "body" : "A programming project seems like an easier way to go than a research project, also as we could continue easier. I've been thinking about visualization of protein interaction data in a non-graph like structure (tables for purifications, color codes for localization and co-expression and simple graphs for sparse interactions y2h, genetic interactions) but never got round to do it.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/aaa17e64c4e3406498b1d797a48f7e08", "date" : "2008-07-12T12:44:19Z" }, { "body" : "Picturing images of pair programming geeks, although not sure anyone here actually does that", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/8e56fae80b7242659bdcd38d085059b0", "date" : "2008-07-12T16:39:31Z" }, { "body" : "I like Roland's ideas.  Those tangled network graphs have never done anything for me in terms of visualisation.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/ed01b1ad0d79410cb633d8142006fad5", "date" : "2008-07-13T23:52:47Z" }, { "body" : "The problem will be the programing language of choice for a programming project :) I am up for anything just for the fun of it but outside Perl I will be less useful. So, yes for a visualization project. A plugin for cytoscape  or we do our own ? what language ? As a possible research project, I never got around to really start this one on domain evolution (<a rel=\"nofollow\" href=\"http://code.google.com/p/domainevolution/\" title=\"http://code.google.com/p/domainevolution/\">http://code.google.com/p...</a>) and it could be something we could get fast results on.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/5fd9379ebd114442bd235d19f1e92e59", "date" : "2008-07-14T01:07:04Z" }, { "body" : "Project wise, Pedro's proposal is very doable and more of a programming exercise than a full blown research project, too. Python is an awesome language and my preferred choice, despite being more confident in Perl. I would leave it up to you, let's see who is in beyond Pedro, Neil and me.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/c7772d2ce14d48f4b72db76c05b3c15d", "date" : "2008-07-14T08:14:32Z" }, { "body" : "Pedro, I've always been impressed by your Google Code project page and initially was going to join up, but other things got in the way.  It would be good to take another look at that.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/83e403d1a41e4b869eda7cd357969d96", "date" : "2008-07-14T10:57:20Z" }, { "body" : "I'd also join in. I'd vote for Python (instead of write-only Perl :). Perhaps we could have a beer Sunday night? By then everyone should be there.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/c0c568222ddf47039084bb8a7479b792", "date" : "2008-07-16T19:57:56Z" }, { "body" : "I'd also would like to contribute. However, I got rather limited experience with Python up until now.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/b5ba918ada534bb4878a27c88e565dc5", "date" : "2008-07-17T09:26:18Z" }, { "body" : "Pedro: I can check out the domain evolution (<a rel=\"nofollow\" href=\"http://code.google.com/p/domainevolution/\" title=\"http://code.google.com/p/domainevolution/\">http://code.google.com/p...</a>) folder OK, but its empty. I would like to be prepared and there are 12 hours of offline travel ahead of me. Sunday would be good for me.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/d4f3dbad44084cef94f45896cad91880", "date" : "2008-07-17T09:28:06Z" }, { "body" : "As I said .. I really never got to the point of actually starting the project :) (very literally nothing in there :). Still, getting the info together (domains from SMART and PDB structures) should be quick enough. Then the different tasks can be set in parallel. We need numbers for domain expansion and correlate that with different possible explanations. Each explanation can be tested by a different person (stability, metabolic cost, specificity, etc). (continues)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/d173f4c5f0934886a7c677c959b58bb5", "date" : "2008-07-17T18:40:13Z" }, { "body" : "It would not be finished in one day but enough could be done to check if there is something there or not. I should say that there is already a Genome Research paper showing that stability of a gene family correlate with its size (number of sequences matching it) <a rel=\"nofollow\" href=\"http://www.genome.org/cgi/content/full/15/3/385\" title=\"http://www.genome.org/cgi/content/full/15/3/385\">http://www.genome.org/cgi...</a> but I think we could explore other explanations.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/f1f5398d34f243d4b729c62f81c39c86", "date" : "2008-07-17T18:46:16Z" }, { "body" : "I wonder whether Nodebox (<a rel=\"nofollow\" href=\"http://nodebox.net/code/index.php/Home\" title=\"http://nodebox.net/code/index.php/Home\">http://nodebox.net/code...</a>), a Python graphics utility, would be useful? I haven't used it yet and have limited experience with building software so I don't really know, but it might be cool to play around with.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/c22bb3f8c93b44038ec4b5b7e9c0a25c", "date" : "2008-07-17T19:41:18Z" }, { "body" : "Nodebox has big drawback that it is only for Macs.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/f6d735f5f0a847a3ab35fd20ab566720", "date" : "2008-07-17T20:49:11Z" }, { "body" : "I have nodebox working on linux (Ubuntu).", "from" : { "name" : "Mitchell J Stanton-Cook", "id" : "mscook", "type" : "user" }, "id" : "e/a4699e8b803d4652a65a89702ae56a92/c/15dc65e33bf741869413c0c4a8e2bd67", "date" : "2008-07-19T09:48:56Z" } ], "body" : "ISMB hackaton ? ", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/a4699e8b/ismb-hackaton", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-07T18:28:26Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-16T19:54:14Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-07T20:47:36Z" }, { "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "date" : "2008-07-07T19:42:18Z" }, { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-07T19:05:38Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-07T18:44:18Z" } ] }
{ "_id" : "e/ab641776df824a909510db8db1450219", "feed_id" : "ismb-2008", "comments" : [ { "body" : "molecular dynamics is computationally expensive on traditional chips. one way around this is to design your own chip. Another approach is to use graphics processing units (GPUs) - a la Folding@home on the Playstation3", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/e9ca1c812265441183345ee0e7693eeb", "date" : "2008-07-21T19:17:32Z" }, { "body" : "GPUs are advancing much faster than CPUs, currently you can do in a day on a GPU what would take a year or more on a CPU", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/a59642dace2c4ee98e1f701d15b5ee0c", "date" : "2008-07-21T19:18:59Z" }, { "body" : "Note: Simbios is a National Center for Biocomputing, so they make everything open and available for download and reuse.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/28b17d35aa8d4e1486d70e3a69e29b54", "date" : "2008-07-21T19:19:38Z" }, { "body" : "OpenMM (open molecular modeling) project - library of methods for MD, code available for AMD and Nvidia GPUs. Isolates hardware-specific issues. Like mentioned before, currently being run on thousands of machines via Folding@home. Library currently links with Gromacs, and looking for collaborators for other MD packages. This project started by Pande group at Stanford", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/8c843d386e3f4744830bd7d4e7e389cd", "date" : "2008-07-21T19:21:50Z" }, { "body" : "Showing a demo of CPU and GPU side by side doing MD calculations on one laptop (i think via virtual machine). GPU is chugging away, spitting out results for every 100 timesteps about 2x/second, it took the CPU a minute to spit out just one.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/060baa19ac834aee8d23dd23d3c6bd46", "date" : "2008-07-21T19:23:45Z" }, { "body" : "Audience question: if GPUs are so great, why aren't we doing everything on GPUs already? Answer: programming on the GPU is a pain right now. [Shirley's note: The industry is currently motivated by video game industry, hopefully this will change as other applications become profitable]", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/0128c46d56714740b4437f2b0046658a", "date" : "2008-07-21T19:25:29Z" }, { "body" : "Now switching over to Simbody - open package for coarse-graining MD simulations as alternative way to speed up calculations. <a rel=\"nofollow\" href=\"https://simtk.org/home/simbody\">https://simtk.org/home/simbody</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/318fb6b8b978430bb5b98c08d2ffdb3f", "date" : "2008-07-21T19:26:19Z" }, { "body" : "Uses internal coordinates to force certain groups into rigid bodies, reduce degrees of freedom by order of magnitude", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/2c3131581a21457d9285fc8d8c57fc56", "date" : "2008-07-21T19:27:52Z" }, { "body" : "Showing sample code for setting degrees of freedom, now showing a demo of 3 residues, first one with no reduction in df, second residue with Simbody defaults, and third residue where there are no df.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/6fb4cfe74d654d14adc00834db71debc", "date" : "2008-07-21T19:29:49Z" }, { "body" : "Now showing demo of a larger molecule with a helix set to rigid and other residues having certain degrees of freedom. This is good if you're not interested in what the helix is doing (assume it is rigid) but are interested in seeing how other parts of the molecule behave; it will speed up your calculations a lot and allow you to see much more.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/cac4672f6ea0436c8d052e5f371b944f", "date" : "2008-07-21T19:31:23Z" }, { "body" : "Audience question: how does rigidifying parts of the molecule affect the dynamics of the non-rigid parts of the molecule? I didn't catch the answer, something about bond lengths", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/6e3ddc48e1874a7895cd34f196da186f", "date" : "2008-07-21T19:32:44Z" }, { "body" : "Pande group and Folding@home: <a rel=\"nofollow\" href=\"http://folding.stanford.edu/Pande/Main\" title=\"http://folding.stanford.edu/Pande/Main\">http://folding.stanford.edu/Pande...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/b8e83486ec254d4fbcde2f6392cd5058", "date" : "2008-07-21T19:33:14Z" }, { "body" : "Simbody also allows you to create arbitrary molecules", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/d48d425618b64b789111105a8b7a43a4", "date" : "2008-07-21T19:36:05Z" }, { "body" : "Simbios (National center for physics based simulation of biological structures) website: <a rel=\"nofollow\" href=\"http://simbios.stanford.edu/\">http://simbios.stanford.edu/</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/17c0a92f06fc4b01bcd8c6475e87ad53", "date" : "2008-07-21T19:37:34Z" }, { "body" : "Disclaimer: my advisor is the PI on the Simbios grant, folks in my lab work on Simbody and SimTK. So I knew most of this stuff already but wanted to report on it to give it a plug for the rest of the ISMB audience :)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/440fb219e0304978b25aad5815807c25", "date" : "2008-07-21T19:44:18Z" }, { "body" : "Talks like these make me weep.  There I was a time I thought my SGI Octane was really fast.", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/22e98415b93244ac8cb37c980c3ad211", "date" : "2008-07-22T00:14:18Z" }, { "body" : "I am lazy.  Is Simbios an Internal Coordinate Dynamics program?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/61e0a03ea227470ea4bc4510d0cd493a", "date" : "2008-07-22T00:14:48Z" }, { "body" : "@Deepak, I think Simbios is the name of the center/organization.  I'm definitely anticipating the release of OpenMM <a rel=\"nofollow\" href=\"https://simtk.org/home/openmm\">https://simtk.org/home/openmm</a> to see how it compares to NAMD and others.", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/c12886e405f246fcbab73d5f5bc612f5", "date" : "2008-07-22T00:39:17Z" }, { "body" : "Right, Simbios is one of the NCBCs (National Center for Biomedical Computation) commissioned by NIH. SimBody is a library they've developed for coarse-graining MD simulations. Simbios also hosts SimTK (Simulation ToolKit), a server housing code and descriptions for dozens of research projects related to physics-based simulation of biological structures, everything from biomechanics of gait to molecular dynamics.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/5c67d6ec64b14d9d94f35cebdc1705d2", "date" : "2008-07-22T02:31:45Z" }, { "body" : "Oh that's very cool.  Would definitely like to try that out", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/ab641776df824a909510db8db1450219/c/83301617137e4dab9b2f050ddd0593db", "date" : "2008-07-22T04:24:16Z" } ], "body" : "TT21: Simbios - Fast molecular dynamics calculations on your laptop", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/ab641776/tt21-simbios-fast-molecular-dynamics", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T19:16:18Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-24T22:42:05Z" }, { "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "date" : "2008-07-22T00:25:32Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-21T23:11:34Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-21T20:07:55Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-21T19:28:03Z" } ] }
{ "_id" : "e/b0eca9851e584c71b7c0e9940be07ab7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Slight title change - protein/RNA sequence, rather than domains", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/f7f1ee7f8e134eaca7ebb4b67a5c90fa", "date" : "2008-07-23T15:18:54Z" }, { "body" : "Starts with overview of coevolution and methods:  parametric (Bayesian, Markov) or non-parametric (mutual info, correlation coefficients etc).  First type incorporate phylogenetic information, but overfitting and cost are issues.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/afeb06a153324f5988c00d254a0b576b", "date" : "2008-07-23T15:20:25Z" }, { "body" : "Figure showing generalised CTMP model for coevolution", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/14730e99700c471b8fb8787907a70ea5", "date" : "2008-07-23T15:22:18Z" }, { "body" : "This looks very applicable to things like protein-peptide interactions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/de3a0ea590cd43869e8c75634ed8c859", "date" : "2008-07-23T15:22:53Z" }, { "body" : "Showing how to construct sequence substitution rate matrices for 2 sites", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/a9b1aa941af3497eb151a0a008b1c558", "date" : "2008-07-23T15:26:43Z" }, { "body" : "First example:  looking at 16S rRNA structure to predict interacting pairs; comparison with 4 other models - CO, WC, WCW, MI; CO model best AROC.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/f7b141eb86e846a9afea6cf93bb5d898", "date" : "2008-07-23T15:29:44Z" }, { "body" : "Now moving to tertiary interactions in rRNA; also works well", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/c8649b3b75d3436e9c9d5936e20578dc", "date" : "2008-07-23T15:30:13Z" }, { "body" : "Now moves onto protein domains; screening of Pfam database", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/e92b4bac922b4dcc8f604d58e0874402", "date" : "2008-07-23T15:31:35Z" }, { "body" : "1.2 x 10e11 all v. all possible pair comparisons", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/c9b67e59ca2d427c8093f2299a67831d", "date" : "2008-07-23T15:32:29Z" }, { "body" : "Showing some statistics that describe co-evolved domains", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/d477492f41f14af49bb17d2c652d1d97", "date" : "2008-07-23T15:33:59Z" }, { "body" : "Coevolving pairs of sites are spatially coupled (shorter pairwise distance - but not necessarily in contact)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/054b6108d1bd4403b09e9d14cad44698", "date" : "2008-07-23T15:35:01Z" }, { "body" : "Examples to illustrate:  Fe/Mn superoxide dismutase; first protein structure that I've seen all conference :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/0657c7dc5feb4d4fa282da6ff4e19c99", "date" : "2008-07-23T15:35:33Z" }, { "body" : "Second example:  ribosomal proteins; coevolving positions are at tRNA binding sites", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/2ac10996a5b644c8845062778ccc420d", "date" : "2008-07-23T15:37:39Z" }, { "body" : "Skips through RNAP (similar to ribosomal story) to phosphoglucomutase:  the coevolving positions are in functionally-important regions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/721bc860d53845bea2e8c169fd172b56", "date" : "2008-07-23T15:39:53Z" }, { "body" : "Wrapping up:  coevolving sites in RNA often physically interact; not so in proteins.  Software is freely available:  www.sns.ias.edu/chyeang", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b0eca9851e584c71b7c0e9940be07ab7/c/8a8645451b134c5ba718e4c490196a06", "date" : "2008-07-23T15:40:47Z" } ], "body" : "HL53:  Chen-Hsiang Yeang - &quot;detecting coevolution in and among protein domains&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b0eca985/hl53-chen-hsiang-yeang-detecting-coevolution", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T15:12:16Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/b2df811da5ba4acba1d0780fc1db15a5", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Discussing the Cancer genome atlas data - ability to visualize and overlay genetic alterations across samples (LOH, CNV, expression).", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/940261937e5b418c9ad4c4ea79e48141", "date" : "2008-07-19T17:54:52Z" }, { "body" : "Aggregation allows ability to detect common alterations of selected subnetworks in majority of samples (e.g., RTK/RAS/PI-3K signaling  in 85% of samples) to delineate underlying cancer program", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/44e7c30032af460787ccb8246afc3c66", "date" : "2008-07-19T17:57:01Z" }, { "body" : "Emphasis on clinical applications - use sub-networks to make drug predictions and attempt to validate these predictions via perturbation experiments", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/caf4e209aa664a7897850016f12f829b", "date" : "2008-07-19T18:00:29Z" }, { "body" : "Leads on this project at  MSKCC are Weiqing Wang and Sven Nelander.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/2b86f193ae5b43109f551fb66ced3e96", "date" : "2008-07-19T18:09:38Z" }, { "body" : "coPIA project - Mutliple perturbation approaches to build predictive network models", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/dfc39aaf1a90458c889f75c0a411d8b0", "date" : "2008-07-19T18:21:40Z" }, { "body" : "In response to question about correlation with clinical phenotype, they saw a high hybrid mutation rate in those patients who were underwent treatment (chemo). They were also able to tease apart differences among the cancer phenotypes.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/b2df811da5ba4acba1d0780fc1db15a5/c/c59fd16726c146519f4455ab0327b5a7", "date" : "2008-07-19T18:30:48Z" } ], "body" : "&quot;There is no such thing as pathway reconstruction..... nor do is there such thing as pathway re-engineering.  Pathways are simply biological models. &quot; - Chris Sander, MSKCC", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b2df811d/there-is-no-such-thing-as-pathway", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T17:46:36Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T02:49:59Z" } ] }
{ "_id" : "e/b51075fb462a425aa056fffb6cb7f0a0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "talk about identifying genetic markers of drug sensitivity in cancer using integrative computational and experimental systems biology", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/42e3c2f28d684df8ab68c2d219b5395e", "date" : "2008-07-20T19:15:07Z" }, { "body" : "they are hiring! ;)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/e624c6d0cb7a4410b5f470ee77afc9eb", "date" : "2008-07-20T19:17:45Z" }, { "body" : "systems pharmacology strategy: want to connect patients to drugs based on biomarkers. (Buzzwords?)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/05921e1a97524b0483134b0338718266", "date" : "2008-07-20T19:19:07Z" }, { "body" : "Definitely, although serious effort as well.  Most companies are using some variation of that strategy", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/c64315b691304dabb5d8097f58379407", "date" : "2008-07-20T19:21:30Z" }, { "body" : "trying to deal with a lot of heterogeneous data; try to get as many kinds of data from the same clinical sample. need to pick particular problems (e.g. target- and pathway based chemotype profiling)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/741f7bf77d914b7f9e3001a1ed46f238", "date" : "2008-07-20T19:23:05Z" }, { "body" : "screenshots of an internal tool to integrate data. wait, it's open source -- Lilly Science Grid", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/487f0095563c4674b5c84c58e0193fb6", "date" : "2008-07-20T19:24:02Z" }, { "body" : "Lou (?) Staudt, NCI: From clinical signatures to new molecular targets", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/2b3674b216eb4a9b87a2290a683be8d0", "date" : "2008-07-20T19:26:44Z" }, { "body" : "They talk about that quite a bit.  The philosophy is, non-competitive, make it available", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/86de3d4666454384b42143585f2ab8ba", "date" : "2008-07-20T19:27:42Z" }, { "body" : "CLBCL: very heterogeneous response to treatment, didn't know initially if there were subgroups or just one group with lots of variation. Could later identify 3 subgroups based on gene-expression signatures. E.g. ABC-DLBCL has a very poor response.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/bcbe3afb339d4f62be84860bf7d9a25b", "date" : "2008-07-20T19:28:38Z" }, { "body" : "Dervied cell lines from cell lines; shRNA screen (synthetic lethality); could identify potential targets for specific subtypes. Using RNAi to try to identify targets, drugs, and patients who might respond to treatment", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/4a8e75d6cc744e19a05e2b691ec37977", "date" : "2008-07-20T19:30:33Z" }, { "body" : "HTS with 14000 siRNA (hmm, what's the chance that not all of the siRNA actually work?). 0.5 million transfections. Could find 53 genes that increase drug sensitivity and where the knock-down could be validated", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/ca73150f624b441daf12c581ed03bf49", "date" : "2008-07-20T19:32:25Z" }, { "body" : "genomic signatures: can take signature library (Lilly generates lots of signatures from public data, less from own screens) and integrate into expression db. matrix: study vs signature. &quot;Can we detect the non-randomness of a signature in unrelated data sets?&quot; Estrogen receptor signature vs. breast cancer: works; ER vs. lung cancer: doesn't work (negative control)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/4719dd718c6f4e51951f0bff2c3ec35b", "date" : "2008-07-20T19:36:04Z" }, { "body" : "they are hiring! (yes, he said it again)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/d0eb0dc6191447cbb5147dd551b454bb", "date" : "2008-07-20T19:41:25Z" }, { "body" : "wonder if Lilly have an Australian arm :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b51075fb462a425aa056fffb6cb7f0a0/c/7e25e4f675cd4909a34732a4e360b037", "date" : "2008-07-20T20:03:00Z" } ], "body" : "Greg Tucker-Kellogg, Lilly/Singapore", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b51075fb/greg-tucker-kellogg-lilly-singapore", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:14:33Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-20T19:25:39Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T19:19:12Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-20T19:18:00Z" } ] }
