Missing components in new website

[alistairewj]

The following components were present in the old website, but are not currently listed anywhere on the new website:

• Research affiliates
  • BIDMC
  • Clinical Decision Making (Peter Szolovits)
  • LCP
  • RLE (Thomas Heldt)
  • Phillips Health Care
• Contact us page = issues & help which is incomplete
• Page describing most recent grant(s) funding MIMIC
• Publications
• Explorer/query builder
• Tutorial (intro to MIMIC)
• Old MIMIC II documentation
• Schema
• FAQs
• Release notes page (currently is a dummy page)

[tompollard]

These have been added (striked out in the list above):

• Research affiliates
• Contact us page = issues & help which is incomplete
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation
• Release notes page (currently is a dummy page)

[tompollard]

Note on the remaining content:

Page describing most recent grant(s) funding MIMIC

• Content is outdated and will be rewritten

Schema

• Content needs to be recreated.

FAQs

• FAQs have been archived and will be covered by new forum

[kpierceHST]

can't check this easily from home. publications should be generated from, or be the same as, the publications file on the lcp site. Something to discuss tomorrow.
K

On 9/16/15 6:37 PM, Tom Pollard wrote:

These have been added (striked out in the list above):

• Research affiliates
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation

---

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#14 (comment)

[kpierceHST]

Hi everyone,

It looks as if the new website has supplanted the old. In principle, that's great -- but I'm concerned that users will be puzzled, and won't be able to find pages they're used to finding (e.g., QueryBuilder). Could you put some sort of an announcement on the home page along the lines of "for the previous site, click here"? Or, perhaps better, put the current site in a subdirectory that can be pointed to from the old site, with a link that says "click here for beta version of new site"?

Thanks,
Ken

On 9/16/15 11:42 PM, Ken Pierce wrote:

can't check this easily from home. publications should be generated from, or be the same as, the publications file on the lcp site. Something to discuss tomorrow.
K

On 9/16/15 6:37 PM, Tom Pollard wrote:

These have been added (striked out in the list above):

• Research affiliates
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation

---

Reply to this email directly or view it on GitHub:
#14 (comment)

[kpierceHST]

Couldn't find a link to publications. Where is it?
K

On 9/16/15 11:42 PM, Ken Pierce wrote:

can't check this easily from home. publications should be generated from, or be the same as, the publications file on the lcp site. Something to discuss tomorrow.
K

On 9/16/15 6:37 PM, Tom Pollard wrote:

These have been added (striked out in the list above):

• Research affiliates
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation

---

Reply to this email directly or view it on GitHub:
#14 (comment)

[alistairewj]

You preempted our e-mail! Because of the short time between now and the
datathon we needed to get the new website up ASAP. We agree we need the
querybuilder in some form - it still exists at the same original URL and
can be accessed through the archive section at
mimic.physionet.org/archive/mimic-ii/

We should probably announce the new site on physionet. However we'd like to
again beta test the website with some internal users first before globally
announcing it, since that strategy seems to have worked well for MIMIC III.

On Thu, Sep 17, 2015 at 9:45 AM, kpierceHST notifications@github.com
wrote:

Hi everyone,

It looks as if the new website has supplanted the old. In principle,
that's great -- but I'm concerned that users will be puzzled, and won't be
able to find pages they're used to finding (e.g., QueryBuilder). Could you
put some sort of an announcement on the home page along the lines of "for
the previous site, click here"? Or, perhaps better, put the current site in
a subdirectory that can be pointed to from the old site, with a link that
says "click here for beta version of new site"?

Thanks,
Ken

On 9/16/15 11:42 PM, Ken Pierce wrote:

can't check this easily from home. publications should be generated
from, or be the same as, the publications file on the lcp site. Something
to discuss tomorrow.
K

On 9/16/15 6:37 PM, Tom Pollard wrote:

These have been added (striked out in the list above):

• Research affiliates
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation

---

Reply to this email directly or view it on GitHub:

#14 (comment)

—
Reply to this email directly or view it on GitHub
#14 (comment)
.

