OSM Proposal to the Open Science Prize

[MedChemProf]

I am starting a thread regarding the OSM's submission to the Open Science Prize. The following is a link to a shared Google Drive folder ( https://drive.google.com/open?id=0B6PPGQnT9f4FLXFlZmluLUFTQWc ).
The folder contains:

1. Rough Draft / Skeleton of the Proposal
2. Team Information Document (each of the proposal contributors will need to complete for inclusion in the proposal when I submit.)
3. To-Do List / Task Completion Tracker
4. Supporting Documents Folder (Open Science Prize Guidelines, FAQ, and recording of Web Meeting discussing the Open Science Prize.)
   Looking forward to everyones input since we are on a tight timeline. I have already made some notes in the proposal itself for needed information from the group. Thanks.

[Daniel-Mietchen]

I suggest to change the sharing of the folder such that everyone with the link can comment. Otherwise, people will have to use other channels to provide feedback, which reduces the likelihood of anyone actually doing it.

[MedChemProf]

I took another look and there does not seem to be a setting for 'comment'. It either looks like you can allow 'viewing' or 'editing'. If the group feels it is better to have me set the permissions to 'editing' I will. They way it is now, if anyone wants to edit I would just need their email to give them editing permissions.

[mattodd]

If that's the choice then I'd set it to "anyone with the link can edit". A revision history is kept and we can keep offline copies in case of accidents.

[MedChemProf]

@Daniel-Mietchen @mattodd I just made the change to "anyone with the link can edit". Below is the link again: https://drive.google.com/open?id=0B6PPGQnT9f4FLXFlZmluLUFTQWc

[mattodd]

Three broad questions:

1. At the moment there is a heavy emphasis on OSM and malaria up-front. Would people be happy if we made the emphasis on the more general practice of making molecules for biological applications? If we want to develop a system that identifies potential collaborators automatically, then the disease focus can be agnostic. Having said that, we can accurately say that the short term application of our work would be in OSM.

2. We can and should make a case that we predict there will be many end users of what we propose, e.g. Royal Society of Chemistry. I don't see this in the funding rules/guidelines, but is there an advantage in securing letters of support for the proposal, or should we aim only to secure email pledges of statements of interest? In which case we can forward a draft proposal to people as soon as it's ready to read, in advance of the deadline.

3. The name of the Thing, to be distinctive. We aim, as I understand it from our discussions, to make something that "understands" what it is we are doing in the lab, and which is then able to work in the background to make connections with other people working on similar science, in real time. This will accelerate progress (through an automated process) and be a positive encouragement for people to work in the open. We need a succinct name for this idea. It's a little like the host of a party who (usefully) goes around making introductions between people with shared common interests. Or as this article puts it "The best you can offer your guests is the unexpected."

[MedChemProf]

@mattodd I think you suggestion to broaden the scope of the application of the proposal makes a lot of sense and may heighten its appeal. I'll hold on making any changes however to hear other thoughts. As you mentioned, we could propose that Malaria is a springboard for the proposal which has broader application.
As far as your second question, there is some latitude to append several documents to the proposal (for which they stressed brevity.) I do not see any reason not to include a set support letters as supplementary documents.
For your third question, are you looking for some sort of acronym? How about: ONLiNE RESPonD (OpeN Laboratory NotEbook Reaction and SPectral Database)

[cdsouthan]

Let me know if you want any input from me. It looks good so far but a few points.

1. Agree with Matt about broadening out e.g. NTDs, rare diseases, anti-Zika, and all non-patenting med chem teams in general.

2. Dont want to bore folk again re PMID 23399051 but it would seem apposite to point out in the documentation that the use of the InChIKey inner layer (in an ELN or anywhere else) already sets the key precendent of instant global sharability/discoverability of chemistry (ie proves the concept and AWK reaction InChIs are being developed).

3. It makes no sense to me not to loop PubChem in somehow. For example, the simple step of the new community ensuring (via an automated substance submission synching) that all discrete structures were indexed with pointers back to our open community would seem an option ( I can follow this up with PC if there is a consensus on it being a good idea

[mattodd]

Hi Chris,

The point about 2) is absolutely well taken, but the researcher doing the work need not know anything about InChis (since they are being calculated and stored as metadata) and need not worry about manually finding connections between research projects (since the system does that for you). Again, coming back to the Google Ads example: let's say I'm writing an email about traveling to Hong Kong. Yes, I can look up flight deals myself, but it's helpful and perhaps serendipitous that suggestions are provided automatically. I don't want to have to remember, when I write the email, what the code for Hong Kong International Airport is. I just want to write in the way I write and have the software note the connections in the background should I need them. The day I last see an InChI fully written out will be a good day.