{ "_id" : "e/b537af2e360446229ca6f69f32d18ff0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The chair notes that the technology track is experiencing &quot;technical issues&quot;.  Ah, the irony.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/9e5b66d9520d4d8bbde5a1066bca38f8", "date" : "2008-07-20T15:51:35Z" }, { "body" : "Here we go then; Jennifer MacDowall from EMBL-EBI.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/ca1675de1c0b4929982ac5747df967e7", "date" : "2008-07-20T15:53:08Z" }, { "body" : "Starts with a basic intro to InterPro and UniProt", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/1c112b354b8648f18487b54f262e1232", "date" : "2008-07-20T15:55:33Z" }, { "body" : "Now giving demo of InterProScan website.  In other news, twitter is &quot;over capacity&quot;.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/26c294302844464583fa473c4fc21b6e", "date" : "2008-07-20T15:58:48Z" }, { "body" : "Running through GO term annotation; kinases as example", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/20b23356ab81430d9809a917fa64650b", "date" : "2008-07-20T16:02:04Z" }, { "body" : "It's a good overview; I've used InterPro a lot though, so nothing new for me so far.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/53c374dcc7614ca780c0f0d0a066ceab", "date" : "2008-07-20T16:02:49Z" }, { "body" : "Summary:  InterPro is a very good resource.  5 minute break before Plasmodium genomes.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b537af2e360446229ca6f69f32d18ff0/c/44057d4d954f4e9ca7e94e8dc98f5ddd", "date" : "2008-07-20T16:09:00Z" } ], "body" : "TT03:  setting up for InterPro", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b537af2e/tt03-setting-up-for-interpro", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T15:47:19Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/b6f28f101f884f0db351f5277cb9b6ad", "feed_id" : "ismb-2008", "comments" : [ { "body" : "So, let's kick things off.  Who is (a) attending ISMB 2008, (b) attending a special pre-conference but not the main event or (c) not attending, but will be in the area?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/4f70bdf023e240598d193409ca8c7531", "date" : "2008-07-07T12:54:12Z" }, { "body" : "I'll attend the main conference only.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/1c2250733ab144cc9201e15f20ce16dc", "date" : "2008-07-07T12:57:15Z" }, { "body" : "(c) - I live in Waterloo, just outside Toronto. If some open-sciency people want to meet up, I'd be keen to meet.  The Duke of York is a pretty good pub near the University of Toronto (<a rel=\"nofollow\" href=\"http://york.thedukepubs.ca/\">http://york.thedukepubs.ca/</a>).  The Linux Caffe (<a rel=\"nofollow\" href=\"http://linuxcaffe.ca/\">http://linuxcaffe.ca/</a>) is a slightly longer walk, but also good.", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/7ce1ad6d733645598146e3db07a493d4", "date" : "2008-07-07T12:58:45Z" }, { "body" : "I live in TO but I am not attending ISMB.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/fd13993265a14f0795d9a14e48b28052", "date" : "2008-07-07T13:18:26Z" }, { "body" : "I won't be there, but let's see what the back channel is like", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/d1bc3afff23c4e96b801710c7e85a2f2", "date" : "2008-07-07T13:26:21Z" }, { "body" : "I'll be at ISMB only and will be in town July 16-24", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/bfa4523fe38c456fa07e345acf4b9672", "date" : "2008-07-07T13:30:33Z" }, { "body" : "I'll be there for the conference and presenting a poster", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/d5c171d39a774c97b27610458b57f1c8", "date" : "2008-07-07T13:31:09Z" }, { "body" : "would be interesting to know where everyone is staying so we can plan something (pub, restaurant, etc). The conference venue is really close to the entertainment district, but we can always arrange something close to UofT.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/89b40d807b1f42688d33eb3f07ffbfb4", "date" : "2008-07-07T13:59:19Z" }, { "body" : "I will be there for the main conference. Update - Actually I will be there from the 17th to the 23rd.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/1f5a98373fd648539e5ad47a5cd3e599", "date" : "2008-07-07T18:22:05Z" }, { "body" : "I will be at the 3Dsig satellite meeting on the 18th-19th but not the main event.", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/81b53c32d0b94fc9ae13a95651b47c63", "date" : "2008-07-07T20:07:47Z" }, { "body" : "LinuxCaffe?  How deliciously geeky and cool.  Must go there.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/60006dbff98143a08389b61fc5327e7b", "date" : "2008-07-08T06:29:37Z" }, { "body" : "I'll be there, between July 17-23 (main conf. + student symposium).", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/93a68419897b4134837925f249a5d05c", "date" : "2008-07-08T09:10:11Z" }, { "body" : "Neil - it's got free wireless, and stacks and stacks of geeky books piled all around, free for the reading.  Plus, it's got a nice atmosphere.", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/2bc5ad3826e74490b3f30b2aac3c5e22", "date" : "2008-07-08T14:42:51Z" }, { "body" : "Now this sounds cool Michael.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/7ca90f99f6d14e58b1f94bdfbcbdff5a", "date" : "2008-07-08T15:53:36Z" }, { "body" : "I am a new member to this room and will be attending ISMB from Jul 18th - Jul 23rd.", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/ce794008938d42d882b750938ed36dc9", "date" : "2008-07-14T10:04:44Z" }, { "body" : "ill be around from saturday through the YEAST meeting following ISMB. see you at the matrix party! woohaa!   <a rel=\"nofollow\" href=\"http://bioinfblog.blogspot.com\">http://bioinfblog.blogspot.com</a>", "from" : { "name" : "sourav", "id" : "sourav", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/05aafeb84e654c0d9b55037426068b2e", "date" : "2008-07-15T23:57:04Z" }, { "body" : "I'll be there for the AFP-Biosapiens satellite meeting on the 18-19th and until late afternoon on the 22nd for the main meeting.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/8d6ad1f3567a4bc3b9765a15879e2ac4", "date" : "2008-07-17T19:34:51Z" }, { "body" : "I'm also interested in an open science meet up, any plans yet for when?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/02e74e26c28f4524b4e460244cc8d7d5", "date" : "2008-07-17T19:35:45Z" }, { "body" : "I will be there for bio-ontologies SIG on the Sunday and the rest of the week - LinuxCaffe here I come", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/ab7dcfb8f1604f56b5290c10ff6d955f", "date" : "2008-07-17T23:20:49Z" }, { "body" : "Linux Caffe is really close to UofT, any idea of a time for a meeting there? It is not close to the subway (but close to streetcars) and I can give a lift for a couple of people to get there if needed.", "from" : { "name" : "pn", "id" : "nuin", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/00fe520f8d71448fa2ae45fac68fe583", "date" : "2008-07-17T23:33:15Z" }, { "body" : "I wish I was staying for the entire conference, but unfortunately I have to leave July 19th to get back to a workshop in Pittsburgh :-/  I'm staying at the InterContinental for anyone who might be interesting in meeting tomorrow or Saturday.  Cheers!", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/30652258497a4c5aa253ec7de5ec6383", "date" : "2008-07-18T03:32:43Z" }, { "body" : "I'll be up in Toronto tomorrow (Friday).  If anyone's interested in meeting up, that'd be great.", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/b6f28f101f884f0db351f5277cb9b6ad/c/88b91c759f844399a7563b3b7d9cd379", "date" : "2008-07-18T03:39:21Z" } ], "body" : "Room created for ISMB 2008", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b6f28f10/room-created-for-ismb-2008", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-07T12:52:49Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/b96c8323b6f042649b925337288fed86", "feed_id" : "ismb-2008", "comments" : [ { "body" : "talking about improving work flows. understand and exploit immune systems.Cerebral was created to help integrate different datasets and help to visualize and ask questions of the data.Visual layout in a pathway view was an important feature requested.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/b96c8323b6f042649b925337288fed86/c/ebd6b0ae40184b83b4b88daf233b1d5e", "date" : "2008-07-18T15:59:30Z" }, { "body" : "bottlenecks identified : 1 interaction data finding; 2 pathway visualization, 3 comparative analysis", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/b96c8323b6f042649b925337288fed86/c/8205d5b0bba74f9eaf4e822bba85ca20", "date" : "2008-07-18T16:06:14Z" }, { "body" : "Generally useful tool for network visualization in particular for gene expression (or other quantitative data) studies across different conditions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/b96c8323b6f042649b925337288fed86/c/da547ef0c16947749ded545ddbac496c", "date" : "2008-07-18T16:17:22Z" } ], "body" : "Jennifer Gardy in Cerebral plugin for Cytoscape - <a rel=\"nofollow\" href=\"http://www.pathogenomics.ca/cerebral/\" title=\"http://www.pathogenomics.ca/cerebral/\">http://www.pathogenomics.ca/cerebra...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/b96c8323/jennifer-gardy-in-cerebral-plugin-for", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T15:55:59Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "tim", "id" : "behindtherabbit", "type" : "user" }, "date" : "2008-07-19T17:09:05Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-18T16:18:36Z" } ] }
{ "_id" : "e/bb2537df38864d39a21c463bb6d301c1", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Oops - reshare from my personal feed.  On we go.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/6a5ef107c4ce4e17a345d4b3015d545a", "date" : "2008-07-20T16:25:13Z" }, { "body" : "Manual gene reannotation aided by comparative studies:  3 genomes used.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/1b8d03e5d55a4fb78845d62c3b7cde3d", "date" : "2008-07-20T16:25:50Z" }, { "body" : "Moving to verification of predicted ORFs; PCR", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/0227ed4b805a4c0cb5f060b909564dc5", "date" : "2008-07-20T16:27:11Z" }, { "body" : "Mentions wikis as a possible annotation tool; citing the S. Salzberg article.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/d0920fdd994848afaa4bc335d54e9e6d", "date" : "2008-07-20T16:29:04Z" }, { "body" : "Manual annotation requires enthusiasm and dedication; doesn't mention crowd-sourcing.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/d5b5446b19104a709ff857fb9b21df38", "date" : "2008-07-20T16:30:19Z" }, { "body" : "And that's lunch.  Anticipation.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/bb2537df38864d39a21c463bb6d301c1/c/3decdeb314894d14bba48de4bda04044", "date" : "2008-07-20T16:33:05Z" } ], "body" : "“PT07:  Plasmodium yoellii genomics” - <a href=\"http://friendfeed.com/e/0e1e9936-c397-45fc-a31e-1330d6729ead\" title=\"http://friendfeed.com/e/0e1e9936-c397-45fc-a31e-1330d6729ead\">http://friendfeed.com/e...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/bb2537df/pt07-plasmodium-yoellii-genomics", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T16:24:51Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/bf0ef4e54af24d13bc957f715682b992", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Given a start point and and end point metabolite how to find paths that link them in a joint model of all known metabolic reactions? She mentioned the problem of pool compounds (water, ATP, etc) and how to possibly identify them. Mentioned a new method that starts with a weighted graph of compounds where &quot;each compound is assigned a weight equal to its connectivity in the network&quot;. Searching thought the &quot;lightest&quot; paths accurately retrieves known pathways. Caveat of analysis is that start and end points are strongly discovery biased. The approach works because intermediate reactions are very connection poor while start and end points are very promiscuous. What is the biologically significance of that ? (ongoing work). NAR paper on webserver for path finding <a rel=\"nofollow\" href=\"http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_2/W326\" title=\"http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_2/W326\">http://nar.oxfordjournals.org/cgi...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/bf0ef4e54af24d13bc957f715682b992/c/fdc1f2ce9c2b46849f5f716918cba5ec", "date" : "2008-07-19T17:22:29Z" } ], "body" : "Shoshana Wodak talked today about finding paths in chemical networks - <a rel=\"nofollow\" href=\"http://biochemistry.utoronto.ca/wodak/bch.html\" title=\"http://biochemistry.utoronto.ca/wodak/bch.html\">http://biochemistry.utoronto.ca/wodak...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/bf0ef4e5/shoshana-wodak-talked-today-about-finding", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T17:15:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/bf8c3724fe754b2e9b2eb353ff5b46f5", "feed_id" : "ismb-2008", "body" : "Has not seen the &quot;obese microbiome&quot; (J. Gordon) in the Amish population", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/bf8c3724/has-not-seen-obese-microbiome-j-gordon-in-amish", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T14:02:10Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/c67be333e8114751820c312392e8984c", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This one is from a recent PNAS paper", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/0740cc69db114342b31ed8f88ec63aa9", "date" : "2008-07-21T18:22:45Z" }, { "body" : "Starts out with an all v. all co-evolutionary profile comparison", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/c858ffb72ea744bc947f100a6368b766", "date" : "2008-07-21T18:23:39Z" }, { "body" : "Builds on mirror tree approach <a rel=\"nofollow\" href=\"http://peds.oxfordjournals.org/cgi/content/abstract/14/9/609\" title=\"http://peds.oxfordjournals.org/cgi/content/abstract/14/9/609\">http://peds.oxfordjournals.org/cgi...</a> (co-evoluti", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/0bbc6d97b94c467c84ee973ad4e44469", "date" : "2008-07-21T18:24:34Z" }, { "body" : "Basically, an integration of interaction data, protein profiles and phylogenetic trees: distinguish protein tree from species tree", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/e8c6756bf9314284b3174d8f001788f2", "date" : "2008-07-21T18:26:21Z" }, { "body" : "Complications due to evolutionary signal", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/30755ab4c8cb49d7a1cc3e591a0aa59a", "date" : "2008-07-21T18:27:04Z" }, { "body" : "high/low throughput complex data behaves quite differently; this was a little unclear to me", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/78ab0a76d1604c859ff61b1d753ea52f", "date" : "2008-07-21T18:33:58Z" }, { "body" : "URL:  ecid.bioinfo.cnio.es", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/0f88ccf486044c20943ef5b283dcd9e2", "date" : "2008-07-21T18:34:59Z" }, { "body" : "Take-home message:  co-evolution an important component in predicting protein complexes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/c67be333e8114751820c312392e8984c/c/26396f7616424cb1bc1b6f5a5893ff68", "date" : "2008-07-21T18:38:41Z" } ], "body" : "HL25 -Prediction of Global Interactomes Based on Genome-wide Coevolutionary Networks", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/c67be333/hl25-prediction-of-global-interactomes-based", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T18:21:54Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-22T00:14:58Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T18:22:29Z" } ] }
{ "_id" : "e/cc1241d673c94da5818111360e7ae36a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Talk by Kimmen Sjolander", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/77c153aa56c94e2ab67992f75b3f8c54", "date" : "2008-07-20T19:23:28Z" }, { "body" : "Their package is called sci-phy:  HMMs for sub-families", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/460578f11e8a4de3ad5a7d5bc5149d21", "date" : "2008-07-20T19:26:13Z" }, { "body" : "Some logistic regression in there too.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/2cda92855062471f8ccbb0433c7edc0b", "date" : "2008-07-20T19:29:31Z" }, { "body" : "Now moving on to PhyloFacts.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/9922430031fb47ac960ff371b10424a3", "date" : "2008-07-20T19:29:46Z" }, { "body" : "And now a package called FlowerPower.  Identifies true remote homologs from a pool of true + false.  Uses psi-blast, muscle, sci-phy pipeline.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/d1404cf79d124baa8a4ffdcb9953b1ee", "date" : "2008-07-20T19:32:16Z" }, { "body" : "Also PhyloBuilder, another web based tool.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/624e71f8d5d6447cafcb10ea2dd18177", "date" : "2008-07-20T19:35:05Z" }, { "body" : "This is all from the Berkeley Phylogenomics Group.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/c90072683ee440e28791db24aaa95aae", "date" : "2008-07-20T19:37:22Z" }, { "body" : "Is anyone talking of PhyloML?", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/fe7d4f1c4b844c1799161311beb34ea6", "date" : "2008-07-20T19:40:02Z" }, { "body" : "didn't catch phyloML, no", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/7ede0b05ea3f4584ba8c0cdd711785dc", "date" : "2008-07-20T19:42:11Z" }, { "body" : "And my first &quot;we are hiring&quot; slide of the day :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/cc1241d673c94da5818111360e7ae36a/c/be92ecf599014b21b9d7aaf849cc3973", "date" : "2008-07-20T19:59:42Z" } ], "body" : "HL13: protein subfamily recognition, classification", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/cc1241d6/hl13-protein-subfamily-recognition", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:23:06Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/cf819f9e90fa4b83bb9f9c4d1f96c384", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This was a general introduction to the power of wikis, lowering the barrier to entry etc. Interesting detail was the ability to open  and copy paste pathway information between WikiPathways and Cytoscape. Numbers - 330 users, 10% editing. They are starting to build portal pages for communities around specific pathways. On development track: bots, more curation tools, web API, contributions scores and awards. I asked about collaboration with journals to publish mature pathway and provide credit to the all authors but I don't think he understood my question. Poster R92 in the main conference.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/cf819f9e90fa4b83bb9f9c4d1f96c384/c/ffe7ac852d7842fba2b4c289f6649235", "date" : "2008-07-19T17:28:48Z" }, { "body" : "It was a good question. Another point I thought they hadn't considered yet was the ability to display discrepancy. The idea of having multiple versions of the models when authors disagree seemed like it could be problematic. It would be good to push for visualization methods that allow us to have a measure of confidence for nodes or edges in the model that can be overlaid on one model", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/cf819f9e90fa4b83bb9f9c4d1f96c384/c/513694a7a93040c8ad972b2fcdaa891f", "date" : "2008-07-19T18:54:52Z" }, { "body" : "My main concern would be the lack of molecular identity... only had a brief look yet, but could not find obvious use of InChI or the likes...", "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "id" : "e/cf819f9e90fa4b83bb9f9c4d1f96c384/c/23e0794ac3074f5aa83552c58a471660", "date" : "2008-07-20T04:50:43Z" } ], "body" : "Martijn van Lersel talked today about WikiPathways - <a rel=\"nofollow\" href=\"http://www.wikipathways.org/index.php/WikiPathways\" title=\"http://www.wikipathways.org/index.php/WikiPathways\">http://www.wikipathways.org/index...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/cf819f9e/martijn-van-lersel-talked-today-about", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T17:25:16Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-20T11:27:30Z" }, { "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "date" : "2008-07-20T04:50:01Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T02:49:40Z" } ] }
{ "_id" : "e/d3958d4289294a5285afb7f591a81b07", "feed_id" : "ismb-2008", "body" : "I summarized some keynotes from 3Dsig in a blog post; Thanks to everyone else for micro-blogging from the main event; it's almost like I'm still at the conference :) - <a rel=\"nofollow\" href=\"http://www.bleedingedgebiotech.com/blog/conferences/impressions-from-ismb-3dsig/\" title=\"http://www.bleedingedgebiotech.com/blog/conferences/impressions-from-ismb-3dsig/\">http://www.bleedingedgebiotech.com/blog...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Adam Kraut", "id" : "adamk", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d3958d42/i-summarized-some-keynotes-from-3dsig-in-blog", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T21:39:17Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-22T18:52:35Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-22T00:13:01Z" } ] }