[alistairewj]

Publications page isn't up yet - on the TODO list!

[kpierceHST]

but this way anyone going to the old site will unexpectedly land at the new. I imagine lots of confused Stanford students. Can't you put it in a subdirectory and point datathon users to it?
K

On 9/17/15 9:49 AM, Alistair Johnson wrote:

You preempted our e-mail! Because of the short time between now and the
datathon we needed to get the new website up ASAP. We agree we need the
querybuilder in some form - it still exists at the same original URL and
can be accessed through the archive section at
mimic.physionet.org/archive/mimic-ii/

We should probably announce the new site on physionet. However we'd like to
again beta test the website with some internal users first before globally
announcing it, since that strategy seems to have worked well for MIMIC III.

On Thu, Sep 17, 2015 at 9:45 AM, kpierceHST notifications@github.com
wrote:

Hi everyone,

It looks as if the new website has supplanted the old. In principle,
that's great -- but I'm concerned that users will be puzzled, and won't be
able to find pages they're used to finding (e.g., QueryBuilder). Could you
put some sort of an announcement on the home page along the lines of "for
the previous site, click here"? Or, perhaps better, put the current site in
a subdirectory that can be pointed to from the old site, with a link that
says "click here for beta version of new site"?

Thanks,
Ken

On 9/16/15 11:42 PM, Ken Pierce wrote:

can't check this easily from home. publications should be generated
from, or be the same as, the publications file on the lcp site. Something
to discuss tomorrow.
K

On 9/16/15 6:37 PM, Tom Pollard wrote:

These have been added (striked out in the list above):

• Research affiliates
• Publications (recent publications anyway)
• Explorer/query builder
• Tutorial (intro to MIMIC)
• PDF documentation / Old MIMIC II documentation

---

Reply to this email directly or view it on GitHub:

#14 (comment)

—
Reply to this email directly or view it on GitHub
#14 (comment)
.

---

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#14 (comment)

[kpierceHST]

for publications on the old site, Dan had set up a nightly cron job (which may still be running...) to grab the file http://lcp.mit.edu/brp_references.html and store it locally for display. I'd suggest something similar: grab http://lcp.mit.edu/lcp_references.html on a regular basis, and style it as you like for display. Or if you'd like, I can generate a subset of that file according to some specifications that you give me.

K

On 9/17/15 9:52 AM, Alistair Johnson wrote:

Publications page isn't up yet - on the TODO list!

---

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#14 (comment)

[tompollard]

Hi Ken,

Sorry we didn't get a chance to warn you before this happened, but with only a week to the hackathon we're feeling under pressure to get the new documentation up as soon as possible. People are asking us lots of questions about the data and it's not sustainable for us to reply to everyone at a personal level.

I don't think that adding the old website to a subdirectory is straightforward because of the structure of the old Joomla site, but we could try to work something out if everyone thinks is a good idea. My feeling is that it makes more sense to provide the necessary information within the structure of the new website.

Instead of embedding the old website within the new website, the idea is that people will come to the new website, think "aha, new website...now where do I go to find the information I need". We could take some additional steps to make things clear to the user community:

• adding an announcement to the front page, saying something like: "If you are looking for MIMIC-II content, including the querybuilder and documention, please refer to our archive: http://mimic.physionet.org/archive/mimic-ii/"
• update the archive page to provide more detailed information. It would be great to go through the technical side of editing the website, but in the meantime you can do this directly by selecting the "Edit this page" in the menu.
• {... more suggestions here :) }

[kpierceHST]

actually it's straightforward; I just did it: http://mimic.physionet.org/oldsite/ .

I do think you should put in a pointer to the old site somewhere. Users may land on the new site and say, Aha, how do I find what I'm looking for? Or they may say, Yikes, I'm on a deadline and they've taken away the page my professor told me to look at. It's start of semester, not a good time to mess with things.

K

On 9/17/15 10:19 AM, Tom Pollard wrote:

Hi Ken,

Sorry we didn't get a chance to warn you before this happened, but with only a week to the hackathon we're feeling under pressure to get the new documentation up as soon as possible. People are asking us lots of questions about the data and it's not sustainable for us to reply to everyone at a personal level.