3. If our focus is creating connections between scientists, can you just firm up the argument for looping in PubChem? I understand the power, in general, but how does that help here? Is the advantage that we can imagine other ELNs/systems that could do what we're trying to do, and which may not talk to our system effectively, then pubchem could be an honest broker that helps spot connections between systems? So I use System X, and you use System Y, and these may not see each other, but if we agree that we'll auto-submit to PubChem then the connection is more likely to be made? This would require an auto-submit and an auto-query function. Perhaps for Stage II of this project?

[MedChemProf]

@cdsouthan Thanks for your comments. I am not sure how or if there will be some sort of link to information in PubChem. I think that is something that would need to be clarified. Certainly your further input or suggestions for changes to the proposal are welcome and invited.

To others, I was hoping for some short term input on the potential budget. The Open Science Prize is for $80k total, but I need some estimates from the group on what piece of that pie they may need for each of the activities. An estimate of your needs is all I need at the moment. I require this not only for the final proposal, but I need to turn in some administrative paperwork earlier to my university and they require to see a budget. Thank you all in advance.

[drc007]

With regard to PubChem I would see this as happening at the completion of an experiment, when you are confident about the final structure spectra etc. Perhaps there should be a "compound creation page" generated when the chemist decides the experiment is complete. This page could be then used to populate the relevant public databases etc.

Update!! The data for the page would presumably be in JSON format and so it should be "easy" for anyone who wanted the data to access it, be it PubChem, RSC ChemSpider, ChEMBL etc.

[mattodd]

Outline budget items would probably need to include money for coding at
Luc's end, and money for an RA in your lab, Chase, to carry out experiments
that we'd use as the basis? If there's spare money we could pay a student
to do related work in my lab, or we could reserve a small pot of money for
a prize for some aspect of the work, e.g. some non-science design elements
(never under-estimate aesthetics in software)? I would advocate for some
money for assistance in project coordination - someone at the centre
helping manage project inputs, project needs, raising awareness of what
we're doing and reaching out to larger organisations for pro bono inputs.

On 3 February 2016 at 23:36, Chase Smith notifications@github.com wrote:

@cdsouthan https://github.com/cdsouthan Thanks for your comments. I am
not sure how or if there will be some sort of link to information in
PubChem. I think that is something that would need to be clarified.
Certainly your further input or suggestions for changes to the proposal are
welcome and invited.

To others, I was hoping for some short term input on the potential budget.
The Open Science Prize is for $80k total, but I need some estimates from
the group on what piece of that pie they may need for each of the
activities. An estimate of your needs is all I need at the moment. I
require this not only for the final proposal, but I need to turn in some
administrative paperwork earlier to my university and they require to see a
budget. Thank you all in advance.

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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
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T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

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[MedChemProf]

@mattodd What I'll do for my internal needs then is to estimate some of the things you mentioned and proportion them assuming that the 'coding' end of things will probably take the lion's share of the funds. Let me know if this does not make sense.

[mattodd]

Fine by me, open to suggestions.
On 4 Feb 2016 12:17 am, "Chase Smith" notifications@github.com wrote:

@mattodd https://github.com/mattodd What I'll do for my internal needs
then is to estimate some of the things you mentioned and proportion them
assuming that the 'coding' end of things will probably take the lion's
share of the funds. Let me know if this does not make sense.

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[mattodd]

Have violently hacked at the proposal. I'd encourage everyone else here to go in and let rip. Very general. Simple language. OSM as a tester community willing and eager to adopt this.

Anyone who wants in also needs to go and fill in some biodata and 50 words of expertise in the other document.

Will come back to this after the weekend. When we've a draft, are people willing to contact organisations to get expressions of interest?