{ "_id" : "e/d401a75f3aa84eab87e0d104edfab07d", "feed_id" : "ismb-2008", "comments" : [ { "body" : "By Francisco De La Vega, Gabor Marth", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/2f24ab380bdf4a11859fcd48b7bbf0fd", "date" : "2008-07-22T14:46:35Z" }, { "body" : "Quite a big audience for this one", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/72c8a7bff61a413a9a4f6784cbcab170", "date" : "2008-07-22T14:47:53Z" }, { "body" : "Why do it?  SNPs, variants, human evolution, personalised medicine - and because we can (cost, technology)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/6202407c421045a4b00c5065e7a18820", "date" : "2008-07-22T14:52:55Z" }, { "body" : "Mentions the 1000 human genomes project and the $1000 genome", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/12ef529171c94b2d9a9fb4df0a21e001", "date" : "2008-07-22T14:53:25Z" }, { "body" : "1000 Genomes project - sequence genomes of 1000+ people from around the world, data to be made available as soon as possible through publicly accessible databases, attempt to create most detailed view of human variation to date. Project website: <a rel=\"nofollow\" href=\"http://www.1000genomes.org/\">http://www.1000genomes.org/</a>, news on the subject: <a rel=\"nofollow\" href=\"http://www.nih.gov/news/health/jan2008/nhgri-22.htm\" title=\"http://www.nih.gov/news/health/jan2008/nhgri-22.htm\">http://www.nih.gov/news...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/dc95e851464d4cb19001c0f3979db00f", "date" : "2008-07-22T14:53:30Z" }, { "body" : "Overview of sequencing technologies: sanger, pyro, short read", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/01c38b7071e24aa9aee00ba431f64761", "date" : "2008-07-22T14:55:04Z" }, { "body" : "Listing pros and cons of the various sequencing technologies. Sanger = long reads and small error rate, but very few reads per run. Pyrosequencing = shorter reads and more bases per run but much higher error rate. Short read sequencing = very short reads, variable error rate, many base pairs per run", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/a75697563dd64d38a7ea6ab54ecc9945", "date" : "2008-07-22T14:56:06Z" }, { "body" : "Short read technology = new computational challenges", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/aad1a39deec643ce9a47775cf736de68", "date" : "2008-07-22T14:56:17Z" }, { "body" : "challenge: how to identify genetic variation in latest generation of sequencing platforms.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/0cb492c9a8c84c6b855e5ab1afbdd1a2", "date" : "2008-07-22T14:57:04Z" }, { "body" : "Next up Gabor Marth <a rel=\"nofollow\" href=\"http://bioinformatics.bc.edu/marthlab/Gabor_Marth\" title=\"http://bioinformatics.bc.edu/marthlab/Gabor_Marth\">http://bioinformatics.bc.edu/marthla...</a> There are links to the software from the lab in the webpage", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/bc82e18adf9b4d669f68db227500566e", "date" : "2008-07-22T14:58:12Z" }, { "body" : "Another quick overview of NGS (next generation sequencing); 454, Illumina/Solexa, AB/Solid, Helicos/Heliscope", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/bc041c39d11b48d5a7bf01a7bb472192", "date" : "2008-07-22T15:00:45Z" }, { "body" : "SNP discovery from re-sequencing.- 1) short read base calling, 2) read mapping, 3) read assembly (produces alignment to the sequence map, 4)visualization", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/cb62dc51f00e460f9318dee5281f1ed0", "date" : "2008-07-22T15:03:00Z" }, { "body" : "Nice overview of how required software components link to tasks", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/09cee5cc81aa4dc2a173e53dc73d7f53", "date" : "2008-07-22T15:05:38Z" }, { "body" : "Challenges:  accurate mapping, appropriate coverage, data quality", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/88b1cc0f39f3411b9a8ac234d1345c2f", "date" : "2008-07-22T15:10:09Z" }, { "body" : "Talking about the problems of placing reads on the genome reference. previous tools to mask repeats do not work well for short reads. Example of a tool that maps positions that are not unique randomly but them assigns probabilities .", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/3639b0cccfa348c1a1ae0047cef9b5a4", "date" : "2008-07-22T15:14:05Z" }, { "body" : "Going through the problem of mapping short reads; then mate pairs and gapped alignment; now talking on &quot;deep multi-individual sampling&quot;", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/482b458bc4194e1a9d83c4be0becd468", "date" : "2008-07-22T15:15:07Z" }, { "body" : "How to cover rare human variation ? more genomes and lower depth or vice versa ? used simulation data to test. 2x to 4X range of coverage for the 1000 genome project ... i did not get how many genomes would be mapped with this coverage.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/10578f4032b24664aa7ef8dbe664dccf", "date" : "2008-07-22T15:18:21Z" }, { "body" : "Simulation:  what coverage required for optimal SNP discovery?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/0864ac821b6a4040b49866e6313bf13e", "date" : "2008-07-22T15:19:28Z" }, { "body" : "Dereck Barnett's work on base error rate. Tested different technologies to calculate the rates of different error types. Also calculated the distribution of reads according to the number of errors. Ex Solexa, most reads have no errors, a bit worse for 454. Both are heavy tailed (very few reads have many errors)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/c29769cdf378470f998358ea2187e918", "date" : "2008-07-22T15:24:17Z" }, { "body" : "This one gets my &quot;poorest keeping to time&quot; award for the meeting so far :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/41fdab990d4446c89976a27799ad85a3", "date" : "2008-07-22T15:28:56Z" }, { "body" : "postdoc positions available in the lab. Peer Bork also advertised positions for metagenomics. It looks like there is a need for more well trained people to analyze data from these new technologies.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/bb7d7ac8b4da47649588e32d0cd09892", "date" : "2008-07-22T15:31:31Z" }, { "body" : "Talk by Goncalo Abecasis - University of Michigan (homepage <a rel=\"nofollow\" href=\"http://www.sph.umich.edu/csg/abecasis/\" title=\"http://www.sph.umich.edu/csg/abecasis/\">http://www.sph.umich.edu/csg...</a>). Giving another introduction to the problems mentioned above of how to deal with the short reads", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d401a75f3aa84eab87e0d104edfab07d/c/33e7829a27784196916b7a97333991be", "date" : "2008-07-22T15:35:57Z" } ], "body" : "SS05:  sequencing thousands of genomes", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d401a75f/ss05-sequencing-thousands-of-genomes", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T14:46:03Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/d53b0eb4416645108ffdc8b8b0fe5681", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Talked about language to specify semi-quantitative model rules that can be used for model verification. The same language could be potentially used to search in a database of of models for implementations to use in synthetic biology. Also, if a model does not work, how would it be possible to search automatically for alternatives that would make it work.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d53b0eb4416645108ffdc8b8b0fe5681/c/65c4f90eb216430e99ea84cf13d64770", "date" : "2008-07-19T17:33:19Z" } ], "body" : "David Gilbert talked today about behaviour driven approach to design in systems biology - <a rel=\"nofollow\" href=\"http://www.brc.dcs.gla.ac.uk/~drg/\" title=\"http://www.brc.dcs.gla.ac.uk/~drg/\">http://www.brc.dcs.gla.ac.uk/~drg...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d53b0eb4/david-gilbert-talked-today-about-behaviour", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T17:30:03Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/d5b274e51d344108853e5974b2a4cccd", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I'm dying to know what an off-target is.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/24a5660c703842c6ba696b10cc38479a", "date" : "2008-07-21T19:16:19Z" }, { "body" : "Let's see how different this is from Fridays' talk (which I only read up on) <a href=\"http://friendfeed.com/e/6610d3ac-07ea-47a4-b7d9-302ba7ed4029/Philip-E-Bourne-talking-on-drug-targets/\" title=\"http://friendfeed.com/e/6610d3ac-07ea-47a4-b7d9-302ba7ed4029/Philip-E-Bourne-talking-on-drug-targets/\">http://friendfeed.com/e...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/d3f8d4848212474eb00cd63ca3bde17a", "date" : "2008-07-21T19:16:22Z" }, { "body" : "Quick primer on drug discovery:  it's expensive, &quot;conventional&quot;, slow and drugs are poorly understood", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/c3b6219000dd4096a2ee379324a8d4c1", "date" : "2008-07-21T19:18:32Z" }, { "body" : "Yep, reusing drugs in the market is hot", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/e66c76ce3f3e4b9c98919b205fc496e8", "date" : "2008-07-21T19:19:18Z" }, { "body" : "Right - an off-target is an alternative binding site; idea is proteome-wide binding site search.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/3d9a282208524808b034f8e3a2382cbe", "date" : "2008-07-21T19:19:34Z" }, { "body" : "My irony detector fails me, Neil. An off-target is a drug target that is not responsible for the primary therapeutic action of the drug, but rather for side effects. (However, Vioxx is a bad example for the effects of off-targets, b/c it was actually too specific and therefore caused an imbalance in some hormone)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/eab74fd884c64ba1be23dd8c6252430f", "date" : "2008-07-21T19:19:45Z" }, { "body" : "Slides thus far are similar to his talk on Friday. Emphasis on unknown receptors and need to characterize protein-ligand binding sites", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/f3696bbbd8f74497beeaba5d6ac48e3b", "date" : "2008-07-21T19:20:07Z" }, { "body" : "what do off-targets tell us? a) nothing b) explain side effect c) new therapeutic usage", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/e2aa1df7063342d5a229d7da996b8ed2", "date" : "2008-07-21T19:20:42Z" }, { "body" : "Apparently quite a few PDB drug-receptor complexes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/8d64d54b12544fd0982fec4feae2769f", "date" : "2008-07-21T19:21:50Z" }, { "body" : "drugs w/ pdb structures: tamoxifen, lipitor, testosteron, sildenafil (missed the 5th example)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/a49b30883f9b4d768e7ba99421691b7e", "date" : "2008-07-21T19:22:05Z" }, { "body" : "the fifth was digoxin", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/b2f0208d4f8147529a86edf9f769b8cc", "date" : "2008-07-21T19:24:25Z" }, { "body" : "&quot;I am to old to compare my method to other methods.&quot;", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/44a80724ec1749539013b55587852fc7", "date" : "2008-07-21T19:27:13Z" }, { "body" : "Quick summary of how to characterise binding sites (geometric potential), then extend to find secondary sites.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/9cb558ecdaa04c45916cbd30b6ad036f", "date" : "2008-07-21T19:27:17Z" }, { "body" : "Key methodology references; Xie and Bourne 2007 BMC Bioinformatics (<a rel=\"nofollow\" href=\"http://www.biomedcentral.com/1471-2105/8/S4/S9\" title=\"http://www.biomedcentral.com/1471-2105/8/S4/S9\">http://www.biomedcentral.com/1471-21...</a>) and Xie and Bourne 2008 PNAS (<a rel=\"nofollow\" href=\"http://www.pnas.org/content/105/14/5441.abstract\" title=\"http://www.pnas.org/content/105/14/5441.abstract\">http://www.pnas.org/content...</a>)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/94ea2dad4acc4ba7ab504a73f3da305d", "date" : "2008-07-21T19:28:47Z" }, { "body" : "An example:  TB; Rossmann fold; targets for entacapone, tolcapone (which are Parkinson's drugs)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/648651e09fde405fb11ef6402d636392", "date" : "2008-07-21T19:29:06Z" }, { "body" : "entacapone &amp; tolcapone are used as COMT inh. in Parkinson, perhaps also useful in TB? Docked into 215 NAD binding proteins. Found ENR, M. tuberculosis potential drug target. Testing under way.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/a828afa617054910a16b3c0763390981", "date" : "2008-07-21T19:32:04Z" }, { "body" : "Wow, Shannon's on fire.  I'm behind your right shoulder by the way.  Hi!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/0666ba33f2844b3a8535a41eb62ee60c", "date" : "2008-07-21T19:32:37Z" }, { "body" : "Example 2:  SERCA; involved in Ca2+ homeostasis", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/87bea1a48c814be282fdebaaeeb03d61", "date" : "2008-07-21T19:34:49Z" }, { "body" : "correction on the quote: &quot;I am too old to compare my method to other methods by showing that we're better on a completely different dataset.&quot;", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/0fb698785ecb489e8838572395ecee0b", "date" : "2008-07-21T19:35:23Z" }, { "body" : "Example 3:  torcetrapib.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/65b10c17ad304543ae4db05e5c0de28d", "date" : "2008-07-21T19:35:39Z" }, { "body" : "In summary:  quite successful at finding off-targets; relating to pathways is the next stage.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/a19851c5ae734231aec52ff3d965e3ec", "date" : "2008-07-21T19:39:28Z" }, { "body" : "Finishes with &quot;the wisdom of the bioinformatics student crowd&quot; - nice.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/8c727a33b4654554a6b20653ebc57c53", "date" : "2008-07-21T19:40:18Z" }, { "body" : "Hmm, the first time I heard this was about 8 years ago, I am a little worried that there's not much in there when you go into the experiment.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/86813f3a7d684762aae870c937d2391c", "date" : "2008-07-21T19:42:59Z" }, { "body" : "Phil posted another talk which has some of the same slides (go about half-way through ppt) (www.sdsc.edu/pb/Talks/Brisbane07_drugs.ppt )", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/d5b274e51d344108853e5974b2a4cccd/c/72b9f1cc635f4063a7ed89b66c5053d2", "date" : "2008-07-21T19:47:14Z" } ], "body" : "HL29:  Phil Bourne - &quot;off targets for some major pharmaceuticals&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d5b274e5/hl29-phil-bourne-off-targets-for-some-major", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T19:11:17Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-21T19:20:17Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T19:17:00Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-21T19:14:02Z" } ] }
{ "_id" : "e/d6012fddb5184b308c43e90ed581fb4c", "feed_id" : "ismb-2008", "comments" : [ { "body" : "The BoF is on Tuesday from 1-2:15pm in room 718B", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/d7b6ba721b4d4a1781c8be600998efb6", "date" : "2008-07-22T03:50:50Z" }, { "body" : "Feel free to suggest or modify topics, volunteer to demo something, etc. I'm hoping this will be very interactive", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/58ed4ab6fbb2482aafd8d09c7c40753d", "date" : "2008-07-22T03:52:15Z" }, { "body" : "Two years ago we already talked about Web 2.0 and actually gave a talk series at EMBL. Back then, we had RSS, delicious, citeUlike, but of course not twitter/friendfeed. I actually think that (as we've proven here) FriendFeed is a really effective way of forming an ad-hoc community, so I guess we should give another talk at EMBL. :) Anyway, we should give people this link as it's a Web 2.0 introduction for scientists: <a rel=\"nofollow\" href=\"http://van.embl.de/cb/web_20_talk_series.shtml\" title=\"http://van.embl.de/cb/web_20_talk_series.shtml\">http://van.embl.de/cb...</a>", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/2140b40e3637453291e7df8bd4ebaae6", "date" : "2008-07-22T03:55:14Z" }, { "body" : "Hmm, I thought publishing it would make it editable by anyone but apparently not. Is there a way to do this?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/4245315678cb4fb48a41495b369a3de0", "date" : "2008-07-22T04:04:40Z" }, { "body" : "This invitation link should work for anyone: <a rel=\"nofollow\" href=\"http://docs.google.com/Doc?id=dv4t5rx_37fh5346gr&amp;invite=d9fqqkk\" title=\"http://docs.google.com/Doc?id=dv4t5rx_37fh5346gr&amp;invite=d9fqqkk\">http://docs.google.com/Doc...</a> (I hope there are no spam-bots trawling for google docs links...)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/8409b4d2336d4cc5871ba979abb8585e", "date" : "2008-07-22T11:54:49Z" }, { "body" : "Cameron had an excellent blog on Friend Feed introduction for scientists (<a rel=\"nofollow\" href=\"http://blog.openwetware.org/scienceintheopen/2008/06/12/friendfeed-for-scientists-what-why-and-how/\" title=\"http://blog.openwetware.org/scienceintheopen/2008/06/12/friendfeed-for-scientists-what-why-and-how/\">http://blog.openwetware.org/science...</a>). I have a few other links related to the use and impact of FF on the blog (<a rel=\"nofollow\" href=\"http://wildtype.wordpress.com/2008/07/22/friend-feeding-frenzy/\" title=\"http://wildtype.wordpress.com/2008/07/22/friend-feeding-frenzy/\">http://wildtype.wordpress.com/2008...</a>)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/ccfc7e7ff6694b17ac44cfcdfcd9f706", "date" : "2008-07-22T13:43:57Z" }, { "body" : "If someone asks about Second Life we could show them Second Nature's homepage (<a rel=\"nofollow\" href=\"http://www.nature.com/secondnature/index.html\" title=\"http://www.nature.com/secondnature/index.html\">http://www.nature.com/secondn...</a>) where Nature hosts talks. A good example of a recent talk was the 23&amp;me talk (<a rel=\"nofollow\" href=\"http://scienceroll.com/2008/06/24/23andme-in-second-life-live/\" title=\"http://scienceroll.com/2008/06/24/23andme-in-second-life-live/\">http://scienceroll.com/2008...</a>). I don't have a lot of experience in Second Life but I don't mind flying around if the connection is good enough.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/d41e075626174d6280ac6dc39fcce84f", "date" : "2008-07-22T16:11:56Z" }, { "body" : "One nice example of the use of second life in science is for archeology  <a rel=\"nofollow\" href=\"http://www.digitalhumanities.org/dh2007/abstracts/xhtml.xq?id=254\" title=\"http://www.digitalhumanities.org/dh2007/abstracts/xhtml.xq?id=254\">http://www.digitalhumanities.org/dh2007...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/18dfc5d4f3e0410fae30d85ad24ec9eb", "date" : "2008-07-22T16:15:37Z" }, { "body" : "Session starting now", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/265a273a131a4ac59c9a29a12dbebe2d", "date" : "2008-07-22T17:13:21Z" }, { "body" : "The google doc was updated as the session was going on with the gist of the discussion", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/f649f0200bec4f2eb19a383b9d82e108", "date" : "2008-07-22T19:52:25Z" }, { "body" : "It went reasonably well.  My fear is always that there will be...silence...but quite a few people contributed.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6012fddb5184b308c43e90ed581fb4c/c/4f58bdae6c0842c89d7d0d6d7c60495e", "date" : "2008-07-22T19:54:39Z" } ], "body" : "Web 2.0 BoF session planning notes - <a rel=\"nofollow\" href=\"http://docs.google.com/Doc?id=dv4t5rx_37fh5346gr\" title=\"http://docs.google.com/Doc?id=dv4t5rx_37fh5346gr\">http://docs.google.com/Doc...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d6012fdd/web-2-0-bof-session-planning-notes", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T03:48:08Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Samuli Eldfors", "id" : "eldfors", "type" : "user" }, "date" : "2008-07-22T19:31:14Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-22T17:18:02Z" }, { "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "date" : "2008-07-22T17:17:51Z" }, { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-22T16:12:05Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-22T13:43:04Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-22T13:12:08Z" }, { "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "date" : "2008-07-22T12:37:59Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-22T03:49:47Z" } ] }