I don't think that adding the old website to a subdirectory is straightforward because of the structure of the old Joomla site, but we could try to work something out if everyone thinks is a good idea. My feeling is that it makes more sense to provide the necessary information within the structure of the new website.

Instead of embedding the old website within the new website, the idea is that people will come to the new website, think "aha, new website...now where do I go to find the information I need". We could take some additional steps to make things clear to the user community:

• adding an announcement to the front page, saying something like: "If you are looking for MIMIC-II content, including the querybuilder and documention, please refer to our archive: http://mimic.physionet.org/archive/mimic-ii/"
• update the archive page to provide more detailed information. It would be great to go through the technical side of editing the website, but in the meantime you can do this directly by selecting the "Edit this page" in the menu.
• {... more suggestions here :) }

---

Reply to this email directly or view it on GitHub:
#14 (comment)

[alistairewj]

Okay that's fine we can put a link to the old site in the archive. We're
not sure if the oldsite gets overwritten when the automatic deployment
scripts kick in so we'll test that now.

On Thu, Sep 17, 2015 at 10:33 AM, kpierceHST notifications@github.com
wrote:

actually it's straightforward; I just did it:
http://mimic.physionet.org/oldsite/ .

I do think you should put in a pointer to the old site somewhere. Users
may land on the new site and say, Aha, how do I find what I'm looking for?
Or they may say, Yikes, I'm on a deadline and they've taken away the page
my professor told me to look at. It's start of semester, not a good time to
mess with things.

K

On 9/17/15 10:19 AM, Tom Pollard wrote:

Hi Ken,

Sorry we didn't get a chance to warn you before this happened, but with
only a week to the hackathon we're feeling under pressure to get the new
documentation up as soon as possible. People are asking us lots of
questions about the data and it's not sustainable for us to reply to
everyone at a personal level.

I don't think that adding the old website to a subdirectory is
straightforward because of the structure of the old Joomla site, but we
could try to work something out if everyone thinks is a good idea. My
feeling is that it makes more sense to provide the necessary information
within the structure of the new website.

Instead of embedding the old website within the new website, the idea is
that people will come to the new website, think "aha, new website...now
where do I go to find the information I need". We could take some
additional steps to make things clear to the user community:

• adding an announcement to the front page, saying something like: "If
  you are looking for MIMIC-II content, including the querybuilder and
  documention, please refer to our archive:
  http://mimic.physionet.org/archive/mimic-ii/"
• update the archive page
  to provide more detailed information. It would be great to go through the
  technical side of editing the website, but in the meantime you can do this
  directly by selecting the "Edit this page" in the menu.
• {... more suggestions here :) }

---

Reply to this email directly or view it on GitHub:

#14 (comment)

—
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#14 (comment)
.

[tompollard]

I've checked the build script and there is no danger of the directory being overwritten with the new builds, so the old site is safe for now :)

I do think we should work towards removing the sub-website at some point though, so let's discuss that once the datathon is out of the way.

@kpierceHST please could you suggest where you'd like the pointer and what you'd like it to say? I'll then add it (and when we have more time, we can run through the process of making updates directly).

[kpierceHST]

Thanks, Tom and Alistair, for accommodating.

For now, I think right on the front page there should be something like "welcome to our new website. If you're looking the old one, here's a link to it." That will do two things: it will let users know that they haven't landed someplace by mistake, and MIMIC hasn't been taken over by a new company entirely; and it will let them get to pages they're used to using if they need them in a hurry (or if they don't see well enough to read the subtle menus on the new site...).

K

On 9/17/15 11:06 AM, Tom Pollard wrote:

I've checked the build script and there is no danger of the directory being overwritten with the new builds, so the old site is safe for now :)

I do think we should work towards removing the sub-website at some point though, so let's discuss that once the datathon is out of the way.

@kpierceHST please could you suggest where you'd like the pointer and what you'd like it to say? I'll then add it (and when we have more time, we can run through the process of making updates directly).