[MedChemProf]

Snow day here, so I had some time to add some edits earlier this morning. I highlighted a few parts of the proposal in underlined, bold red where some additional input from the group is required. I also added an estimated budget for some focused discussion. Not heading outside anytime soon:

[cdsouthan]

If its OK I will make an extended comment on my blog, bits of which (sans weather pictures...) can then be subsumed over into the proposal as the drafters see fit (style is then consistant). I guess this whole thing is open anyway (no concerns on overlap with others) so that saves me pontificating here.

[mattodd]

Absolutely - but please also feel free to add in specifics to the proposal as well as biodata if you want in. Also feel free to disseminate this writing process widely - happy to involve people if interested.
Amazing snow @MedChemProf . The contrast could not be greater with Sydney right now.

[MedChemProf]

@mattodd - Yet another snow day, so I spent more time editing the proposal. Please everyone have a look. Also, I will need individuals to fill in their details on the Team Information document. I added some names for those whom I thought would be contributing, but those are not exclusive.
Also, would the group be in favor of scheduling another Google Hangouts meeting to discuss the progress so far? I will propose this Thursday at 4:00PM EST (http://www.timeanddate.com/worldclock/fixedtime.html?msg=OSM+Open+Science+Prize+Google+Hangout+Discussion&iso=20160211T16&p1=911&ah=1&am=30), but counter offers welcomed. Please let me know.

[mattodd]

A Hangout's a good idea - make it open to all. Could we possibly do an hour later? 9am is a lot easier than 8am for me. I'll do another round of edits shortly (next 24 hr) and alert a few people to this draft.

[MedChemProf]

@mattodd Google Hangout time changed to 5PM EST on Thursday, February 11th to discuss the Open Science Prize proposal (other can find their city and time by following this link: http://www.timeanddate.com/worldclock/fixedtime.html?msg=OSM+Open+Science+Prize+Google+Hangout+Discussion&iso=20160211T17&p1=911&ah=1&am=30 )
Link to Google Hangout: https://talkgadget.google.com/hangouts/_/lh7afwttp3ohfcbl3uep35lnqaa
Discussion to focus on current status of Open Science Prize proposal from the OSM, suggestions for changes or modifications, and timeline to complete supplementary materials such as a brief demo video or walk through of the proposed project.
If needed, the link to the shared Google Drive folder of materials ( https://drive.google.com/open?id=0B6PPGQnT9f4FLXFlZmluLUFTQWc ).

[drc007]

Sorry I missed the meeting life is a bit hectic at present.
A few thoughts.

For me the real attraction is SCINDR however much of the proposal appears to focus on the ELN with little detail on how SCINDR will be implemented. Do you run the risk it will be regarded as yet another ELN?
Whilst the ELN would be a key access point, perhaps you should mention that SCINDR would be "open" so that there could be multiple entry points?
@madgpap Would the ChEMBL group be open to using UniChem as a datasource? This would give access to multiple databases.
There are open source ELN (for example http://www.ncbi.nlm.nih.gov/pubmed/23645817 and http://www.myexperiment.org/home) so we need to be careful about claims of novelty.
Do you have to use Chrome? It would be good for the demo to be accessible using any web browser. If you are going to provide a link I'm not sure you can expect reviewers to be willing to install Chrome first.

"Our pilot study will involve demonstrating that SCIND can do XYZ" This is a key part, what do we hope to demonstrate?

[cdsouthan]

I couldn't make it either - what are rough timelines now? I'd still like to add some aspects and personal specs but am preparing for an immunopharmacolgy (day-job) meeting this Monday. Some questions 1) many folk are working on open reaction capture/ archiving e.g. ChemSpider, NextMove (patent extraction), Alex Clark, othe groups on reaction InChIs etc. Do we need to mention where they are at? 2) do most reactions have intermediates that can be defined by normal chemistry database rules (i.e. can be specifed and searched) even if they might be tough to get in a pot? 3) don't want to keep banging on about PMID 23399051 but I think Mat thought I was refering to full InChI strings not just the Keys. The point is the 14-characters of the connectivity layer already constitue a skeletal but de-facto SCIND. If anyone, anywhere, anytime, reduces their reaction componants (but the rare rather than common ones) and product design to just the 14 characters, Google (as manual or auto call-out) finds this anywhere else on the globe in ~ 0.3 secs (i.e. aha - now I know someone else is also working with this core structure). It just needs to be under any url (that also shows who to contact of course) the googlbot can get to - not even an ELN.