{ "_id" : "e/d6ac91c0e88842f9b392cc1879823019", "feed_id" : "ismb-2008", "comments" : [ { "body" : "CBW? I'd like to stay with poster but join you later possibly. Would rather meet around 8 and go for dinner.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/3cbd069107974ee19e88278bca74af57", "date" : "2008-07-21T19:18:34Z" }, { "body" : "I would also like to browse around the posters a bit. Perhaps meet at 8 in the lobby of the Intercontinental and head off to the Elephant and Castle (?) for drinks and food and hopefully catch up with the CBW folks if they're still there.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/62e848c1852f476aabf6f87876792bac", "date" : "2008-07-21T19:39:38Z" }, { "body" : "I have poster duty too; happy to skip out early, but if 8 is a consensus, fine.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/91d9c0fefd7543d0bccf7c1da8e0c1bd", "date" : "2008-07-21T20:52:32Z" }, { "body" : "That sounds great, count me in", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/b18215d75b16499f9a642c38c7fedaa3", "date" : "2008-07-21T20:56:20Z" }, { "body" : "Sounds great but I am going to see the Radiohead - Nosferatu mashup (<a rel=\"nofollow\" href=\"http://www.blogto.com/photo_gallery/2008/07/radioheadnosferatu_mash_returns_to_cineforum/\" title=\"http://www.blogto.com/photo_gallery/2008/07/radioheadnosferatu_mash_returns_to_cineforum/\">http://www.blogto.com/photo_g...</a>) at 9. I can't resist!", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/a1dd12660e57403e916e86638e5bfaa9", "date" : "2008-07-21T21:06:22Z" }, { "body" : "Ok, so plan is to meet in Intercontinental lobby at 8", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/3fad88c9f53843e5a59bba1686f446ba", "date" : "2008-07-21T21:32:54Z" }, { "body" : "ok, 8pm", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6ac91c0e88842f9b392cc1879823019/c/d98bb1c439a44f56adfffab3e70d87a8", "date" : "2008-07-21T23:08:24Z" } ], "body" : "Would people interested in the BoF want to get together tonight? Are people planning to go to the CBW event?", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d6ac91c0/would-people-interested-in-bof-want-to-get", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T19:13:50Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/d6af6373897d483d975e5204ef127f96", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Here we are at the big finale", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/1d4f635fa8b04546aa7dded4e4b83d86", "date" : "2008-07-23T17:58:26Z" }, { "body" : "It has been fun :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/5ade299a3f6f4478b40377a8de720b5d", "date" : "2008-07-23T18:05:20Z" }, { "body" : "october to end of November each year submissions of names for awards", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/e189d68c88294e30a25e6c039cb332e8", "date" : "2008-07-23T18:07:36Z" }, { "body" : "Lab homepage <a rel=\"nofollow\" href=\"http://www.cbse.ucsc.edu/staff/hausslerlab.shtml\" title=\"http://www.cbse.ucsc.edu/staff/hausslerlab.shtml\">http://www.cbse.ucsc.edu/staff...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/a08d213a78534ea1bfdf5016522b9c7e", "date" : "2008-07-23T18:08:53Z" }, { "body" : "Very, very long introduction to the speaker", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/500373a7a8c440d9aba0d5a77a014c38", "date" : "2008-07-23T18:10:56Z" }, { "body" : "The application Powerpoint has quit unexpectedly :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/024de07259734c58a88719417146194e", "date" : "2008-07-23T18:14:29Z" }, { "body" : "reconstruction of genome evolution. looking at segment duplications and genome evolution. Second trend - trying to unite the different scales of genome evolution from large scale re-arrangements to point mutations.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/7f41df6dd57749c39a3f9caef3e1d27d", "date" : "2008-07-23T18:15:48Z" }, { "body" : "the slides are not working but he is doing a good job of improv", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/b9ccc7f294ef4be3b3555080f02a5ea6", "date" : "2008-07-23T18:16:12Z" }, { "body" : "ah the slides are back", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/5d4ebfa9db0e44f299d703cd397ff1e5", "date" : "2008-07-23T18:16:24Z" }, { "body" : "Jiam Ma, Bernard Suh and Brian Raney, work on evolution of history of a mammalian chromosome (rat)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/79610e7a086f49449643bf728d08aa72", "date" : "2008-07-23T18:17:00Z" }, { "body" : "Showing rat chromosome X as example of evolutionary changes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/76425fe0b2954945b59445709d70112f", "date" : "2008-07-23T18:17:14Z" }, { "body" : "Duplication and integration graphs that would make nice wall decorations too", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/36a7315543234ea5913c6fcc0f11ef1e", "date" : "2008-07-23T18:18:12Z" }, { "body" : "Evan Eicher- Morpheus: new genes by segmental duplication. Is Morpheus a tool ?  No, it is a gene.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/3655c03c716a422990c4f86ff43b69a5", "date" : "2008-07-23T18:18:25Z" }, { "body" : "Morpheus (Evan Eichler) - new genes by segmental duplication", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/d919c4e45215495aab66146628b2d370", "date" : "2008-07-23T18:18:32Z" }, { "body" : "The demise of a acyltransferase 3 by a stop codon in the chimp/human lineage. The last protein of that particular fold", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/d18eac006558466ca464248baae92f6d", "date" : "2008-07-23T18:19:46Z" }, { "body" : "Second example:  gene loss; mutation to stop codon before the human-chimp branch", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/092a6c49b87b4bec9809cff6ffc01f41", "date" : "2008-07-23T18:20:09Z" }, { "body" : "zooming in to single base reconstruction , mutation to STOP condon for a gene in the divergence with orangutan (~15My)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/cb5cbe9cb8f8480f8a42db4f90868070", "date" : "2008-07-23T18:20:29Z" }, { "body" : "Reconstruction of evolutionary history of placental mammals", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/23e0afe0e63740ee926622dfbd871c80", "date" : "2008-07-23T18:21:40Z" }, { "body" : "project for the community : reconstruct the evolutionary history of genomes (totally agree that this is going to be exciting, I am interested in having this information for ascomycota, I think Ian has nice tools for this)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/f05b7c1a6030487eaf2f5db3d72a3bd7", "date" : "2008-07-23T18:22:37Z" }, { "body" : "Nicely illustrated with photos of mammals next to the tree", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/69d2fc866b1d4d54aed40d4bbe0376b1", "date" : "2008-07-23T18:24:18Z" }, { "body" : "Genome evolution:  infinite sites model; covers (1) speciation, (2) duplication and (3) break/rearrange; shows some breakpoint graphs", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/0cd12784ed8b483e85781256e36a7ee2", "date" : "2008-07-23T18:25:32Z" }, { "body" : "the infinite sites model of genome evolution - 2-breakpoint rearrangements (different groups use this)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/4f91f93c7049468e84895850a8c480fe", "date" : "2008-07-23T18:25:48Z" }, { "body" : "2-breakpoints rearrangements - pair  the 4 ends together randomly", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/af98400518144bbba30efe8f061d4193", "date" : "2008-07-23T18:26:25Z" }, { "body" : "Reusing breakpoints - intractable problem for &gt;= 3 genomes; explains how to get around this by not using same breakpoint twice", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/50a04283ece34e9fbbf9358f486e979e", "date" : "2008-07-23T18:30:16Z" }, { "body" : "Neutral drift, negative selection, positive selection all now recognisable for multi genomes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/87dd8396b4b0413ea4a98dace185cc39", "date" : "2008-07-23T18:34:05Z" }, { "body" : "The new method looks interesting but I could not keep up with it. something about using all positions instead of breakpoints in many more genomes to reconstruct the ancestral states.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/c6a037b3ebad4258931b171600c0ba02", "date" : "2008-07-23T18:34:11Z" }, { "body" : "~ 5% human genome under negative selection", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/757809e3caa24ac498db329c08e2853d", "date" : "2008-07-23T18:34:44Z" }, { "body" : "Some regions might change from negative to positive selection. Search for human accelerated regions (of positive selection ?) Har1 example", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/5bea0909f4194e72af64151278b2edc3", "date" : "2008-07-23T18:35:16Z" }, { "body" : "Mentions the HAR1 gene (human accelerated region); conserved structural RNA; specific expression in developing cerebral cortex; expressed with cortical development protein Reelin", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/598921052d4648519b23b7e5cf211204", "date" : "2008-07-23T18:35:45Z" }, { "body" : "I'm glad I stuck around for this talk - beautiful stuff", "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/4dc855be9beb4e589d5c015751be44f2", "date" : "2008-07-23T18:39:51Z" }, { "body" : "collaboration with Pierre Vanderhaeghen <a rel=\"nofollow\" href=\"http://dev.ulb.ac.be/pvdhlab/\">http://dev.ulb.ac.be/pvdhlab/</a> to experimental test the role of HAR1 in human brain development", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/8d8954be3aca4ada89b23aee1dd9590b", "date" : "2008-07-23T18:41:07Z" }, { "body" : "Where and how do functional RNA structures arise ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/ab087c52fa54460394c898863f4e9b75", "date" : "2008-07-23T18:41:49Z" }, { "body" : "Moving now to ultra-conserved regions; ~ 500 000 in human; example - cluster of elements near ARX gene shown to act as enhancers (lacZ fusion)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/1dd5e5e3320e4919b5d2ecb64ea77186", "date" : "2008-07-23T18:44:11Z" }, { "body" : "It's a fantastic combination of hard math and soft biology (embryonic development)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/cbc80e225f30466cb9c107b4b2613118", "date" : "2008-07-23T18:45:17Z" }, { "body" : "Elements absent from invertebrates; how do so many appear relatively quickly?  links this to transposons", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/187d90193829470f9362959e2f8d4bc6", "date" : "2008-07-23T18:46:27Z" }, { "body" : "Talking about their work on ultra conserved regions, Experimental tests for these regions (expression patterns). Many ultra-conserved regions but all arose recently (evolutionary time). How can these all be created so rapidly ? possibly due to some form of transposon mediated copy", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/0464d78ad02b447799d1bbf602c2dca9", "date" : "2008-07-23T18:46:52Z" }, { "body" : "One such ancient transposon strongly matches coelacanth - how cool is that!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/f70405b7324f498d99d7adce7e494b3f", "date" : "2008-07-23T18:48:18Z" }, { "body" : "comment: the evolution of vertebrates was facilitated by transposons", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/f924c644081a41d0a6d4adc8f483978e", "date" : "2008-07-23T18:50:18Z" }, { "body" : "The grand challenge: The reconstruction of the evolutionary history of each base of the human genome (applause)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/5f758c0ca8d44d569ceb91f53fd31bf5", "date" : "2008-07-23T18:52:23Z" }, { "body" : "Again, the grand challenge of human molecular evolution is to be able to reconstruct the evolutionary history of each base. (it really shows that he is passionate about evolution :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/666d62712d174ed7aedb49d440ece527", "date" : "2008-07-23T18:52:34Z" }, { "body" : "Hmm; he almost goes with the &quot;mammals at top of the ladder&quot;, but then takes a step back.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/ab2761b2b65349d880b74772fb853b74", "date" : "2008-07-23T18:53:49Z" }, { "body" : "And that's it.  Let's understand the history of mammals through their genomes.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/046eab72fbe64220842dc50d6861de86", "date" : "2008-07-23T18:54:21Z" }, { "body" : "question: are the evolutionary breakpoints related to cancer breakpoints ? general response - the breakpoints are re-used so maybe", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/d6af6373897d483d975e5204ef127f96/c/7deb05d6041943f29757ce0f4052ace4", "date" : "2008-07-23T18:55:04Z" } ], "body" : "Keynote 8:  David Haussler - &quot;100 million years of evolutionary history of the human genome&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/d6af6373/keynote-8-david-haussler-100-million-years-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T17:58:06Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Jason Stajich", "id" : "stajich", "type" : "user" }, "date" : "2008-07-23T20:22:51Z" }, { "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "date" : "2008-07-23T18:38:32Z" }, { "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "date" : "2008-07-23T18:16:09Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-23T18:07:11Z" }, { "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "date" : "2008-07-23T18:05:50Z" }, { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-23T18:05:12Z" } ] }
{ "_id" : "e/dc070742c4f64b71b4df146ad7f595c4", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Talk by Han-Yu Chuang from Trey Ideker's group", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/6b06dafb092c4ef59564928a3b91651a", "date" : "2008-07-22T15:21:32Z" }, { "body" : "issue again of breast cancer metastasis and poor ability to predict via expression (sample heterogeneity, poor correspondence among data sets). Key idea:  overlaying relevant pathway information should improve results", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/2ea573f632504b9db0328d39edeee1b4", "date" : "2008-07-22T15:23:27Z" }, { "body" : "Combined two data sets (van de Vijver et al NEJM and Wang et al Lancet) using overalpping gene set ~8000 genes. PPI data from public databases (Bind, reactome etc)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/81734b5f85eb4aa59f7a617ec2ba39fd", "date" : "2008-07-22T15:25:11Z" }, { "body" : "assessment of subnetworks (using greedy search for local maximum to id subnetworks) - considering as discriminant features", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/68cd152c94314c5187b4e81c25d4ef1c", "date" : "2008-07-22T15:26:31Z" }, { "body" : "Search artifact therefore use permutation tests - global (to randomize relationship between expression and PPI). Local permutation test to handle topology bias.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/4d800e86f9c9490d8a91dc49a5ec0466", "date" : "2008-07-22T15:28:47Z" }, { "body" : "Results are set of markers with functional relationships to each other", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/75ed8cc0d91a433db2cbb8d436882d56", "date" : "2008-07-22T15:31:12Z" }, { "body" : "Reserved one data set for examination of classification accuracy. However, given choice of requirement of overlap at beginning, seems this could potentially over-inflate accuracy estimates", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/1a172828858746bc9bb42d37ee046444", "date" : "2008-07-22T15:35:25Z" }, { "body" : "Discussion of other related work: use of module maps for targeted therapy - Wong et al. Cancer Research 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/dc070742c4f64b71b4df146ad7f595c4/c/03118f380b464e6ab02751fe5212fb21", "date" : "2008-07-22T15:38:17Z" } ], "body" : "HL35: Pathway based diagnosis of cancer and metastasis", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/dc070742/hl35-pathway-based-diagnosis-of-cancer-and", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T15:20:31Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/dc858c27f524402aab57d56c80fe4fc7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "one level above the ISMB registration desk; Neil says &quot;where all the smokers are&quot;", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/da7061f35be94239b38d85d6b8acf97e", "date" : "2008-07-20T23:10:07Z" }, { "body" : "sure, I'll go.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/50b175f6d88e42e39dab2c898fa029ad", "date" : "2008-07-20T23:31:57Z" }, { "body" : "Great, should be there on time", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/bad50585a14f4e6682a593f86d7db7cd", "date" : "2008-07-20T23:34:11Z" }, { "body" : "sorry, missed the deadline. Which pub/bar are you all in?", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/23e057fe40274712baeccad231cc1422", "date" : "2008-07-21T00:21:49Z" }, { "body" : "missed this but would be interested to hear if any good discussions transpired", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/7372a22276b1411a8aa02af58450f763", "date" : "2008-07-21T02:25:50Z" }, { "body" : "Missed due to Dark Knight IMAX screening.. too bad", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/dc858c27f524402aab57d56c80fe4fc7/c/d93c8a314a364256907b10f62b2fe791", "date" : "2008-07-21T05:23:09Z" } ], "body" : "Beer tonight, meet 8 pm at the south exit of MTCC", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/dc858c27/beer-tonight-meet-8-pm-at-south-exit-of-mtcc", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T23:09:41Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/dcd08a8b213948b3996be31cf345eec7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "A project underway at FEBS Letters in collaboration with the MINT data base", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/7cdbbd71d603467da029aa90cb65eff0", "date" : "2008-07-23T15:52:42Z" }, { "body" : "Large gap between articles on PPI and publications of low throughput experiments", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/67a0498591c44798955a91a914926e5e", "date" : "2008-07-23T15:54:25Z" }, { "body" : "started working in structured information due to experimental work going on in the lab. Explained the creation of MINT and the iMEX consortium. The annotation by curators are not covering no-where near enough the increasing number of pubmed articles", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/ac5e1b050fc74968b8c4b1838fc40ace", "date" : "2008-07-23T15:54:37Z" }, { "body" : "The principle of structured digital abstracts (SDA) <a rel=\"nofollow\" href=\"http://www.febsletters.org/article/S0014-5793(08)00194-4/fulltext\" title=\"http://www.febsletters.org/article/S0014-5793(08)00194-4/fulltext\">http://www.febsletters.org/article...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/66b41b79e8eb45b4ac3474c1d73b4827", "date" : "2008-07-23T15:56:08Z" }, { "body" : "Project started in January, first issue (see above link) in April 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/d26395d4e80340b2bb6c7eb52a37d482", "date" : "2008-07-23T15:57:03Z" }, { "body" : "Link to press release with useful information <a rel=\"nofollow\" href=\"http://www.eurekalert.org/pub_releases/2008-04/e-fls040208.php\" title=\"http://www.eurekalert.org/pub_releases/2008-04/e-fls040208.php\">http://www.eurekalert.org/pub_rel...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/dfe675ca622d46d68396a50745db8f3b", "date" : "2008-07-23T15:57:43Z" }, { "body" : "The authors can reject doing the structured abstract, I think this is where it might fail, if most people don't want to do it.3 in 4 accepted .. not bad, only 30 structured abstracts so far. 16 out of 30 authors filled a survey about the process.Some points: 1h of average time to do it. 6/10 had some difficulty. the most difficult task was the find the uniprot ID (wow). 2/16 said that this could affect their decision to publish there again", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/dfe35ed8adfb4777b8ff3811460f36a6", "date" : "2008-07-23T15:58:33Z" }, { "body" : "161 articles published, 30 with SDA", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/fb4bfe2e26fb4ca0930a79b9122bd015", "date" : "2008-07-23T16:00:59Z" }, { "body" : "90% wrong assignment on taxonomy", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/8a14358c3c7342a1b13025ec12a7ea13", "date" : "2008-07-23T16:05:29Z" }, { "body" : "The data is almost insignificant in relation to the whole field but the information int he FEBS experiment will be useful for publishing world.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/46e613900c8f4875af7976e50f46a640", "date" : "2008-07-23T16:09:34Z" }, { "body" : "The general problem so far has been that authors make mistake so curators still have to spend considerable time on the process. Pubmed did not accept to add the structured abstract to the Pubmed abstract.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/0e549103badd4911a4a2512db1db15be", "date" : "2008-07-23T16:11:33Z" }, { "body" : "in the future they hope to have more journals participating and more types of information captured (they focus on articles that describe protein-protein interactions)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dcd08a8b213948b3996be31cf345eec7/c/89ac199aef03474998a652f18e48fc6a", "date" : "2008-07-23T16:12:46Z" } ], "body" : "SS07: The future of scientific publishing - G. Cesarini on Structured Digital Abstracts", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/dcd08a8b/ss07-future-of-scientific-publishing-g", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T15:51:21Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/dfd8376fc6cb488797162f8a3f716503", "feed_id" : "ismb-2008", "comments" : [ { "body" : "An excellent line up", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/54fa8ec72d8b4597b582e57c57c45c56", "date" : "2008-07-21T14:36:21Z" }, { "body" : "Mark Gerstein on protein function (from networks)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/913f69cad443412bbe5c8fb6448c0f1b", "date" : "2008-07-21T14:50:32Z" }, { "body" : "Human variation (SNP and CNV) in networks", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/a8b9d126b8994dc386af049105f1c98a", "date" : "2008-07-21T14:52:48Z" }, { "body" : "As a side note Mark Gerstein has a few &quot;life streams&quot; (<a rel=\"nofollow\" href=\"http://gerstein.info/streams/\">http://gerstein.info/streams/</a>)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/5b4f3110e17f4fb586f69aaba1d3db68", "date" : "2008-07-21T14:53:00Z" }, { "body" : "positive selection largely takes place at the network periphery (in the human interactome), Nielsen et al. PLoS Biol 2005", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/bc75eddd2cef44aebbd2de422e73f60e", "date" : "2008-07-21T14:55:42Z" }, { "body" : "Use human variation data (SNPs and copy number variation) mapped to human interaction networked. Discussing the differences between adaptive and neutral evolution. Looked for proteins under positive selection in the interactome using sequence analysis.proteins under positive selection were found at the periphery of the networks", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/14b76285aceb470ea10a649e91cd27b6", "date" : "2008-07-21T14:55:47Z" }, { "body" : "poorly connected proteins (on the periphery) are also closer to the outside of the cell. I wonder if this is not a technical problem of finding interactions for membrane proteins for example.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/ea6565c381284d0ab61baa39cba47fc6", "date" : "2008-07-21T14:58:56Z" }, { "body" : "Some of work on networks he was mentioning was done by P. Kim (<a rel=\"nofollow\" href=\"http://homes.gersteinlab.org/people/pmkim/\" title=\"http://homes.gersteinlab.org/people/pmkim/\">http://homes.gersteinlab.org/people...</a>)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/a1306c75607d469283f0acf51e7f53e0", "date" : "2008-07-21T15:00:34Z" }, { "body" : "Adaptive evolution on the periphery, example CD4 and HIV.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/a57711f5f19347329b620f543e9ef72c", "date" : "2008-07-21T15:00:58Z" }, { "body" : "Well, there is also the problem of biased gene conversion which inflates the number of proteins appearing to be under positive selection. Would be interesting to explore this critically.