---

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#14 (comment)

[kpierceHST]

so it turns out that my script for approving mimic users no longer works, because it pointed to a location on the old site.

ditto for the display of grantees:

I can fix things, but not today.

On 9/17/15 10:19 AM, Tom Pollard wrote:

Hi Ken,

Sorry we didn't get a chance to warn you before this happened, but with only a week to the hackathon we're feeling under pressure to get the new documentation up as soon as possible. People are asking us lots of questions about the data and it's not sustainable for us to reply to everyone at a personal level.

I don't think that adding the old website to a subdirectory is straightforward because of the structure of the old Joomla site, but we could try to work something out if everyone thinks is a good idea. My feeling is that it makes more sense to provide the necessary information within the structure of the new website.

Instead of embedding the old website within the new website, the idea is that people will come to the new website, think "aha, new website...now where do I go to find the information I need". We could take some additional steps to make things clear to the user community:

• adding an announcement to the front page, saying something like: "If you are looking for MIMIC-II content, including the querybuilder and documention, please refer to our archive: http://mimic.physionet.org/archive/mimic-ii/"
• update the archive page to provide more detailed information. It would be great to go through the technical side of editing the website, but in the meantime you can do this directly by selecting the "Edit this page" in the menu.
• {... more suggestions here :) }

---

Reply to this email directly or view it on GitHub:
#14 (comment)

[tompollard]

@kpierceHST this should be fixed as high priority, so I'll deal with it now. Added as new issue #18.

[tompollard]

Interestingly, the old website has a directory containing the old, old website:
https://mimic.physionet.org/oldsite/old_website/

Can this one be removed, or does it need to stay?

[tompollard]

Couldn't find a link to publications. Where is it?

Please see latest comments on issue #8. The publications have been added at: http://mimic.physionet.org/about/publications/

The list only appears to include publications with at least one LCP author. We should review whether these are the most appropriate publications to be displayed on the MIMIC website.

I would prefer to include a list of the best publications using MIMIC, regardless of the affiliation of the authors.

[kpierceHST]

I've set it to read-only, so it's there but not accessible. Doubt we need it around but can we throw it in an archive somewhere?
K

On 9/17/15 11:57 AM, Tom Pollard wrote:

Interestingly, the old website has a directory containing the old, old website:
https://mimic.physionet.org/oldsite/old_website/

Can this one be removed, or does it need to stay?

---

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#14 (comment)

[tompollard]

Great, thanks @kpierceHST. The content is archived with the archived version of the old website (in the directory above 'HTML' on the server). I guess it may be best to archive the content somewhere else on the server instead, so I'll look into this...

[tompollard]

I think all of the useful content from the old website has been copied across, so I'm closing this issue. The front page of the new site (http://mimic.physionet.org/) includes an announcement pointing people to the archived version of the old website and documentation.

[kpierceHST]

Actually, this list does contain a few works by only non-lcp authors. Their publications are listed in the various brp_*.bib files.

I suggest the following:

• create mimic__.bib files that include the publications you'd like to see listed but that have no lcp authors (i.e., are not included in the lcp__.bib files).
• add a field in lcp_*.bib files to flag mimic-relevant publications
• adjust the script that generates publications.html files so it spits out a list of mimic-flagged entries combined with entries from mimic_.bib files. (That is, adapt the way the brp_references.html file is currently generated.)
• put the mimic_references.html file somewhere so that the new mimic site can find and display it.

I can take care of all of this, if you'll sent me a list of relevant publications (subset of http://lcp.mit.edu/publications.shtml plus other papers with only non-lcp authors.) I think this is by far the simplest approach: one set of bib files, non-overlapping insofar as possible.

K

On 9/18/15 12:18 PM, Tom Pollard wrote:

Couldn't find a link to publications. Where is it?

Please see latest comments on issue #8. The publications have been added at: http://mimic.physionet.org/about/publications/

The list only appears to include publications with at least one LCP author. We should review whether these are the most appropriate publications to be displayed on the MIMIC website.

I would prefer to include a list of the best publications using MIMIC, regardless of the affiliation of the authors.

---

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#14 (comment)