[mattodd]

Thanks @drc007 - all pertinent, central points. @lpatiny the proposal is here, and you should be able to change anything. Taking Chris' points in turn:

1. "For me the real attraction is SCINDR however much of the proposal appears to focus on the ELN with little detail on how SCINDR will be implemented. Do you run the risk it will be regarded as yet another ELN?"
   Answer: It's the intention that SCINDR is centre stage. We need more in the proposal on how we propose to create and run SCINDR, yes. If the ELN is mentioned too much, that's not good.

2. "Whilst the ELN would be a key access point, perhaps you should mention that SCINDR would be "open" so that there could be multiple entry points?"
   Answer: I'm sure @lpatiny would intend SCINDR to be open source.
   Follow-on: The idea was suggested that we could run SCINDR with the "pay for secrecy" model, as a way to finance it. Is that still possible if it's open source? The idea would be that we'd run the ELN and SCINDR for e.g. companies for a fee, as a service, if they wanted to keep both private. The fee-payers can see what's in the public domain, but they keep their own material private. It's not clear this works, but given that SCINDR must be open source, there is nothing to stop people taking it and using it internally (in the same way an open source ELN can be used internally), yet there remains a simplicity in being involved with, and supporting, the open source project given that Software-as-a-Service type arrangements mean you i) don't have to hire people to take care of SCINDR and ii) get updates applied automatically.

3. "@madgpap Would the ChEMBL group be open to using UniChem as a datasource? This would give access to multiple databases."
   Answer: Isn't that public domain in any case? So SCINDR could just interrogate it for similarity to compounds in the ELN?

4. "There are open source ELN (for example http://www.ncbi.nlm.nih.gov/pubmed/23645817 and http://www.myexperiment.org/home) so we need to be careful about claims of novelty."
   Answer: It's not claimed that an open source ELN is novel. Labtrove's also open source. But we could clarify (Luc?) what it is about this ELN that is different, besides the clear benefit that this team is familiar with it.

5. "Do you have to use Chrome? It would be good for the demo to be accessible using any web browser. If you are going to provide a link I'm not sure you can expect reviewers to be willing to install Chrome first."
   Answer: Agreed. Luc? I think it's developed on Chrome and so is guaranteed to work there. Ought we to factor in some of the prize money to ensure the prototype also works on other browsers?

6. ""Our pilot study will involve demonstrating that SCIND can do XYZ" This is a key part, what do we hope to demonstrate? "
   Answer: Yes - we need remaining text in the proposal to describe the technical aspects, and also that something will be clearly achieved by the prototype. We will need to define and refine these few crucial sentences in response to where Luc gets up to by the end of the month. It'll be last minute, and is the part that now needs writing, but will not take many words.

Notes to everyone:
a) Deadline is end of the month, so we've 2 weeks left.
b) If you want in, you need to add yourself to the team page, and will need to make clear what you bring to the party. Note 1st person writing style and strict character/Word limits. Ping @MedChemProf for access if you can't edit for any reason.
c) We should meet up again this coming week. My 9 a.m. is again good if it can be stomached by the Europe guys.
d) We have a graphic v1! The image is intended to get across the simple idea that SCINDR is automatically watching what two researchers are doing and will effect an introduction so that they can work together. Again ping @MedChemProf with suggested improvements etc.

[alintheopen]

Hi all new video is up https://www.youtube.com/watch?v=joarvBnTQ_k

with updated script. Please let me know if I need to fix something.

Cheers

Alice

On Fri, Feb 26, 2016 at 2:18 PM, Alice Williamson <
alice.e.williamson@gmail.com> wrote:

ha - said this to Mat yesterday. New video is tinder not finder ;)

On Fri, Feb 26, 2016 at 12:27 PM, Chase Smith notifications@github.com
wrote:

@alintheopen https://github.com/alintheopen @mattodd
https://github.com/mattodd One off the wall question. This may just be
due to my ears hearing an Australian accent, but in the draft video, the
word 'SCINDR' seemed to rhyme with the word 'Finder'. Was that the intent?
Or should the word 'SCINDR' rhyme with 'Tinder'?

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[drc007]

Brilliant, and my mother thinks it is wonderful!

[drc007]

OK for me to add a link to the video on my website?