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/50394a41ff02410cb2d8f0a73361d710", "date" : "2008-07-21T15:02:29Z" }, { "body" : "but the cd4 example is clearly not influenced by that", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/cb67e5c273b7425287ae5050ae39a862", "date" : "2008-07-21T15:03:03Z" }, { "body" : "On CD4 protein, surface residues that interact with HIV gp120 are under positive selection", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/ed344e1031d34ddcab693c187ff0311c", "date" : "2008-07-21T15:03:23Z" }, { "body" : "Can use structures to find mutually exclusive protein-protein interactions (Kim et al. Science 2006)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/e3dd5b5c4ec841be88fce30de9641266", "date" : "2008-07-21T15:05:54Z" }, { "body" : "Hmm, Mark Gerstein mostly talked about previously published results... HIV being the only disease-related topic he mentioned", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/727c7dc7eea045fabb06fe7ecf8140cb", "date" : "2008-07-21T15:06:57Z" }, { "body" : ":) Acknowledgments: Co-author network", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/2c7c1b2e3a994cdc90eeb56fa2e8a635", "date" : "2008-07-21T15:07:55Z" }, { "body" : "This session is packed.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/8225a8bda1914787841f15e2efd058cd", "date" : "2008-07-21T15:08:21Z" }, { "body" : "But the CD4 stuff is at least relevant, not just some OMIM mapping without a cause", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/6e6192f61e1d44bd9ec6808fa66e3ba7", "date" : "2008-07-21T15:09:37Z" }, { "body" : "Next up: Haiyuan Yu, former grad student in Mark Gersteins lab, now post-doc with Marc Vidal", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/04bbdd1209d1465190da453c0cb6dfe2", "date" : "2008-07-21T15:11:53Z" }, { "body" : "Haiyuan Yu talking about &quot;High Quality Binary Protein Interaction Map Reveals Properties of Yeast Interactome Network&quot;", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/01b61cf9b70740cf9d3d39e4e51c5100", "date" : "2008-07-21T15:12:00Z" }, { "body" : "There we go again: Christian von Mering's infamous &quot;Y2H isn't reliable&quot; figure :)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/8e7eaa050f574e4e855f4dee27a3a45c", "date" : "2008-07-21T15:13:42Z" }, { "body" : "yeast two hybrid evangelism :) Ito non core is very noisy should not be used for analysis. (the net is very slow today)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/d7dc73df84754c1b96e499db866c622f", "date" : "2008-07-21T15:16:28Z" }, { "body" : "RTFP, we do say that Ito core is superior to the whole data set, but its only ~850 interactons.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/0773ce856b3a4f549dff5f94086cea9b", "date" : "2008-07-21T15:16:41Z" }, { "body" : "To compare literature curated interaction with Y2H they used only the literature curated that are supported by one report. He says that that is the fair comparative test. Using different methods to compare Y2H with literature curated interactions", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/76bbeefb01424d74b10eb5c91ce85f09", "date" : "2008-07-21T15:18:03Z" }, { "body" : "interaction re-tested by Y2H- core Y2H from previous tests retest very well. The literature curation re-test at similar or even lower quality. pull down interaction re-test worse than Y2H but he stresses that the interaction types are different and that the tests that they are using Y2H and PCA detect binary interactions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/3e6bed633b3c4e06b5cb03b4e6108720", "date" : "2008-07-21T15:20:58Z" }, { "body" : "Its fractions, not absolute numbers and only the specificity, not sensitivity, so...", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/1122d08c669a470281d453551d95c3ba", "date" : "2008-07-21T15:21:17Z" }, { "body" : "He suggests that MIPS or other complex interactions data can not be used directly to benchmark binary interactions. He defines a set of high quality binary interactions for benchmarking.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/16164bf4fe9348b7bb16304f0d21c6f1", "date" : "2008-07-21T15:23:42Z" }, { "body" : "re-mapped yeast interaction network repeated 3X. 2930  interactions among 2000 proteins (combining also previous interactions)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/68d02e5cda5c4df390a9fc16ae6177fd", "date" : "2008-07-21T15:26:03Z" }, { "body" : "ongoing project: look for mutants that disrupt particular interactions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/6ce1dc1157ca4541bd45787b9fad3b5f", "date" : "2008-07-21T15:28:11Z" }, { "body" : "Its  a good map, just very incomplete and its quite hard to envisage how to close it.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/bd87e4647b9b4001a079b0536877567a", "date" : "2008-07-21T15:28:11Z" }, { "body" : "Again, a talk that didn't address disease at all even though Marc Vidal is doing some work on this (Yıldırım et al. Drug-target network. Nature Biotechnology (2007) vol. 25 (10) pp. 1119-26)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/1c5f138dafa54dc78e0d7180b24c49df", "date" : "2008-07-21T15:28:49Z" }, { "body" : "I remember from another talk that they were mentioning a maximum coverage of Y2H of 20% but I am not sure. They were saying that basically we will need many different methods to get higher coverage.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/5a779249f2224a97a12ed52aa4ea7b2f", "date" : "2008-07-21T15:29:24Z" }, { "body" : "The problem is  just that all interaction screens provide different aspects - binary (y2h), complexes (apms), functional interaction (genetic) - and just throwing them together won't cut it.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/e3b05e7ce8cf465ba9dce775849c7b7f", "date" : "2008-07-21T15:33:05Z" }, { "body" : "Frederick P. Roth - Mouse Functional Linkage Graphs and Complex Disease", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/77377cd32fda45c2ba4dfe004ad763d4", "date" : "2008-07-21T15:33:31Z" }, { "body" : "Fritz Roth: Functional prediction in mouse as a competition", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/97ff5f7c9f304a179c102ba760bbe173", "date" : "2008-07-21T15:34:36Z" }, { "body" : "He is talking about MouseFunc (<a rel=\"nofollow\" href=\"http://hugheslab.med.utoronto.ca/supplementary-data/mouseFunc_I/\" title=\"http://hugheslab.med.utoronto.ca/supplementary-data/mouseFunc_I/\">http://hugheslab.med.utoronto.ca/supplem...</a>) predicting function for mouse", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/0b05a825e0754efdaed3e00d22ff2bde", "date" : "2008-07-21T15:35:29Z" }, { "body" : "Precision of functional association (36 top novel predictions) precision between 72 to 83%. Evaluated by other lab.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/394ae87c3c454fbd8973143042b5a0fe", "date" : "2008-07-21T15:43:53Z" }, { "body" : "There are a number of real improvements in this work, the limitation to 31-100 GO term specificity in particular", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/dc5e1d0bf1c3467b99ac7d44ef3c5fa9", "date" : "2008-07-21T15:44:52Z" }, { "body" : "I wish the speakers would go more into detail, it's a special session after all", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/be30170422c1406983b0a9a3b70b7d06", "date" : "2008-07-21T15:48:26Z" }, { "body" : "Next one! Trey Ideker", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/7dad2ee8ab9c4aa6a9c0ee77d5045d4d", "date" : "2008-07-21T15:49:40Z" }, { "body" : "plug for Cyotscape plug-ins, most popular: Bingo w/ 5000 downloads in last year", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/a5e64cea6f8f4209a4753efa2a3b37a2", "date" : "2008-07-21T15:51:44Z" }, { "body" : "One last though about Roth's talk. He was another researcher mentioning the need to understand how many different mutations together might cause disease.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/8ce0d704f94f496f8ddf8b85e77779c6", "date" : "2008-07-21T15:53:06Z" }, { "body" : "based on pathway assembly, study disease using networks: network-based disease diagnosis; functional separation of disease gene families; moving from GWAS to network-wide &quot;pathways&quot; association (PAS)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/65b12e8b83764d898b3ec34c41933693", "date" : "2008-07-21T15:54:07Z" }, { "body" : "Is it really necessary to advertise Cytoscape? Sounds like advertising Blast to me.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/703a10182eb749d393203da7da6231f4", "date" : "2008-07-21T15:54:40Z" }, { "body" : "General description of his Trey Ideker's lab. How to combine different interaction networks and to study them to understand evolution, function and disease. First work on networks and disease, combining gene expression profiles and protein interactions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/caa415cb85314121980495509275e6c4", "date" : "2008-07-21T15:56:45Z" }, { "body" : "Tuesday 2:45 , 718B talk by members of his lab on dissection function in large transcription networks. All of the disease work was referenced for other talks. He is going to talk about the position effects of transcription factor binding sites in the sub-telomere", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/06bd248457604f238c8b476970490ef6", "date" : "2008-07-21T16:01:08Z" }, { "body" : "position effects in the genome: order matters, even in eukaryotes; look at distance from nearest telomere in yeast. transcription factors have particular binding profile, bimodal distribution of telomere distances", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/b2692f4fd3db486492163056618e7c59", "date" : "2008-07-21T16:02:36Z" }, { "body" : "Some TFs bind in a bi model distribution along the genome. Some of them bind the sub-telomere in a condition dependent fashion", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/d8a42e26d15a43049f1fc005c14bce93", "date" : "2008-07-21T16:02:58Z" }, { "body" : "He said these distance effects were unpublished and not talked about before, but this was also shown in Barcelona in April or May", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/bbbbd1be9bde4fd08e22e71e44b462ae", "date" : "2008-07-21T16:03:16Z" }, { "body" : "He suggested in a previous talk that this could be due to physical localization of transcription withing the nucleus. More intuitive could be that it is some sort of condition dependent sequestration of TFs", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/e70d1dea4e504b93a7fe2dae698b42a2", "date" : "2008-07-21T16:04:14Z" }, { "body" : "condition-specific behavior: changes in environmental tradition sometimes leads to appearance of another telemore distance mode", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/61c85adc2bd14e2dac1dd4d32676559c", "date" : "2008-07-21T16:04:40Z" }, { "body" : "Lat talk: Nevan Krogan <a rel=\"nofollow\" href=\"http://kroganlab.ucsf.edu/\">http://kroganlab.ucsf.edu/</a> (disclaimer, I am biased :)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/6d6d126f992f4ec2a4ee28865619df8a", "date" : "2008-07-21T16:09:21Z" }, { "body" : "Last talk of the session: Nevan Krogan", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/bac21195a1364329a732ffe0d831cacb", "date" : "2008-07-21T16:09:38Z" }, { "body" : "how to combine protein and genetic interaction networks. Starting by introducing quantitative genetic interactions.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/0d160209254a4385a0fc6ee0d3d73589", "date" : "2008-07-21T16:10:55Z" }, { "body" : "epistatic interactions measured by colony size - EMAPs a good methods papers on this is <a rel=\"nofollow\" href=\"http://genomebiology.com/2006/7/7/R63/abstract\" title=\"http://genomebiology.com/2006/7/7/R63/abstract\">http://genomebiology.com/2006...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/2babe31fd5a44ec794d32de49b1a0496", "date" : "2008-07-21T16:14:01Z" }, { "body" : "using correlation of genetic interactions between gene pairs to predict complex and functional association.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/8c4aa3b3ef524a3ab008ea19b9507ba0", "date" : "2008-07-21T16:15:16Z" }, { "body" : "Genetic Map of 743 Genes Involved in Chromosome Biology; Collins et al, Nature, 2007. Pairs of genes coding for physically interacting proteins often have similar genetic ixn profiles and positive genetic ixns", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/7fd311f58c104acb8c27db25e3b77a0e", "date" : "2008-07-21T16:15:35Z" }, { "body" : "Talking about Assem's work on S. pombe genetic interaction map on DNA machinery", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/ae44d558d7be4158a1d4d19ff68e95a2", "date" : "2008-07-21T16:16:39Z" }, { "body" : "550 S.pombe genetic interaction map that is comparable (orthologous as well) to the one in S. cerevisiae", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/bd628756cc864749b02430767bb79c66", "date" : "2008-07-21T16:18:42Z" }, { "body" : "He is talking about the RNAi cluster found within the genetic interaction network. A new component of RNAi machinery was found in the map. Follow up experiments confirm the result", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/e53d75965c6c4ed9a4ebe5a471f423b6", "date" : "2008-07-21T16:21:52Z" }, { "body" : "how conserve are genetic interaction between S. cerevisiae and S. pombe ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/ce95b10199394636b8f63405d9347235", "date" : "2008-07-21T16:22:17Z" }, { "body" : "the conservation of genetic interactions (S scores) between pairs of proteins  is very low R=0.14 but higher if they interact (defined by co-complex).", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/484d7c4851414e568bdaf6e52adbdb7b", "date" : "2008-07-21T16:24:17Z" }, { "body" : "conservation is found at the level of modules (complexes) but not between them", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/c123b6df4cd64982a0ea127779b368d8", "date" : "2008-07-21T16:24:58Z" }, { "body" : "Best conservation at the complex level - but complexes are often in the nucleus and the nucleus is best conserved. Not a contradiction to what is presented but softens the generality, I would think.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/fcebc929e9664ce3a39280759a918eb0", "date" : "2008-07-21T16:25:48Z" }, { "body" : "genetic interactions within modules not conserved", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/9a0308c1ac7a42b98aa234873cbb1986", "date" : "2008-07-21T16:28:31Z" }, { "body" : "Bonus talk! Frank Alber, USC: Determining the subunit architectures of macromolecular assemblies. [Interaction networks? Disease? Hello?]", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/7bb169f278f14666bb0e5be873e696f7", "date" : "2008-07-21T16:32:07Z" }, { "body" : "Frank Alber on subunit architectures of complexes", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/a585ec7d21df4150ac189bdea2d694a9", "date" : "2008-07-21T16:33:14Z" }, { "body" : "Frank Alber talk on determining big macromolecular assemblies structures by integrating different structural data.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/f9890ad1bd224a2ba09ec175b83fb305", "date" : "2008-07-21T16:33:30Z" }, { "body" : "Introduction to nuclear pore complex. used developed computational approach and experimental data: copy numbers, sedimentation coefficients, imuno-electron microscopy (15 to 20nm resolution), shape from electron microscopy, affinity purification for proximity information", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/b7d516d30a054620a132e070b6928aa5", "date" : "2008-07-21T16:39:47Z" }, { "body" : "used all the constraints to build optimized models of protein localization probability within the complex and used known structures to fill the structure. Nice pictures and movie of the whole complex", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/90c1890b38e64281869a672bd75a564e", "date" : "2008-07-21T16:45:16Z" }, { "body" : "Stunning display of the 450 proteins in the nuclear pore complex. Amazing work, really.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/dfd8376fc6cb488797162f8a3f716503/c/1b76125ffdc2477a86a505adc2310c67", "date" : "2008-07-21T16:47:36Z" } ], "body" : "Interaction Networks and Disease Room 701A - <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/special_session_details.php#session3\" title=\"http://www.iscb.org/ismb2008/special_session_details.php#session3\">http://www.iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/dfd8376f/interaction-networks-and-disease-room-701a", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T14:33:26Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Hsuan-Cheng Huang", "private" : true, "id" : "hchuang", "type" : "user" }, "date" : "2008-08-13T08:53:26Z" }, { "from" : { "name" : "Euan", "id" : "stew", "type" : "user" }, "date" : "2008-07-23T21:06:45Z" }, { "from" : { "name" : "Thomas Lemberger", "id" : "thomaslemberger", "type" : "user" }, "date" : "2008-07-21T15:38:04Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T14:58:35Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-21T14:41:55Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T14:36:05Z" } ] }
{ "_id" : "e/e068af46ea0341f48a91a430a99f5ee5", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Moving onto humans as a microbial environment - &quot;2nd human genome project&quot;", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/fd4be56e1c1445b4a8e5bed03f371196", "date" : "2008-07-20T13:17:46Z" }, { "body" : "Let's not forget those human-colonising archaea!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/d282f30c0b4b4eaf9b0bac71b0591e15", "date" : "2008-07-20T13:20:06Z" }, { "body" : "Significant cross-talk between microbial/human genes; doesn't supply evidence or examples though", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/6a98ad89c1b2474fa3007e150d081388", "date" : "2008-07-20T13:22:16Z" }, { "body" : "Still defining goals, methods and tools required to study human microbiome - ideas welcome", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/e338db501c0b4cd681d0fdda9604e6a2", "date" : "2008-07-20T13:27:17Z" }, { "body" : "Moving to the wondrous diversity of the GI tract...", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/e8b8c37d31e44abba2e13894ba5e057a", "date" : "2008-07-20T13:30:16Z" }, { "body" : "Are &quot;singletons&quot; ever interesting or should we just discard them?", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/4c36347c8d744a5496967cb5098bbcc5", "date" : "2008-07-20T13:32:49Z" }, { "body" : "Microbiome compositions not &quot;random&quot;, but lots of variation between individuals", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/8b1277c8fcae4b86940197363ea35698", "date" : "2008-07-20T13:38:00Z" }, { "body" : "Metagene - gene calling software for metagenomes", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/380fbbe549954e96b6f728a0fe5a1f91", "date" : "2008-07-20T13:39:55Z" }, { "body" : "Metaproteomic analysis gives better data than gene prediction", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/e1f7a72649794bf3ab73a91191d07781", "date" : "2008-07-20T13:43:16Z" }, { "body" : "Wrapping up: how to define a core microbiome?  What are the big questions in human metagenomics?  New tools required!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/e068af46ea0341f48a91a430a99f5ee5/c/d7eb0afa2b344cdb87ff9745350f491c", "date" : "2008-07-20T13:44:03Z" } ], "body" : "In theory metagenomics can access 100% of environment - I wonder?", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e068af46/in-theory-metagenomics-can-access-100-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T13:14:42Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/e1772f637a424a9a86b01d2110c6880f", "feed_id" : "ismb-2008", "comments" : [ { "body" : "trust from paid curations, a level of user ability and searchabiliyt from the crowd", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/dd98e0c2c30f425eb7c3b218766d881c", "date" : "2008-07-20T18:12:08Z" }, { "body" : "Seems to be a relatively uncontroversial starting question, the Panel seem in agreement that both add value and should exist together - I think I would agree to", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/54fd4bf618bc4fa8ae0fb410f4e7ffb0", "date" : "2008-07-20T18:15:49Z" }, { "body" : "Panel: Helen Parkinson (Array Express, EBI), Mark WIlkinson (Uni British Columbia), Phil Bourne (UCSD), Matt Cockerill (Biomed Central)", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/7940c4919b104c1eb3c0ac5ae933ad06", "date" : "2008-07-20T18:18:17Z" }, { "body" : "Frank, it's a somewhat obvious answer.  Glad to hear that people seem to think so", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/ea8a73fff6514b22b5ba79f0fcdbddd1", "date" : "2008-07-20T18:18:28Z" }, { "body" : "Agghh! battery is dying!", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/e8701486d7ca453b9f38f161aafaa542", "date" : "2008-07-20T18:20:19Z" }, { "body" : "Back with some juice", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/e1772f637a424a9a86b01d2110c6880f/c/17ea98e8b96540788d7a6f23b1a5057c", "date" : "2008-07-20T19:35:04Z" } ], "body" : "Bio-ontologies Panel session Question 1: Curation vs Crowd sourcing - Should databases be developed by the cmmunity rather than professional curators?", "feed_name" : "ISMB 2008", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e1772f63/bio-ontologies-panel-session-question-1", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:11:10Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/e189d8b768a5439ebe43aa72bb6e509a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Claire M. Fraser-Ligget point of view on the microbiome is nicely sober, discussing problems rather than trying to impress.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/e189d8b768a5439ebe43aa72bb6e509a/c/868c52e604d24f4db0dc25f887da98cc", "date" : "2008-07-20T13:31:48Z" } ], "body" : "Please, don't say superorganism  <a href=\"http://friendfeed.com/search?q=%23keynote\">#keynote</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e189d8b7/please-don-t-say-superorganism-keynote", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T13:19:59Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d", "feed_id" : "ismb-2008", "comments" : [ { "body" : "David W. Andrews talking about high throughput microscopy to look at protein localization in S. cerevisiae <a rel=\"nofollow\" href=\"http://www.dwalab.com/\">http://www.dwalab.com/</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/57ded213d8b5496a9d6988b24fcdd965", "date" : "2008-07-20T18:24:49Z" }, { "body" : "Fully automated high content microscopy of gene deletion library (work by Mathew Henderson and Tony Collins). Screen looking for ER defects. There are problems with differences in expression of GFP in the populations. Image analysis of localization correlation of two fluorophores, cell structure features and what he called texture features (no clue what they are) allows them to look for genes implicated in ER formation.