On 27 Feb 2016, at 09:54, alintheopen notifications@github.com wrote:

Hi all new video is up https://www.youtube.com/watch?v=joarvBnTQ_k

with updated script. Please let me know if I need to fix something.

Cheers

Alice

On Fri, Feb 26, 2016 at 2:18 PM, Alice Williamson <
alice.e.williamson@gmail.com> wrote:

ha - said this to Mat yesterday. New video is tinder not finder ;)

On Fri, Feb 26, 2016 at 12:27 PM, Chase Smith notifications@github.com
wrote:

@alintheopen https://github.com/alintheopen @mattodd
https://github.com/mattodd One off the wall question. This may just be
due to my ears hearing an Australian accent, but in the draft video, the
word 'SCINDR' seemed to rhyme with the word 'Finder'. Was that the intent?
Or should the word 'SCINDR' rhyme with 'Tinder'?

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[alintheopen]

Sure! If everyone is happy with it that is! Glad your Ma approves Chris! ;)

On Saturday, 27 February 2016, Chris Swain notifications@github.com wrote:

OK for me to add a link to the video on my website?

On 27 Feb 2016, at 09:54, alintheopen <notifications@github.com
javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

Hi all new video is up https://www.youtube.com/watch?v=joarvBnTQ_k

with updated script. Please let me know if I need to fix something.

Cheers

Alice

On Fri, Feb 26, 2016 at 2:18 PM, Alice Williamson <
alice.e.williamson@gmail.com
javascript:_e(%7B%7D,'cvml','alice.e.williamson@gmail.com');> wrote:

ha - said this to Mat yesterday. New video is tinder not finder ;)

On Fri, Feb 26, 2016 at 12:27 PM, Chase Smith <
notifications@github.com
javascript:_e(%7B%7D,'cvml','notifications@github.com');>
wrote:

@alintheopen https://github.com/alintheopen @mattodd
https://github.com/mattodd One off the wall question. This may
just be
due to my ears hearing an Australian accent, but in the draft video,
the
word 'SCINDR' seemed to rhyme with the word 'Finder'. Was that the
intent?
Or should the word 'SCINDR' rhyme with 'Tinder'?

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<
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[cdsouthan]

Nice, probably a while since Chris swirled a reaction flask in anger but hey.....

[MedChemProf]

@alintheopen The new video is fantastic. Other than the youtube version, do you have it saved in another format? In the Open Science Prize site, they have a section for uploading the video in one of the following formats: File Types Supported:
AVI (preferred)
Quicktime (.mov)
MPEG (.mpg, .mpeg, .mp4)
Windows Media (.wmv)
Flash Video (.flv, .f4v)
(Videos uploaded must be smaller than 1000MB in size. If you get an error while uploading, please try uploading a different file format.)
Also, if you happen to make any additional changes, I did finally upload a new picture to the shared site in a folder called Pics. I have no problem with my picture in its current state in the video however.

[mattodd]

Absolutely great, Alice, well done!

Nice support letter from WHO/TDR is in the shared Drive folder, Chase. And
I made a few other tweaks/comments. Anything not resolved by closing time -
Chase you have discretion to ignore/override.

On 28 February 2016 at 04:48, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen The new video is fantastic.
Other than the youtube version, do you have it saved in another format? In
the Open Science Prize site, they have a section for uploading the video in
one of the following formats: File Types Supported:
AVI (preferred)
Quicktime (.mov)
MPEG (.mpg, .mpeg, .mp4)
Windows Media (.wmv)
Flash Video (.flv, .f4v)
(Videos uploaded must be smaller than 1000MB in size. If you get an error
while uploading, please try uploading a different file format.)
Also, if you happen to make any additional changes, I did finally upload a
new picture to the shared site in a folder called Pics. I have no problem
with my picture in its current state in the video however.

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.

MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

[Daniel-Mietchen]

If file size is an issue, I suggest to link prominently to the YouTube version.

[MedChemProf]

Only open issues at the moment are:

1. Is there a 'name' of the ELN at http://eln.cheminfo.org/ and where would some one look for the source code @mattodd @lpatiny
2. Can the video be placed in the shared folder for me to retrieve and upload or should I just try and capture it from the youtube link? @alintheopen
   Thanks

[cdsouthan]

All looks tops to me, good job. Have pinged PubChem again for spport lett, but good we have some anyway.

[alintheopen]

https://www.youtube.com/watch?v=Y8Oq53efBE8
new youtube video with Chase's lab photo and mp4 uploaded to share folder.

Fingers crossed!

On Mon, Feb 29, 2016 at 8:02 AM, cdsouthan notifications@github.com wrote:

All looks tops to me, good job. Have pinged PubChem again for spport lett,
but good we have some anyway.

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[lpatiny]

The lab notebook is based on many projects. Among them:
http://github.com/npellet/visualizer http://github.com/npellet/visualizer
https://github.com/cheminfo-js/openchemlib-extended https://github.com/cheminfo-js/openchemlib-extended
https://github.com/cheminfo/chemcalc-js https://github.com/cheminfo/chemcalc-js

On Feb 28, 2016, at 2:21 PM, Chase Smith notifications@github.com wrote:

Only open issues at the moment are:

1. Is there a 'name' of the ELN at http://eln.cheminfo.org/ http://eln.cheminfo.org/ and where would some one look for the source code @mattodd https://github.com/mattodd @lpatiny https://github.com/lpatiny
2. Can the video be placed in the shared folder for me to retrieve and upload or should I just try and capture it from the youtube link? @alintheopen https://github.com/alintheopen
   Thanks

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[mattodd]

Pubchem email of support being uploaded to Drive folder now. Will need to be incorporated into the existing PDF.

[mattodd]

OK, but can we call the ELN something ("Patinage"?) and link to one most
relevant source? It'd be useful to try to do both, just to make it easier
for the referees to read and check.

On 29 February 2016 at 20:00, lpatiny notifications@github.com wrote:

The lab notebook is based on many projects. Among them:
http://github.com/npellet/visualizer <http://github.com/npellet/visualizer

https://github.com/cheminfo-js/openchemlib-extended <
https://github.com/cheminfo-js/openchemlib-extended>
https://github.com/cheminfo/chemcalc-js <
https://github.com/cheminfo/chemcalc-js>

On Feb 28, 2016, at 2:21 PM, Chase Smith notifications@github.com
wrote:

Only open issues at the moment are:

1. Is there a 'name' of the ELN at http://eln.cheminfo.org/ <
   http://eln.cheminfo.org/> and where would some one look for the source
   code @mattodd https://github.com/mattodd @lpatiny <
   https://github.com/lpatiny>
2. Can the video be placed in the shared folder for me to retrieve and
   upload or should I just try and capture it from the youtube link?
   @alintheopen https://github.com/alintheopen
   Thanks

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#371 (comment)
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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

[MedChemProf]

@mattodd It appears you moved the PubChem Letter to the trash on the shared site. Was that an error or are you going to replace it with another? Thanks. Also, I can work with the links that @lpatiny provided to finish off the proposal.

[MedChemProf]

@mattodd I saw that you tweeted about creating a Slack channel for the OSM. Did you post the channel name?

[mattodd]

Yes, sorry, corrected version coming hopefully in a moment.

On 29 February 2016 at 23:28, Chase Smith notifications@github.com wrote:

@mattodd https://github.com/mattodd It appears you moved the PubChem
Letter to the trash on the shared site. Was that an error or are you going
to replace it with another? Thanks. Also, I can work with the links that
@lpatiny https://github.com/lpatiny provided to finish off the proposal.

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#371 (comment)
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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
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T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
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http://opensourcepharma.net/

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[lpatiny]

Well the ELN for us is “just” a view in the github.com/npellet/visualizer project so it is currently not really a project by itself.

We just have a github project for tracking the issues.

https://github.com/cheminfo/eln-couch https://github.com/cheminfo/eln-couch

But the real link to provide is always http://eln.cheminfo.org http://eln.cheminfo.org/

On Feb 29, 2016, at 1:24 PM, Mat Todd notifications@github.com wrote:

OK, but can we call the ELN something ("Patinage"?) and link to one most
relevant source? It'd be useful to try to do both, just to make it easier
for the referees to read and check.