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/91df831bc9e14d6d92d7c1753287a3a8", "date" : "2008-07-20T18:37:39Z" }, { "body" : "Second talk by Gaudenz Danuser (<a rel=\"nofollow\" href=\"http://www-bioeng.ucsd.edu/wibe/members/profiles/danuser.shtml\" title=\"http://www-bioeng.ucsd.edu/wibe/members/profiles/danuser.shtml\">http://www-bioeng.ucsd.edu/wibe...</a>) imaging of cell migration. Interested in measuring cell adhesion by microscopy.Looking for molecules that effect cell motility (velocity) or/and cell adhesion.Introduction to fluorescent speckle microscopy (provides a &quot;stochastic sampling of microtubule dynamics&quot;. Used the method to look at different sub structures at the leading edge. Looked at contraction and boundary forces and see how they change over time.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/a8c45aab2ef04890895e75745d32324c", "date" : "2008-07-20T18:50:13Z" }, { "body" : "General comment: We have proteomics (which molecules), we have molecular biology (how to manipulate) and now imaging (what happens). Suggests that big contribution of computation is to relate image events to molecular mechanism.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/18104a80b9544adcbe89125f3a843761", "date" : "2008-07-20T19:13:45Z" }, { "body" : "Chris Bakal &quot;Towards Describing the Systems Architecture of Cell Morphogenesis&quot;. What shape do cells take for a given condition ? What methods can be used to model signaling systems at different localizations in the cell ? He is mostly talking about a Science paper <a rel=\"nofollow\" href=\"http://www.sciencemag.org/cgi/content/abstract/316/5832/1753\" title=\"http://www.sciencemag.org/cgi/content/abstract/316/5832/1753\">http://www.sciencemag.org/cgi...</a>", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/82f76f06b8a84d1286ae8f7aa45797a9", "date" : "2008-07-20T19:22:02Z" }, { "body" : "Pedro met this newbee, Thanks Pedro", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/db2ee44170cc468bb3f2a981c8cfb0c5", "date" : "2008-07-20T19:48:05Z" }, { "body" : "Bisque - Integration computer visions and dbs by BS Manjunath <a rel=\"nofollow\" href=\"http://vision.ece.ucsb.edu/manjunath/\" title=\"http://vision.ece.ucsb.edu/manjunath/\">http://vision.ece.ucsb.edu/manjuna...</a>", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/3314f95b8f544bc3bfc18a637cf58827", "date" : "2008-07-20T19:50:04Z" }, { "body" : "He along with others have created BioSegmentation database", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/e3c9ef32f4f64bc9b4b886856e8e624d/c/265804d7d333440bb91c235035ea9d7b", "date" : "2008-07-20T20:16:11Z" } ], "body" : "Frontiers in cell imaging: Automated image analysis - <a rel=\"nofollow\" href=\"http://www.iscb.org/ismb2008/special_session_details.php#session2\" title=\"http://www.iscb.org/ismb2008/special_session_details.php#session2\">http://www.iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e3c9ef32/frontiers-in-cell-imaging-automated-image", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T18:22:43Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/e977af9c28f84ca29badf6465fe40cd0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "So the red shirts were just available for volunteers ? I was already thinking that I just didn't get one.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/e977af9c28f84ca29badf6465fe40cd0/c/b25483e91b584278a014036e7995a46d", "date" : "2008-07-20T19:29:08Z" }, { "body" : "I am wearing one!!!!!!", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/e977af9c28f84ca29badf6465fe40cd0/c/a66f7a48a16a40d1a8596d9cc7d27651", "date" : "2008-07-20T19:47:19Z" }, { "body" : "How did you get one ?", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/e977af9c28f84ca29badf6465fe40cd0/c/ecc16411b87b467ab87b293dc2ee87a6", "date" : "2008-07-20T19:49:01Z" }, { "body" : "Volunteer, of course", "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "id" : "e/e977af9c28f84ca29badf6465fe40cd0/c/ccc01c1b453a4a2999ac7ee7a5e1f39c", "date" : "2008-07-20T19:53:13Z" } ], "body" : "The volunteers here are called red shirts.  I wonder how many will survive the meeting :)", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e977af9c/volunteers-here-are-called-red-shirts-i-wonder", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:27:45Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "date" : "2008-07-20T20:27:29Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-20T19:45:29Z" }, { "from" : { "name" : "Saravanamuttu Gnaneshan", "id" : "gnani", "type" : "user" }, "date" : "2008-07-20T19:37:36Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T19:28:34Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-20T19:28:03Z" } ] }
{ "_id" : "e/e9dc49c9a3f64d71883cbce3853a772c", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Emphasis that this wrt hierarchal levels this is an organelle level study –  use case is phagosome", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/e9dc49c9a3f64d71883cbce3853a772c/c/5e1df4314c9e4c4aa024bf4da97b56b9", "date" : "2008-07-21T16:06:04Z" }, { "body" : "Known positives, 1st and second neighbors. Examine edges between 1st and 2nd to knowns. Weight edges and use slider to optimize threshold. Estimates of precision and recall.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/e9dc49c9a3f64d71883cbce3853a772c/c/9739f8da311d42d5beb816538666fdbc", "date" : "2008-07-21T16:11:44Z" }, { "body" : "Requires at  least 2 connections from initial  optimization study.  He noted that there is room for automated methods  and methodology work.", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/e9dc49c9a3f64d71883cbce3853a772c/c/9251a83a846f4b7e89b42c54898c139c", "date" : "2008-07-21T16:15:36Z" }, { "body" : "Case study: Exocyst function – role in internalization. Experimental data indicates there are different paths of internalization (e.g. Internalization of e.coli versus others)", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/e9dc49c9a3f64d71883cbce3853a772c/c/275ffac702a34532a95c8b5a06a252ef", "date" : "2008-07-21T16:15:55Z" }, { "body" : "See website for more info and software <a rel=\"nofollow\" href=\"http://baderlab.bme.jhu.edu/baderlab/index.php/Main_Page\" title=\"http://baderlab.bme.jhu.edu/baderlab/index.php/Main_Page\">http://baderlab.bme.jhu.edu/baderla...</a> (alias is www.baderzone.org) . Love the Boris and Natasha image!", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "id" : "e/e9dc49c9a3f64d71883cbce3853a772c/c/cc8dd222870b46b58f90fcb5262674b0", "date" : "2008-07-21T16:22:10Z" } ], "body" : "HL22: Systems Biology of Phagosome", "feed_name" : "ISMB 2008", "from" : { "name" : "Shannon McWeeney", "id" : "wildtype", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/e9dc49c9/hl22-systems-biology-of-phagosome", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T16:05:05Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/ea2317c3b96142d48630d27d49d47229", "feed_id" : "ismb-2008", "comments" : [ { "body" : "This year, ISMB will auto-generate posts for each talk around 10 minutes before the start of the talk, so that the live-blogs can be linked to the ISMB homepage. I hope we'll have lots of coverage!", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/80d639f11c13459eaee59d5faa66c433", "date" : "2009-06-23T09:36:21Z" }, { "body" : "ISMB will also advertise this on their homepage and in the conference newsletter, so hopefully we'll get many new contributors.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/7ab7ddea1c9c4280b6f25530b9b31bc3", "date" : "2009-06-23T09:36:47Z" }, { "body" : "Only 4 days to go!  Would love to be there and catch up/meet new faces, but vicarious participation via copious microblogging will be the next best thing :-)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/80bbee8c6e6f457c92a856050872fa39", "date" : "2009-06-23T09:42:11Z" }, { "body" : "Will we be able to micro-blog the SIGs from this room as well?", "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/0b0a66a6f1084183900912696281c807", "date" : "2009-06-23T09:57:10Z" }, { "body" : "Yes, no problem. We will generate posts for each SIG meeting.", "from" : { "name" : "Bettina", "id" : "tina001", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/d98eb60e636340c081d771617ab4fa9f", "date" : "2009-06-23T10:21:12Z" }, { "body" : "@Bettina - thanks :)", "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/0562586afbf9451888ca171b4ee2b255", "date" : "2009-06-23T12:33:21Z" }, { "body" : "This doesn't look like a room - it's actually a &quot;friend&quot;, even though it's a conference &quot;friend&quot;. Is this because you don't want people starting topics there? As it stands, we'll only be able to comment on existing topics, and not post interesting links etc EXCEPT as they relate to an already-started topic. Perhaps this is deliberate to keep things on-topic. Is this what you were going for? Just curious... :)", "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/9609cc4ea92b45b1a3bd2f2e96121398", "date" : "2009-06-24T08:30:26Z" }, { "body" : "you're right, I didn't realize this. I brought it to the attn of the admins. It might be deliberate (because of the integration with the ISMB website), but then one should probably create another room to coordinate meet-ups etc.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/3a2a38820d6a4c4f80e67969505e0453", "date" : "2009-06-24T08:36:33Z" }, { "body" : "Thanks, Michael. Yes, the idea was to keep it more organized. We will create another room for the &quot;ismbeccb2009-talk&quot; where everyone is welcome to post but please use the official &quot;ismbeccb2009&quot; conference room for all discussions regarding the presentations (Highlights, Proceedings Track, Technology Track, SIGs and Keynotes).", "from" : { "name" : "Bettina", "id" : "tina001", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/04742c4a24de4b9a985709f9c13355b7", "date" : "2009-06-24T10:00:03Z" }, { "body" : "@Bettina - thanks for the reply. While I'm not 100% sure that splitting things up like this will work (people might not switch that much between the two), I can see the reasoning and hope it works well. Perhaps these reasons should be added to the taglines of the ISMB &quot;friend&quot; and the ISMB talk group you mentioned, so that when people go to one, they see both what it's for and how to get to the other one... Thanks! :)", "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/a778f19b27664c0e9004b48c21e8a844", "date" : "2009-06-24T10:46:00Z" }, { "body" : "Ok, its true, switching between groups might not work. I talked with my supervisor and we  decided now to change the settings. So now everyone of you should be able to post in the ismbeccb2009 room.", "from" : { "name" : "Bettina", "id" : "tina001", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/fde9659c6d2d4156a47a5f982bb890a9", "date" : "2009-06-24T14:36:06Z" }, { "body" : "@Bettina - thanks, looks good. Looking forward to the start of the conference on Saturday! :)", "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "id" : "e/ea2317c3b96142d48630d27d49d47229/c/1f867b5feb274d5aa28116e1ca4e4dd1", "date" : "2009-06-24T15:02:32Z" } ], "body" : "The official room for ISMB/ECCB 2009: <a href=\"http://friendfeed.com/ismbeccb2009/\" title=\"http://friendfeed.com/ismbeccb2009/\">http://friendfeed.com/ismbecc...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/ea2317c3/official-room-for-ismb-eccb-2009", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2009-06-23T09:34:27Z", "to" : [ { "name" : "Michael's feed", "id" : "biocs", "type" : "user" }, { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" }, { "name" : "The Life Scientists", "id" : "the-life-scientists", "type" : "group" }, { "name" : "Science 2.0", "id" : "science-2-0", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel MacArthur", "id" : "dgmacarthur", "type" : "user" }, "date" : "2009-06-24T20:44:24Z" }, { "from" : { "name" : "Mickey Kosloff", "id" : "mkosloff", "type" : "user" }, "date" : "2009-06-24T18:54:15Z" }, { "from" : { "name" : "Anne Tuukkanen", "id" : "anniina", "type" : "user" }, "date" : "2009-06-24T16:01:52Z" }, { "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "date" : "2009-06-24T05:35:44Z" }, { "from" : { "name" : "Reinhard Schneider", "id" : "r8709", "type" : "user" }, "date" : "2009-06-23T14:21:47Z" }, { "from" : { "name" : "Konrad Förstner", "id" : "konradfoerstner", "type" : "user" }, "date" : "2009-06-23T14:08:22Z" }, { "from" : { "name" : "Cass Johnston", "id" : "cassj", "type" : "user" }, "date" : "2009-06-23T12:58:40Z" }, { "from" : { "name" : "Ruchira S. Datta", "id" : "ruchira", "type" : "user" }, "date" : "2009-06-23T11:46:31Z" }, { "from" : { "name" : "Brad Chapman", "id" : "chapmanb", "type" : "user" }, "date" : "2009-06-23T11:38:20Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2009-06-23T11:21:15Z" }, { "from" : { "name" : "Daniel Swan", "id" : "dswan", "type" : "user" }, "date" : "2009-06-23T10:15:55Z" }, { "from" : { "name" : "Allyson Lister", "id" : "allyson", "type" : "user" }, "date" : "2009-06-23T09:56:30Z" }, { "from" : { "name" : "Egon Willighagen", "id" : "egonw", "type" : "user" }, "date" : "2009-06-23T09:44:03Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2009-06-23T09:37:17Z" } ] }
{ "_id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5", "feed_id" : "ismb-2008", "comments" : [ { "body" : "OK, this open doc could be used to collect ideas for the report. If you want to contribute, please leave a message here, preferably with what you would like to add. For now, the document only contains some scribbles and nothing of general interest.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/0b7f8c08695249c6ac520279b58e4366", "date" : "2008-08-03T17:37:59Z" }, { "body" : "I have now added the first notes on the literature mining results to the document. I will try to make a figure out of it tomorrow - just a simple plot showing the growth of the terms that I have found.", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/231788c935a846a89e61eae14f97fd6f", "date" : "2008-08-09T18:16:19Z" }, { "body" : "I've added a draft of my writeup for the Web 2.0 BoF. Feel free to edit!", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/3a8fd015e4264d518620bb546131bf4f", "date" : "2008-08-10T02:38:45Z" }, { "body" : "Just to make sure everyone notice: I have gone through out manuscript and made a few comments. I think the manuscript is in a quite good shape, so we should be able to finish it quickly once we are all over the NAR database deadline on September 15 :-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/b683a46b5d524e648a59cb2535d77801", "date" : "2008-09-10T16:09:31Z" }, { "body" : "I added a (draft) small report on the BioPathways SIG. I can trim it down to fit as a box or maybe it can just go in supplementary I don't really now. I will check the main article tomorrow.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/c1255eb271744b00a49d1326c4061b3f", "date" : "2008-09-11T22:10:22Z" }, { "body" : "Added few subtle changes to FriendFeed collage.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/986d861e38ab4894a97b1edda8811173", "date" : "2008-09-23T12:17:17Z" }, { "body" : "Can I get access to it? I am on the Short Read way.", "from" : { "name" : "Steve Wu", "id" : "seekerwjk", "type" : "user" }, "id" : "e/eb8a8628bee94edba5c7ca3da57c1fb5/c/6b07e1f8c12e4d43aa39fc4a73fbbb39", "date" : "2008-11-03T11:47:56Z" } ], "body" : "ISMB 2008 report - <a rel=\"nofollow\" href=\"http://docs.google.com/Doc?id=ddft5j63_368gvbtsgdn&amp;invite=d6gdh93\" title=\"http://docs.google.com/Doc?id=ddft5j63_368gvbtsgdn&amp;invite=d6gdh93\">http://docs.google.com/Doc...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/eb8a8628/ismb-2008-report", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T18:22:48Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-08-10T10:16:00Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-08-05T05:48:14Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-08-03T18:03:44Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-22T19:26:11Z" }, { "from" : { "name" : "Adrian Heilbut", "id" : "adrianh", "type" : "user" }, "date" : "2008-07-22T18:26:19Z" } ] }
{ "_id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Some of the topics included reproducibility (is it possible, even in silico? what are the criteria? can we institute a badge of some sort to indicate compliance with the criteria? The story of the Russians and the sapphire-lasing study is telling, video logging may help), URL and data citation/impact factors as opposed to just publications, (dis)incentives to go open, blogging and recruitment/exposure, good research practices and their lack of adoption (version control as an example)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/46e3fb3953eb4e6d9bb292278e4af8f9", "date" : "2008-07-19T04:06:50Z" }, { "body" : "Greg also asked what the desired outcome of the PSB workshop is, and I didn't have a good answer. Michael N brought up the good point that for OA to really get momentum, they first got a lot of powerhouses - funding agencies, namely - to buy-in, and signed declarations helped a lot. So perhaps using reflections on all the other Open * meetings this year we can devise a productive agenda with concrete outcomes (one of which may be drafting a declaration that we will promote to big names).", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/e2bf44f4647c445aa99311ea624c99da", "date" : "2008-07-19T04:10:34Z" }, { "body" : "Greg also mentioned that about 9 years ago people were talking about very much open sciencey things (as open source was starting to take off) with the same fervor, but nothing has happened in the intervening time and now we are back at that point. What needs to happen to make sure that that doesn't happen this time? Are things different now, and how?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/5c77125b9e0f4faa962a235416823107", "date" : "2008-07-19T04:13:32Z" }, { "body" : "Another interesting thought was if in the next few years, students will gravitate towards PIs who adopt more open practices, who blog, who are more willing to incorporate &quot;Web 2.0&quot; tools into their work and research. Michael N and Greg both agreed that their blogging was a major reason their students joined their labs. Will students indirectly effect change by placing a new type of selective pressure on schools and faculty?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/e4bff22256e1428cb48690f1910aa8e9", "date" : "2008-07-19T04:19:45Z" }, { "body" : "This meeting got me thinking that open science is very ill-defined, other than as &quot;a nice idea&quot;.  Need to get my own thoughts in order on what it all means.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/4bbb959115a2441d990aa45eec8ccddb", "date" : "2008-07-19T14:32:13Z" }, { "body" : "I agree. OA is very well defined and this is a good thing. But it will be hard to sell open science to big names unless we know what it is, exactly, that we're selling. This may mean breaking open science down into a few core components which may be easier to define individually, and a declaration (or two, or three) may come out of that more naturally.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/068acfc6d4394ccba49132cd93bdd957", "date" : "2008-07-19T14:42:43Z" }, { "body" : "Neil, which is why I think scientists should think about marketing and branding, not because these are good things per se, but because if you can wrap an idea around something, it's easier to convey", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/418ff43b3b324bdfb7a76f7e10c7104b", "date" : "2008-07-19T16:41:42Z" }, { "body" : "I think the branding/definition thing is good. I think for instance it is clear to most people what Open Notebook Science is, partly because Jean-Claude and others are active in defending the definition of the term. Maybe some other terms to cover 'full data disclosure on publication' 'publishing all results' and similar more precise things.", "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "id" : "e/ecf6b1da5ced4eaeb3c5659cdae5af06/c/ce3437e2923e4755b911fc5df6791ff0", "date" : "2008-07-19T19:03:02Z" } ], "body" : "A good group got together for a blogger/open science meetup type thing at the Loose Moose. Greg Wilson, Pedro, Neil, Michael Kuhn, Michael Nielsen, Joe Anderson, and myself.", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/ecf6b1da/good-group-got-together-for-blogger-open", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-19T04:03:33Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-21T12:23:37Z" } ] }