On 29 February 2016 at 20:00, lpatiny notifications@github.com wrote:

The lab notebook is based on many projects. Among them:
http://github.com/npellet/visualizer <http://github.com/npellet/visualizer

https://github.com/cheminfo-js/openchemlib-extended <
https://github.com/cheminfo-js/openchemlib-extended>
https://github.com/cheminfo/chemcalc-js <
https://github.com/cheminfo/chemcalc-js>

On Feb 28, 2016, at 2:21 PM, Chase Smith notifications@github.com
wrote:

Only open issues at the moment are:

1. Is there a 'name' of the ELN at http://eln.cheminfo.org/ <
   http://eln.cheminfo.org/> and where would some one look for the source
   code @mattodd https://github.com/mattodd @lpatiny <
   https://github.com/lpatiny>
2. Can the video be placed in the shared folder for me to retrieve and
   upload or should I just try and capture it from the youtube link?
   @alintheopen https://github.com/alintheopen
   Thanks

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#371 (comment)
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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

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[MedChemProf]

@mattodd @lpatiny The one problem I have with that link is that it only works with Chrome which the reviewers may not use while evaluating the proposal.

[drc007]

"OK, but can we call the ELN something ("Patinage"?) "

I'd suggest something that might be easier to associate with a Lab Notebook, "MyResearch", "Discoveries" etc.

[mattodd]

We may have to recommend its use here and say that with Prize support it is
the intention that Firefox will be supported in the future?

On 29 February 2016 at 23:50, Chase Smith notifications@github.com wrote:

@mattodd https://github.com/mattodd @lpatiny
https://github.com/lpatiny The one problem I have with that link is
that it only works with Chrome which the reviewers may not use while
evaluating the proposal.

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Reply to this email directly or view it on GitHub
#371 (comment)
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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

CRICOS 00026A
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[drc007]

You should say you will aim to support all modern desktop and mobile browsers.

On 29 Feb 2016, at 12:53, Mat Todd notifications@github.com wrote:

We may have to recommend its use here and say that with Prize support it is
the intention that Firefox will be supported in the future?

On 29 February 2016 at 23:50, Chase Smith notifications@github.com wrote:

@mattodd https://github.com/mattodd @lpatiny
https://github.com/lpatiny The one problem I have with that link is
that it only works with Chrome which the reviewers may not use while
evaluating the proposal.

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#371 (comment)
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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

CRICOS 00026A
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use is strictly prohibited. If you receive this email in error, please
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[MedChemProf]

I changed the phrasing to: "A prototype of the new ELN that will be adapted to run SCINDR is already online at http://eln.cheminfo.org/ (requires the use the ‘Google Chrome’ browser for the current version. The aim will be to eventually support all modern web browsers)."

[lpatiny]

We should probably explicitly specify it next to the link. We plan to make it compatible with Edge and possibly Firefox but Safari is definitely excluded because apple is ages behind at the point of view of implementation of javascript standards.

On Feb 29, 2016, at 1:50 PM, Chase Smith notifications@github.com wrote:

@mattodd https://github.com/mattodd @lpatiny https://github.com/lpatiny The one problem I have with that link is that it only works with Chrome which the reviewers may not use while evaluating the proposal.

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[MedChemProf]

Complete proposal has been submitted (Executive Summary; Proposal; Team Information; Video; and Letters of Support) @mattodd @alintheopen @cdsouthan @drc007

[mattodd]

Congrats everyone, it's a great proposal that will lead to something
genuinely useful if funded.

On 1 March 2016 at 06:27, Chase Smith notifications@github.com wrote:

Complete proposal has been submitted (Executive Summary; Proposal; Team
Information; Video; and Letters of Support) @mattodd
https://github.com/mattodd @alintheopen https://github.com/alintheopen
@cdsouthan https://github.com/cdsouthan @drc007
https://github.com/drc007
[image: capture]
https://cloud.githubusercontent.com/assets/14179120/13406258/874650a8-def0-11e5-8729-7b038c9eb3ce.PNG

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MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

[Daniel-Mietchen]

I just noticed that the HTTP link doesn't "work" in FireFox, but the HTTPS link does:

• http://eln.cheminfo.org/
• https://eln.cheminfo.org/

[MedChemProf]

Thanks for spotting that. I noticed the problem, but did not have a solution. In the proposal I added a note to view the link in Chrome presently and other modern browsers would be added later. I also added a screen shot of the ELN into the proposal to further cover the issue.

[alintheopen]

Prize has been submitted, so closing. Other related discussions #372 are ongoing.