{ "_id" : "e/ef87914fc3c5494388adc518e9991fb4", "feed_id" : "ismb-2008", "comments" : [ { "body" : "PA plays &quot;don't let the sun go down on me&quot;...", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/96aa44c765b648d6960bcc4032a35777", "date" : "2008-07-22T20:48:25Z" }, { "body" : "systems biology of human metabolism", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/9f1f67165e1e4e0b9579f7312ac118c5", "date" : "2008-07-22T20:51:39Z" }, { "body" : "Kicks off with an iphone joke :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/c825b96104ca4d338512e8222a6f7fec", "date" : "2008-07-22T20:51:57Z" }, { "body" : "Who would start with an iPhone joke :) ?", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/a1460a0c6d384fd2aa398da9b79f8cb6", "date" : "2008-07-22T20:53:42Z" }, { "body" : "1. paradigms 2. Links and nodes (network bioogy) 3. Maps and functional states 4. Workflows and knowledge bases 5  Reconstruction 6. Human reconstruction of the metabolic network 7. Application", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/208fc25dbedc44dea880a91b9e41fcc5", "date" : "2008-07-22T20:54:09Z" }, { "body" : "Talk outline looks mighty ambitious", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/df4709fb61b94fd4afc75bc66d14a470", "date" : "2008-07-22T20:54:10Z" }, { "body" : "components, networks, models, phenotypes (the paradigm)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/02dd671a576c4c5683f37da02fa183d8", "date" : "2008-07-22T20:55:21Z" }, { "body" : "omics to knowledge base to in silico modeling to validation and discovery", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/633f94011dd543f5b91475d7962e609c", "date" : "2008-07-22T20:55:44Z" }, { "body" : "Systems biology: components -&gt; networks -&gt; computational models -&gt; phenotypes", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/b8d8f777b5e14080a1bd231f79f53aa4", "date" : "2008-07-22T20:56:04Z" }, { "body" : "Conversion of biochemical data to query-able format", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/dfa01de512cb4c2186416cf0ccda403d", "date" : "2008-07-22T20:56:19Z" }, { "body" : "1. maps to database, 2. knowledge base 3. query tools 4. validation and discovery of missing parts, synthetic biology", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/ad8dadb72a7a41e8800e71f595af6ad4", "date" : "2008-07-22T20:57:11Z" }, { "body" : "So, his paradigm for sysbio maps to a large, structured and detailed knowledge base", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/212348c6202b44f0a45c2ecd5ad71294", "date" : "2008-07-22T20:58:47Z" }, { "body" : "Various levels of modelling; detailed chemical kinetic knowledge the most specific", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/ae745546b1254f26b957a06708770e4d", "date" : "2008-07-22T20:59:29Z" }, { "body" : "general property of cells - prototypical transformation are bi-linear.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/fc6ca202d9e54f0fb07bc0a9bf1d5b58", "date" : "2008-07-22T21:00:12Z" }, { "body" : "Molecular biology links are fundamentally bi-linear, e.g. bimolecular reactions and interactions", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/0a6b2677d165499dbc5ec8c97b80c290", "date" : "2008-07-22T21:01:09Z" }, { "body" : "Network links constrained by chemistry", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/e25789834835483b9e5c3585cbedba75", "date" : "2008-07-22T21:02:01Z" }, { "body" : "Metabolic networks cannot be randomized for statistical evaluatiuon - no pyruvate will go to isocitrate just so.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/a9d6e4a6aca04ea286f8e749b03985a5", "date" : "2008-07-22T21:02:43Z" }, { "body" : "relative rates are fixed by thermodynamics but absolute rates are highly variable inside the cell. General comment, links are very constrained by the physical attributes of the nodes. Interesting comment about problems in creating a random network with little knowledge of atomic information.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/311cc204dd2248b3bd4119d6fd8dd331", "date" : "2008-07-22T21:02:58Z" }, { "body" : "Can now visualise pathways in context of entire metabolic network", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/a454ec24592e4d0da93f8b18d20cc05e", "date" : "2008-07-22T21:03:24Z" }, { "body" : "nice thing about genome scale models is that we can look at pathways in the context of the whole model. &quot;Pathways are models networks are reality&quot;  Uwe Sauer", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/658e1b56f4904760860d885acfd7fc44", "date" : "2008-07-22T21:03:50Z" }, { "body" : "Analogy between road maps and traffic (functional states) and biological networks. Getting closer to flux balance analysis", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/3a5b1ba26d9043629814db9ee3c206d6", "date" : "2008-07-22T21:04:31Z" }, { "body" : "Network topology fixed, but functional states vary constantly - nice analogy with traffic on highways through the day", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/7c6634e2ad21499a9c22938c649ae84a", "date" : "2008-07-22T21:05:49Z" }, { "body" : "Cobra suite <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/17406635\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/17406635\">http://www.ncbi.nlm.nih.gov/pubmed...</a> (a recent in Nature Protocols)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/417bdd91df224458b959572307f8c0a2", "date" : "2008-07-22T21:06:45Z" }, { "body" : "contained based models work also because evolution creates systems that are optimized for some function. It is not easy to know what are these functions that are optimized.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/ee03ea0aa55d414f9e09f33c9b222d85", "date" : "2008-07-22T21:07:16Z" }, { "body" : "COBRA software available as Matlab package", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/405e120e87b7485aa8fed077dbf5b869", "date" : "2008-07-22T21:08:28Z" }, { "body" : "OK, vectors and matrix operations, sysbio at last", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/3f741db328274a82924c84852b300e40", "date" : "2008-07-22T21:10:24Z" }, { "body" : "I hope he does not say biblioome", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/c91d2d531b334895a586e01a1a5a92c1", "date" : "2008-07-22T21:10:41Z" }, { "body" : "Moving on from fluxes and matrix operations to workflows + knowledge bases; mentions EcoCyc as example", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/e237c36084924eb68017d3cc608522c8", "date" : "2008-07-22T21:11:05Z" }, { "body" : "@pedro uwe sauer (eth)was the author of the pathways quote", "from" : { "name" : "Ildefonso Cases", "private" : true, "id" : "icases", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/027e613fce534be98fbcfcc1fbc9b9d0", "date" : "2008-07-22T21:12:47Z" }, { "body" : "Tables:  rows are metabolites; columns are reactions; must be balanced (like balancing reactions in high school, but larger scale); you then map this to the metabolome as well as you can", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/9ab6184dbaac42fc830174ff86be0eb0", "date" : "2008-07-22T21:14:50Z" }, { "body" : "@Ildefonso thanks", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/84bb14c1b395479d8e88c36f2e820f27", "date" : "2008-07-22T21:14:58Z" }, { "body" : "Metabolic reconstruction 1. Genome annotation 2. Model to perform tests (gaps etc) 3. Simulation, 4. Validation (go back to 2. if problems arise).", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/68f20026c3154381acdb876d2556f103", "date" : "2008-07-22T21:15:47Z" }, { "body" : "The human metabolic and regulatory network is 10k by 15k today", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/eb3c2b7cba734a61892a48d89c50b44f", "date" : "2008-07-22T21:16:37Z" }, { "body" : "Feis  2008 Nature reviews Microbiology (new review on the subject) I don't think it is available", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/5f27e17b668d4a078fc7e8c0bace0a5b", "date" : "2008-07-22T21:17:59Z" }, { "body" : "Showing plot of available genome-scale reconstructions over time", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/4915a44e257840a9a76741f72f040422", "date" : "2008-07-22T21:18:43Z" }, { "body" : "An idea for community effort for 2D annotation. Example of yeast reconstruction jamboree, accepted in Nature Biotech (out in a few months) Slamonella/Klebsiella jamboree September 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/35b95832b1c54748bd1b05f01388de34", "date" : "2008-07-22T21:19:56Z" }, { "body" : "Talking now about community annotation efforts; kind of like hackathons", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/83813e3e026448efa2573555c9ac8acf", "date" : "2008-07-22T21:20:18Z" }, { "body" : "Annotation jamborees to come: Salmonella and human (in 2008)", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/0a8392efc2314bdfbe5b9f37a572d9c7", "date" : "2008-07-22T21:20:28Z" }, { "body" : "2 years , 7 people to build the human metabolic network from literature 1134 genes, PNAS.. He could have mentioned another human reconstruction that was published in MSB", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/144c0ae7acfa45ebaafd404d48892362", "date" : "2008-07-22T21:22:17Z" }, { "body" : "RECON 1 knowledgebase - is it available somewhere?", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/5fb21129dde140179a455f5a6598042e", "date" : "2008-07-22T21:22:31Z" }, { "body" : "Dimensions:  3D (ultrastructural reconstruction); 4D - states over time", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/dacbdf604c734be5b6e0cd0de354afc7", "date" : "2008-07-22T21:23:12Z" }, { "body" : "3D reconstruction of transcription in E. coli - spatial and temporal aspects of the network", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/05db5bcf8765445fa88f1b5d6120b331", "date" : "2008-07-22T21:24:07Z" }, { "body" : "Last topic - what can we (the audience) do with reconstructions", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/4d6b2060b18c47159f12824a9d23a7c3", "date" : "2008-07-22T21:24:35Z" }, { "body" : "&quot;ask not what you can do for your reconstruction but what the reconstruction can do for your&quot; ... phenotypic behavior, network analysis, bacterial evolution, metabolic engi, biological discovery. (<a rel=\"nofollow\" href=\"http://www.nature.com/nbt/journal/v26/n6/abs/nbt1401.html\" title=\"http://www.nature.com/nbt/journal/v26/n6/abs/nbt1401.html\">http://www.nature.com/nbt...</a>)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/49d691a64fc84f30a0346549da99bffb", "date" : "2008-07-22T21:25:12Z" }, { "body" : "Ask not what you can do for reconstruction - Ask what reconstruction can do for you", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/c6f2d7e0eb9c4f5c84242c611dbd52c0", "date" : "2008-07-22T21:25:47Z" }, { "body" : "Uses:  metabolic engineering; evolution; network analysis; phenotypic behaviour; discovery (missing parts)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/7a6ab7fd0e874525adbad3f60482d54e", "date" : "2008-07-22T21:25:49Z" }, { "body" : "A lot more people working in these type of models. Mentions recent paper by Barabasi (<a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/18599447\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/18599447\">http://www.ncbi.nlm.nih.gov/pubmed...</a>)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/89b94b2480e8402aa0ab069cdba7426f", "date" : "2008-07-22T21:27:43Z" }, { "body" : "Prediction of missing reactions or even missing pathways", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/c6b1596895494cbf83d49327ed59c4d3", "date" : "2008-07-22T21:28:46Z" }, { "body" : "Knowledge gaps: reactions, metabolites", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/db41cd8ac06a4a95ac8dab887794a003", "date" : "2008-07-22T21:29:05Z" }, { "body" : "Covering some uses of the RECON 1 knowledge base", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/3a9292a24beb46e3b04f152d0736dd0c", "date" : "2008-07-22T21:30:10Z" }, { "body" : "@Lars, I think Recon 1 is a reference to that human model in Duarte et al PNAS, and I think it is all available.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/fdd0fb44e57b47868f1f808573f9788e", "date" : "2008-07-22T21:30:12Z" }, { "body" : "Q10 synthesis gaps <a rel=\"nofollow\" href=\"http://www.ncbi.nlm.nih.gov/pubmed/17088549\" title=\"http://www.ncbi.nlm.nih.gov/pubmed/17088549\">http://www.ncbi.nlm.nih.gov/pubmed...</a>", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/d00c45f1682f45d0a0c236a171f9c73e", "date" : "2008-07-22T21:32:26Z" }, { "body" : "@Pedro, that is also how I understand it now :-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/b359972ce824402d9bbb6e02fcfa377e", "date" : "2008-07-22T21:33:26Z" }, { "body" : "co-sets - Using metabolic networks to predict the cause of SNPs (concept MSB paper 2006). several examples of how SNPs associated with phenotypes that could be predicted by the network. Mentions again the Barabasi paper linked above", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/9c487530d05e4baea808beac8685260c", "date" : "2008-07-22T21:35:03Z" }, { "body" : "Recon 1 + gene expression map to localize the map by tissue. (lost me on nthe application ) I think the reference was Nature Biotech 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/0603956142f34e639f2607f7b5abbd72", "date" : "2008-07-22T21:36:29Z" }, { "body" : "Construction of tissue-specific models by combining Recon 1 and tissue expression data", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/ac6ad935358343649efc4ed1ae34e8f1", "date" : "2008-07-22T21:36:38Z" }, { "body" : "Multi-omics data integration; basically mapping all sorts of datasets onto each other; gives example of mapping OMIM to expression profiles", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/274d6eef756b4aa0b48c7367ad4e2cb6", "date" : "2008-07-22T21:36:57Z" }, { "body" : "Proud to be on time.", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/89127b1598594191b54ba433fb3e2988", "date" : "2008-07-22T21:38:40Z" }, { "body" : "Wrapping up.  I thought it was a pretty impressive overview.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/10862b62ed414c8fa10442591b3c71f4", "date" : "2008-07-22T21:38:52Z" }, { "body" : "connectivity map data set (Lamb et al); expression data mapped to recon 1 metabolic network gen set; identified metabolic signatures for 540 expr. profiles; case study: anti diabetic drugs cluster very well; can see systemic down-=stream effects of drugs; one co-set includes HMG-CoA reductase (interesting to check other targets in the co-set if they are drug targets)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/c9de5133988245569dc52debd051e1ce", "date" : "2008-07-22T21:39:03Z" }, { "body" : "Hypothesis: members of the same co-set should have identical effect on cell state -&gt; implications for drug development by suggesting alternative targets", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/97ead74b2fe441e08222d2371b620c62", "date" : "2008-07-22T21:39:46Z" }, { "body" : "Well done everyone - this was an awesome coverage of the talk :-)", "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/8a0db48bc6c94fccbe34b0b281ad5a8e", "date" : "2008-07-22T21:41:03Z" }, { "body" : "Yes, great coverage. Useful for me.", "from" : { "name" : "Michael Barton", "id" : "michaelbarton", "type" : "user" }, "id" : "e/ef87914fc3c5494388adc518e9991fb4/c/92e18afe0e62477fbeea07cc248c0dfe", "date" : "2008-07-23T10:51:39Z" } ], "body" : "Keynote 6:  Bernhard Palsson - &quot;systems biology: an era of reconstruction and interrogation&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/ef87914f/keynote-6-bernhard-palsson-systems-biology-era", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T20:44:25Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Hsuan-Cheng Huang", "private" : true, "id" : "hchuang", "type" : "user" }, "date" : "2008-08-13T08:54:23Z" }, { "from" : { "name" : "Burke Squires", "private" : true, "id" : "burkesquires", "type" : "user" }, "date" : "2008-07-23T15:57:02Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-23T12:57:07Z" }, { "from" : { "name" : "Cameron Neylon", "id" : "cameronneylon", "type" : "user" }, "date" : "2008-07-23T00:17:28Z" }, { "from" : { "name" : "Sutee Dee", "id" : "thaiyoshi", "type" : "user" }, "date" : "2008-07-22T22:36:46Z" }, { "from" : { "name" : "Thomas Lemberger", "id" : "thomaslemberger", "type" : "user" }, "date" : "2008-07-22T21:24:45Z" }, { "from" : { "name" : "Lars Juhl Jensen", "id" : "larsjuhljensen", "type" : "user" }, "date" : "2008-07-22T20:53:27Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-22T20:52:10Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-22T20:49:37Z" } ] }
{ "_id" : "e/f060ab3bf1a34677b7b09ed8519defb6", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Uh oh, no slides  &quot;unstructured digital publishing&quot;", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/74ed537b82a64ec6bd88d2bd46de6868", "date" : "2008-07-23T16:20:18Z" }, { "body" : "Matt Cockerill (BioMed Central), Claire Bird (Oxford University Press), Catherine Nancarrow (Public Library of Science)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/a8882c61189d4ce9938ffbfd98fc9c64", "date" : "2008-07-23T16:21:02Z" }, { "body" : "PLoS, BMC and OUP", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/f241e575ad324f3b9a6f40717644b27a", "date" : "2008-07-23T16:21:16Z" }, { "body" : "MC: quality control function of scientific publishing; peer-review can be a rate-limiting resource for sharing scientific knowledge; need efficient process; will see more sharing of reviews between journals", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/5e5e3cdde9704f26b978acd2c9805fff", "date" : "2008-07-23T16:22:42Z" }, { "body" : "MC: reviews should separate soundness from how exciting the research is", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/032bd63eda4c43d88ba08497e8d08d38", "date" : "2008-07-23T16:23:21Z" }, { "body" : "Validation processes", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/94c16796078c48f08e4240f42373212b", "date" : "2008-07-23T16:23:32Z" }, { "body" : "MC: medical community more open to open peer review than biologists, might change (Biology Direct)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/c9734411086c4593a6b4b62a64511d0a", "date" : "2008-07-23T16:24:57Z" }, { "body" : "Open peer review - the Matt Cockerill mentions medical journals and Biology Direct", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/cf1dd34b33ca4793b8ad1c2edb933772", "date" : "2008-07-23T16:25:08Z" }, { "body" : "Matt Cockerill talked about re-using reviews from higher impact journals to lower impact journals, talked about lower tier (PLoS ONE and BMC Notes), open peer review (works in medicine and Biology Direct)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/ff9e505ca2444be9bb30f4514ea14306", "date" : "2008-07-23T16:25:57Z" }, { "body" : "much more information structured, needs open access", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/51cc9b744b2f48238b086988665b4f21", "date" : "2008-07-23T16:26:13Z" }, { "body" : "Fast talkers and slow internet connections", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/9cabc030065247ec80c8fe01952b5dbb", "date" : "2008-07-23T16:26:34Z" }, { "body" : "MC: would be nice to have full text so that more meta-analysis can be performed", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/f2c0f1929b774fa3aa0af9b609bdf99c", "date" : "2008-07-23T16:26:36Z" }, { "body" : "CB: expects to see new networks and tools that can complement impact factors", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/5086416afee74c89a9304e7eb2f0e563", "date" : "2008-07-23T16:28:58Z" }, { "body" : "Claire Bird ... quality of data and re-usability of the article is important and integrity of the publishing process needs to be sustained. community will decide the limits of usefulness of a publication.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/b699ae9f21be47b3aa93cf558e42e7b3", "date" : "2008-07-23T16:29:11Z" }, { "body" : "Catherine Nancarrow - alternative peer review model ? self-organizing community online. How comments , ranking etc could be counted for career progress", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/0f1e1b5c0aa2466cb1304102ed43f4a3", "date" : "2008-07-23T16:30:02Z" }, { "body" : "CB: is there an alternative to the current model? Discussion recently: self-organizing communities on the web [hmm, didn't Nature try this?]", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/76bdeeb03f734eeb8d4694de87ccfbb7", "date" : "2008-07-23T16:30:05Z" }, { "body" : "Question by Pedro: We can't find out currently how many people download a paper. MC: Publishers recognize this, think about how to share access data; perhaps fully open citation base [Thomson won't like this]", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/cd6643dee538440c9c95d39bc653fe20", "date" : "2008-07-23T16:33:45Z" }, { "body" : "Q: Cooperativity and data-sharing – author lists and order is an incentive against data sharing; &quot;support&quot; scientists don't get the credit they deserve; perhaps author list in alphabetical order would be more egalitarian. CN: Require author contributions in the meta-data. Strive to be as transparent as possible. MC: With the right collection of data, these &quot;hidden&quot; contributions could be measured", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/330efdf615ac49789c76ff94e06a3078", "date" : "2008-07-23T16:36:42Z" }, { "body" : "Peter Karp - maybe we could have an ontology of contributions (sounds interesting)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/fb342d52477c4866a15d373bc9262137", "date" : "2008-07-23T16:37:06Z" }, { "body" : "Q: Perhaps we could have an ontology of contributions? Or the author contr. could be aggregated", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/a9c0ceb658fb4541a3a9a2d73cebf2d8", "date" : "2008-07-23T16:37:31Z" }, { "body" : "Reactome developer - it has been very difficult to have Reactome tracked in Pubmed.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/b37e1627c70a4bdcbc18331cb0f1a8e1", "date" : "2008-07-23T16:39:08Z" }, { "body" : "Q: someone from Reactome; complains that it took a long time to have the database listed in PubMed; is there a way to make this more visible [didn't fully understand this] MC: Interested to talk to UniProt guys, current tools are drived towards journal articles, but they should also track DBs", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/18c0fde34f014fe0acf6fd4626f3af63", "date" : "2008-07-23T16:39:27Z" }, { "body" : "Discussion about Open Access (not really about publishing on well)", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/49de890dd0734a64b7b958b17b3ca9e1", "date" : "2008-07-23T16:47:06Z" }, { "body" : "MC: NIH repository policy might lead to freely accessible publications, which are still under restrictive licenses (re: text-mining)", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f060ab3bf1a34677b7b09ed8519defb6/c/1214f8db3924441891e8c93d4c9368c5", "date" : "2008-07-23T16:48:57Z" } ], "body" : "SS07: The future of scientific publishing - The publishers view", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f060ab3b/ss07-future-of-scientific-publishing", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T16:20:06Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Michael Habib", "id" : "habib", "type" : "user" }, "date" : "2008-08-08T12:47:49Z" }, { "from" : { "name" : "Rafael Sidi", "id" : "rafaelsidi", "type" : "user" }, "date" : "2008-07-26T22:47:21Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-23T16:26:05Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-23T16:23:37Z" } ] }
{ "_id" : "e/f170db0bbd934842a28b2953b0de59e0", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Struggling with the internet ;-)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f170db0bbd934842a28b2953b0de59e0/c/3a72bdaf76a24dcd92304159e0877900", "date" : "2008-07-22T17:22:53Z" }, { "body" : "discussions starting now..", "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "id" : "e/f170db0bbd934842a28b2953b0de59e0/c/5def5ea860074616a6d4255769c466ce", "date" : "2008-07-22T17:25:55Z" }, { "body" : "Nice to see two shiny Macs on the desk", "from" : { "name" : "Michael Barton", "id" : "michaelbarton", "type" : "user" }, "id" : "e/f170db0bbd934842a28b2953b0de59e0/c/b0ab9d70965a4c288310d976ec2f106b", "date" : "2008-07-22T18:07:19Z" }, { "body" : "Even though one of them was running XP ;)", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f170db0bbd934842a28b2953b0de59e0/c/05504f2102ab4b38ac3683fec8099bd2", "date" : "2008-07-22T18:24:31Z" } ], "body" : "“Pedro and Shirley” - <a href=\"http://friendfeed.com/e/f686ef0b-3bff-4ae7-8833-2d1efb7a179f\" title=\"http://friendfeed.com/e/f686ef0b-3bff-4ae7-8833-2d1efb7a179f\">http://friendfeed.com/e...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f170db0b/pedro-and-shirley", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-22T17:22:53Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "thumbnails" : [ { "url" : "http://i.friendfeed.com/c544da7b139307ef145b98771975c0dba6ae2d58", "height" : 150, "link" : "http://i.friendfeed.com/dc6e69a04981d84e982f711b2f41f50c78bdcd02", "width" : 200 } ], "likes" : [ { "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "date" : "2008-07-23T00:04:03Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-22T19:28:24Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-22T18:25:47Z" }, { "from" : { "name" : "Michael Barton", "id" : "michaelbarton", "type" : "user" }, "date" : "2008-07-22T18:07:26Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-22T17:50:55Z" }, { "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "date" : "2008-07-22T17:25:29Z" }, { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-22T17:23:15Z" } ] }
{ "_id" : "e/f2d0aa5b67c945ac9638733316d95aef", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Went to the information desk and asked. People there were surprised to hear that there even is a videocast. So even though, from a technical point of view, everything is in place, there is no recording.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f2d0aa5b67c945ac9638733316d95aef/c/672b62835ad341feab0462db7eafb8da", "date" : "2008-07-20T20:33:39Z" }, { "body" : "ISMB sent me a fax to sign to allow them to record my talk and to make derivatives such as videos that would enhance a publication. My talk is for the PLoS track so I assumed that it was for them to record the talks to add to SciVee.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/f2d0aa5b67c945ac9638733316d95aef/c/7668a632acea4814ac6c0bbf07bfee54", "date" : "2008-07-21T03:14:12Z" }, { "body" : "cool", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f2d0aa5b67c945ac9638733316d95aef/c/ed132c73776d49aea557cb6302b7677f", "date" : "2008-07-21T05:26:12Z" }, { "body" : "1) glad you liked it; was my idea and a hell of work; 2) no recording because (i) everyone else felt this is too low quality, (ii) actually, not that simple to record what is streamed is it?", "from" : { "name" : "Burkhard Rost", "id" : "br42", "type" : "user" }, "id" : "e/f2d0aa5b67c945ac9638733316d95aef/c/aaefdc3ef76941298155da67147c6965", "date" : "2008-07-27T01:31:32Z" } ], "body" : "Does anyone know, whether the live video feeds of each presentation they are streaming to the iMacs next to the Biomed Central stand are recorded in any way ?", "feed_name" : "ISMB 2008", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f2d0aa5b/does-anyone-know-whether-live-video-feeds-of", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:19:48Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T19:21:02Z" } ] }
{ "_id" : "e/f57985d88b6649b2ac0f7f5d6405e615", "feed_id" : "ismb-2008", "comments" : [ { "body" : "knowing a protein's location in the cell is important because it often provides clues as to its function, determines who it interacts with, what pathways it's involved in, and when it goes wrong it has implications for disease", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/725afdcf36d84adaa71240f9494ae384", "date" : "2008-07-20T19:48:43Z" }, { "body" : "Sequence can provide hints - localization signal sequences, general amino acid composition of the protein, hydrophobic areas indicating transmembrane regions would also fall here", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/7ee33c1fe3fc47a686205819940b6cb3", "date" : "2008-07-20T19:51:08Z" }, { "body" : "Expert rule-based systems as well as machine learning methods exist but can we do better?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/45b754063e004b39952d4db0a80a0e71", "date" : "2008-07-20T19:51:39Z" }, { "body" : "How can we use text to help with prediction? We DON'T want information extraction, rather we want information retrieval - not trying to &quot;understand&quot; text, but rather identifying relevant documents and classifying them (text categorization)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/a5b7523682804e248332370e77f3443f", "date" : "2008-07-20T19:54:45Z" }, { "body" : "Extract features from text and combine with features from sequence into an SVM", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/760e1a458a5a4c19a15b7701bc14057b", "date" : "2008-07-20T19:55:14Z" }, { "body" : "Text for a protein = Medline titles and abstracts referenced in Swiss-prot entry", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/5213f8f59b514c21bb55fabbe61b2074", "date" : "2008-07-20T19:55:44Z" }, { "body" : "Hmm ... so no text analysis?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/695ce80543014551a1370f72275e4966", "date" : "2008-07-20T19:56:42Z" }, { "body" : "Features = terms found in text (stop words removed, words stemmed, and bigrams as well as unigrams considered)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/acc24b385e5d4c9ca05e2cbaf8a34f62", "date" : "2008-07-20T19:56:47Z" }, { "body" : "Another in the plethora of SCL predictors.  More is good, I suppose.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/200ad3cc3496429e8ad29db152fe4784", "date" : "2008-07-20T19:58:21Z" }, { "body" : "Proteins with known subcellular localization used as training set for text feature selection --&gt; determine distinguishing terms for that particular localization (terms that are found frequently in that localization group and not in other groups), terms are weighted by the probability that it describes a protein in that group", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/05ceafe5e77443c99ef2a77d96dd10a7", "date" : "2008-07-20T19:59:14Z" }, { "body" : "SherLoc does 5-10% better than TargetP on various test sets. She also shows results if you use text alone, sequence alone (MultiLoc), and combined (SherLoc). Text alone doesn't improve, sequence alone does better by a bit, and SherLoc (combined) does best", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/db68869bd36e4711b6ddb6169dfc0828", "date" : "2008-07-20T20:04:37Z" }, { "body" : "What if no pubmed references exist for your protein? - HomoLoc (use references for homologous proteins), PubLoc (do a pubmed search for abstracts with that protein), or DiaLoc (you provide the text description about the protein, we'll predict based on that text): <a rel=\"nofollow\" href=\"http://epiloc.cs.queensu.ca/DiaLoc.html\" title=\"http://epiloc.cs.queensu.ca/DiaLoc.html\">http://epiloc.cs.queensu.ca/DiaLoc...</a>", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/1c84852dfaa346f586e402ba8e2fcbd4", "date" : "2008-07-20T20:08:47Z" }, { "body" : "Hmm. She said that localization can tell us about the function, interactions, etc. But then during the Q&amp;A she says that the way people talk about a protein - describing what it does, essentially - can help you predict where it localizes if it isn't already known. Seems tricky to have it both ways but I suppose it's possible to know a lot about what a protein does but not know where it localizes, as well as the other way around.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/fc1aee439cc84bb19653c9c88858d08e", "date" : "2008-07-20T20:14:27Z" }, { "body" : "@Deepak, no, it sounds like they did not do any analysis, just retrieved the documents and broke them up into terms for use as features in the SVM.- idea being that the SVM w/feature selection would extract the informative terms useful for prediction.", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f57985d88b6649b2ac0f7f5d6405e615/c/aab5da58fdc34d6b94c946502bd23d21", "date" : "2008-07-21T15:59:31Z" } ], "body" : "HL16: SherLoc - Predicting protein subcellular location using sequence data and cues from text (Hagit Shatkay)", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f57985d8/hl16-sherloc-predicting-protein-subcellular", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T19:46:28Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/f5f9c8852d6643fcbb2bc4eaeeb00de7", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Claire hits us with the phrase &quot;global microbial pan-genome&quot;.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/f5f9c8852d6643fcbb2bc4eaeeb00de7/c/e807142666834434ad7532b28e1075e8", "date" : "2008-07-20T13:11:13Z" } ], "body" : "Claire M. Fraser-Ligget is introduced with her h-index (81) by the chairman, she immediatly apologizes. Nice.", "feed_name" : "ISMB 2008", "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f5f9c885/claire-m-fraser-ligget-is-introduced-with-her-h", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T12:58:38Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-20T16:43:30Z" }, { "from" : { "name" : "Mr. Gunn", "id" : "mrgunn", "type" : "user" }, "date" : "2008-07-20T16:34:13Z" }, { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-20T13:10:41Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-20T13:00:16Z" } ] }
{ "_id" : "e/f7ada144f3bc4eaab48343587bd5015a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "Hilmar Lapp commented at lunch at how small a fraction of ISMB ppl actually contribute here. I guess it's ~10 contributing and ~30 room members out of 1500-2000 people.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/4669196bd8994fd180b6074bb621eeca", "date" : "2008-07-20T17:53:20Z" }, { "body" : "This meeting is our chance to make it less so!", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/4822c32b16b944a4840f544f36f51eb1", "date" : "2008-07-20T17:54:02Z" }, { "body" : "Technorati finds 6 recent blog posts about ISMB", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/8e2e5805bd5b4c6cafa62e82636718a4", "date" : "2008-07-20T17:55:28Z" }, { "body" : "I am surprised it is that high.  I am sure at Bio-IT World it was 1 contributing :)", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/d3758461878c4fd8954f4f64ca46e4be", "date" : "2008-07-20T17:55:57Z" }, { "body" : "What about Twitter?", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/48e606bd39a244488cb551224af4d008", "date" : "2008-07-20T17:56:03Z" }, { "body" : "Perhaps next time a &quot;Birds of a Feather&quot; event might be a good idea in order to raise awareness?", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/9d06c35336714818b96983c6f816d904", "date" : "2008-07-20T17:57:29Z" }, { "body" : "Well, it always has to start somewhere. Obviously there is room for a lot more people, but I am quite satisfied with the way it goes.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/369ac78ceb6d4cd0b4c9f7f5e5da3e2c", "date" : "2008-07-20T18:02:40Z" }, { "body" : "To be clear, I also think that this is working quite nicely. I got a good impression of what went on yesterday despite enjoying the day roaming around Toronto.", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/0057d856ad0a4be1bdc02b6b9916b706", "date" : "2008-07-20T18:09:36Z" }, { "body" : "Heck, I am not there and I am enjoying the discussion ... now when all of you start carrying camcorders and streaming live, it will be even cooler", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/ffad917eb904495aa0992573549b2a4c", "date" : "2008-07-20T18:19:44Z" }, { "body" : "There seems to be space in the program for Monday (or even Tuesday) to have a BoF session, depends on if they'll let us announce one. Perhaps the theme should be &quot;science blogging&quot;?", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/dd11385f2f6545f091aa8dc15103fdb1", "date" : "2008-07-20T19:15:00Z" }, { "body" : "Sounds awesome Shirley", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/490616808ca841bd814ce4cf63b17db8", "date" : "2008-07-20T19:16:20Z" }, { "body" : "Go for it", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/237c721e89c64982ae4fb2bc1d6cbeab", "date" : "2008-07-20T19:20:25Z" }, { "body" : "Deepak: in fact they are already streaming the presentations to a handful of special iMacs. I wonder if they are recorded and will be made available.", "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/3d205d77a74d4bca8941eed730ca101e", "date" : "2008-07-20T19:21:52Z" }, { "body" : "Ah ... I hope they are.", "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "id" : "e/f7ada144f3bc4eaab48343587bd5015a/c/d2323ebbf8804104bc26df63b09a5be5", "date" : "2008-07-20T19:28:15Z" } ], "body" : "I guess FF is still very obscure", "feed_name" : "ISMB 2008", "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/f7ada144/i-guess-ff-is-still-very-obscure", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-20T17:51:36Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/fbd6b6206fae47429ce373a1a0a5749e", "feed_id" : "ismb-2008", "comments" : [ { "body" : "I guess we should prepare a little bit :) Any ideas ? I have some slides from a talk on Open Science (my connection is to slow to put them online now). Do we prepare an introduction before the discussion for those that less aware (examples of tools: blogs, wikis, video, screencast, friendfeed, social networks) ? Roland suggested we could use the time to draft a conference report from the aggregated info.", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/aac39cf0982543b48c95a08f1d982229", "date" : "2008-07-21T03:07:45Z" }, { "body" : "I like both ideas. Perhaps a quick intro w/ Pedro's help, and then move on to the &quot;task&quot;", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/bbe0dcfb1b2c4def88e9b4159a404b26", "date" : "2008-07-21T14:35:13Z" }, { "body" : "Not sure I'll be able to make it up, but this looks like a great idea!", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/a9cf4e5bece0430483de3bf065dea174", "date" : "2008-07-21T15:12:54Z" }, { "body" : "@Michael, the security lady may also turn you away if you don't have a conference badge, unless we do some distraction techniques ;)", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/f5f0cfbdefe2446e8cfde38e6b5d9c47", "date" : "2008-07-21T16:24:03Z" }, { "body" : "Hah!  I'd forgotten about that.  In any case, it's unlikely I can make it (3 hour round trip).", "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/aba12c770a224235aed266d50cba2a80", "date" : "2008-07-21T16:27:40Z" }, { "body" : "Just to remind myself: we should put in a plug for Michael Barton's bioinformatics career survey during the session", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/fb9f8ddf9eb841f88f9d21ebb583c475", "date" : "2008-07-21T21:51:04Z" }, { "body" : "I knew I had 3 things to mention ... forgot about the survey", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/fbd6b6206fae47429ce373a1a0a5749e/c/42fc65aa9a244304897ee5d60057bce8", "date" : "2008-07-21T21:53:30Z" } ], "body" : "Science blogging and Web 2.0 BoF in room 718B on Tuesday! - <a rel=\"nofollow\" href=\"http://iscb.org/ismb2008/bof.php\" title=\"http://iscb.org/ismb2008/bof.php\">http://iscb.org/ismb200...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Shirley Wu", "id" : "shwu", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/fbd6b620/science-blogging-and-web-2-0-bof-in-room-718b-on", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-21T02:27:22Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "date" : "2008-07-21T16:28:59Z" }, { "from" : { "name" : "Michael Nielsen", "id" : "michaelnielsen", "type" : "user" }, "date" : "2008-07-21T15:11:47Z" }, { "from" : { "name" : "Michael Kuhn", "id" : "biocs", "type" : "user" }, "date" : "2008-07-21T11:17:27Z" }, { "from" : { "name" : "Daniel Jurczak", "id" : "djurczak", "type" : "user" }, "date" : "2008-07-21T05:22:22Z" }, { "from" : { "name" : "Frank", "id" : "fgibson", "type" : "user" }, "date" : "2008-07-21T04:07:10Z" }, { "from" : { "name" : "Roland Krause", "id" : "spitshine", "type" : "user" }, "date" : "2008-07-21T03:55:05Z" }, { "from" : { "name" : "sourav", "id" : "sourav", "type" : "user" }, "date" : "2008-07-21T03:06:09Z" }, { "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "date" : "2008-07-21T03:01:31Z" } ] }
{ "_id" : "e/fc5c08bac3794211a135bc66591bf0d5", "feed_id" : "ismb-2008", "comments" : [ { "body" : "A probabilistic framework for modeling indels on phylogenetic trees", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/bab09f16bafa4afe86cf7ccefcc99897", "date" : "2008-07-23T14:48:39Z" }, { "body" : "This is a method from computational linguistics finding application in bioinformatics", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/7625816fec4e44d195fcd7c2062078b7", "date" : "2008-07-23T14:49:04Z" }, { "body" : "Some example apps:  Ortheus, SAPF, Indelign, GConstructor, Tree-HMM - and several more", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/87421f30a67d4c05b88e14bc0ec44a4e", "date" : "2008-07-23T14:49:59Z" }, { "body" : "Nice animation of evolving DNA sequence showing substitutions, indels, duplications - TKF91 model", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/25d535e5389a4c28ae7294b07e490cc4", "date" : "2008-07-23T14:51:37Z" }, { "body" : "Transducer is stochastic finite-state machine; very similar to pair HMMs, but slightly different probabilistic output (conditional)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/b0a16360bf4047a18c821cdbe9d400a1", "date" : "2008-07-23T14:52:41Z" }, { "body" : "Second animation shows string transducers on a tree", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/20f602e78fbd4379a3695da665033d5f", "date" : "2008-07-23T14:56:24Z" }, { "body" : "Scales poorly - states increase exponentially with taxa; various ways around this (monte carlo HMM, Gibbs sampling)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/a66803cf912c4209967cafec6f00644e", "date" : "2008-07-23T14:58:33Z" }, { "body" : "Phylocomposer - uses Graphviz to visualise transducers in various contexts: e.g. alignment, trees; allows design of your own operations", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/aefa494ad1414864ae4a796863aab919", "date" : "2008-07-23T15:03:03Z" }, { "body" : "HMMoC (HMM Compiler) - automated generation of code in C++", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/92479dfca4474c0b85f79e567e076cf0", "date" : "2008-07-23T15:05:49Z" }, { "body" : "Benchmarking statistical alignments (BAliBase) - improvements over e.g. Clustal using affine-gap transducers.", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/9016b099205a4d49b58a40551953fd5b", "date" : "2008-07-23T15:09:13Z" }, { "body" : "Also applicable to RNA structural alignments", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/aa784b3fad2641bcb48f0ed2547087a7", "date" : "2008-07-23T15:09:42Z" }, { "body" : "It's all at biowiki.org", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/92347c22262044a3b6214ab64890386b", "date" : "2008-07-23T15:10:19Z" }, { "body" : "A questioner says RNA clustering by structure is &quot;the simplest clustering problem he ever did&quot; :)", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fc5c08bac3794211a135bc66591bf0d5/c/ddffc399192643318b60e2b65a822254", "date" : "2008-07-23T15:15:05Z" } ], "body" : "HL49:  Ian Holmes - &quot;Transducers&quot;", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/fc5c08ba/hl49-ian-holmes-transducers", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-23T14:48:04Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/fe2b0786888747838bd8bb8dac17c65d", "feed_id" : "ismb-2008", "comments" : [ { "body" : "And 2007:  <a rel=\"nofollow\" href=\"http://www.tweetclouds.com/user_pages/ismb2007_1221460825.html\" title=\"http://www.tweetclouds.com/user_pages/ismb2007_1221460825.html\">http://www.tweetclouds.com/user_pa...</a>", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "id" : "e/fe2b0786888747838bd8bb8dac17c65d/c/f0fba7e38e2c4e5183b7aaef72ddce81", "date" : "2008-09-15T06:44:36Z" } ], "body" : "ISMB 2008 selected abstracts:  Tweet Cloud - <a rel=\"nofollow\" href=\"http://www.tweetclouds.com/user_pages/ismb2008_1221460804.html\" title=\"http://www.tweetclouds.com/user_pages/ismb2008_1221460804.html\">http://www.tweetclouds.com/user_pa...</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Neil Saunders", "id" : "neilfws", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/fe2b0786/ismb-2008-selected-abstracts-tweet-cloud", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-09-15T06:44:13Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group" }
{ "_id" : "e/ff99ad585d0e4db2931bb201c923c56a", "feed_id" : "ismb-2008", "comments" : [ { "body" : "paper in press in MSB, database and pathway analysis tools on immune related pathways.Curated interactions &gt; 4000", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ff99ad585d0e4db2931bb201c923c56a/c/d929a3b3e0954abe858a26b2f0e7c3f2", "date" : "2008-07-18T15:39:22Z" }, { "body" : "Correction on the name :) - Geoff Winsor", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "id" : "e/ff99ad585d0e4db2931bb201c923c56a/c/773a4b49a19042bdb6a3030570d0b758", "date" : "2008-07-18T15:40:19Z" } ], "body" : "Geof Winsor  talking about InnateDB - <a rel=\"nofollow\" href=\"http://innatedb.ca/index.jsp\">http://innatedb.ca/index.jsp</a>", "feed_name" : "ISMB 2008", "from" : { "name" : "Pedro Beltrao", "id" : "pedrobeltrao", "type" : "user" }, "url" : "http://friendfeed.com/ismb-2008/ff99ad58/geof-winsor-talking-about-innatedb", "feed_description" : "For anyone interested in following ISMB 2008, Toronto.  Arrange meet-ups, micro-blog the talks and whatever else you like.", "date" : "2008-07-18T15:37:35Z", "to" : [ { "name" : "ISMB 2008", "id" : "ismb-2008", "type" : "group" } ], "feed_type" : "group", "likes" : [ { "from" : { "name" : "Deepak Singh", "id" : "mndoci", "type" : "user" }, "date" : "2008-07-18T16:18:44Z" } ] }