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.

[mattodd]

Everyone - looking forward to meeting up in a few hours - @lpatiny if you've a chance to look at your two sections in the proposal, that'd be great. We should think (in the meeting) about what is needed for the video. Everyone else - please give the proposal a read and see if anything is off. We need to be wrapping up the text at this stage. Good news - DNDi were kind enough to provide a letter of support, which is in the Drive folder. I am waiting on RSC (not yet replied) and USAID (who have). It'd help if people could think about other possible organisations to contact for this purpose - I'm stepping back from that for lack of time, but I feel our case would be stronger with more up-front acknowledgement that we're doing something genuinely useful.

[drc007]

Who did you contact at RSC?

Sent from Chris's iPhone

On 23 Feb 2016, at 10:35, Mat Todd notifications@github.com wrote:

Everyone - looking forward to meeting up in a few hours - @lpatiny if you've a chance to look at your two sections in the proposal, that'd be great. We should think (in the meeting) about what is needed for the video. Everyone else - please give the proposal a read and see if anything is off. We need to be wrapping up the text at this stage. Good news - DNDi were kind enough to provide a letter of support, which is in the Drive folder. I am waiting on RSC (not yet replied) and USAID (who have). It'd help if people could think about other possible organisations to contact for this purpose - I'm stepping back from that for lack of time, but I feel our case would be stronger with more up-front acknowledgement that we're doing something genuinely useful.

— Reply to this email directly or view it on GitHub.

[mattodd]

Kiera McNeice, who I believe was willing to convey the request through to Richard Kidd. If you've a way in to these guys via another channel, that would I'm sure be helpful.

On 23 February 2016 at 21:45, Chris Swain notifications@github.com wrote:

Who did you contact at RSC?

Sent from Chris's iPhone

On 23 Feb 2016, at 10:35, Mat Todd notifications@github.com wrote:

Everyone - looking forward to meeting up in a few hours - @lpatiny if you've a chance to look at your two sections in the proposal, that'd be great. We should think (in the meeting) about what is needed for the video. Everyone else - please give the proposal a read and see if anything is off. We need to be wrapping up the text at this stage. Good news - DNDi were kind enough to provide a letter of support, which is in the Drive folder. I am waiting on RSC (not yet replied) and USAID (who have). It'd help if people could think about other possible organisations to contact for this purpose - I'm stepping back from that for lack of time, but I feel our case would be stronger with more up-front acknowledgement that we're doing something genuinely useful.

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— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187648199 .

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

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[drc007]

Will use my contacts

Sent from Chris's iPhone

On 23 Feb 2016, at 10:49, Mat Todd notifications@github.com wrote:

Kiera McNeice, who I believe was willing to convey the request through to Richard Kidd. If you've a way in to these guys via another channel, that would I'm sure be helpful.

On 23 February 2016 at 21:45, Chris Swain notifications@github.com wrote:

Who did you contact at RSC?

Sent from Chris's iPhone

On 23 Feb 2016, at 10:35, Mat Todd notifications@github.com wrote:

Everyone - looking forward to meeting up in a few hours - @lpatiny if you've a chance to look at your two sections in the proposal, that'd be great. We should think (in the meeting) about what is needed for the video. Everyone else - please give the proposal a read and see if anything is off. We need to be wrapping up the text at this stage. Good news - DNDi were kind enough to provide a letter of support, which is in the Drive folder. I am waiting on RSC (not yet replied) and USAID (who have). It'd help if people could think about other possible organisations to contact for this purpose - I'm stepping back from that for lack of time, but I feel our case would be stronger with more up-front acknowledgement that we're doing something genuinely useful.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187648199 .

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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[drc007]

Done, and also

https://twitter.com/RSC_CICAG/status/702125170304151552

[MedChemProf]

Is anyone else having trouble calling in to the Google Hangout?

[drc007]

Yep.

Message to try again later

On 23 Feb 2016, at 19:00, Chase Smith notifications@github.com wrote:

Is anyone else having trouble calling in to the Google Hangout?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187842438.

[lpatiny]

I'm on https://hangouts.google.com/call/fil7iealpnhq3atkzm5h4dfovia But I'm alone apparently

[drc007]

Now logged in

On 23 Feb 2016, at 19:01, Chris Swain swain@mac.com wrote:

Yep.

Message to try again later

On 23 Feb 2016, at 19:00, Chase Smith <notifications@github.com mailto:notifications@github.com> wrote:

Is anyone else having trouble calling in to the Google Hangout?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187842438.

[cdsouthan]

@mattodd if you can point me to the draft letter of recomendation I can get it out to EB at PubChem

[alintheopen]

Hi all, I just got thrown out of the video call! Sorry for disappearing - Luc I sent you an email (thank you for the kind offer of help with the ELN) and I'll put the storyboard together now and then get back to you all.

Cheers

Alice

On Wed, Feb 24, 2016 at 6:02 AM, cdsouthan notifications@github.com wrote:

Me too now - cant see u

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187842960 .

ALICE WILLIAMSON | Postdoctoral Research Fellow and Postdoctoral Teaching Fellow School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY Lab 532 | Chemistry Building F11 | The University of Sydney | NSW | 2006

E alice.williamson@sydney.edu.au | W www.opensourcemalaria.org

T +61 431318280 | Twitter @all_isee https://twitter.com/all_isee

[lpatiny]

Is there a service where we could retrieve the safety information based on a SMILES ?

[drc007]

ChemSpider might be the best source

eg

http://www.chemspider.com/Chemical-Structure.259.html?rid=53eb1e8a-4a2e-4366-97d9-57f9a7f04ac8 http://www.chemspider.com/Chemical-Structure.259.html?rid=53eb1e8a-4a2e-4366-97d9-57f9a7f04ac8

Then scroll down to safety section.

There is an API that you should be able to use

http://www.chemspider.com/AboutServices.aspx? http://www.chemspider.com/AboutServices.aspx?

There is a Python wrapper for the API but I guess you will want to use javascript?

Cheers

Chris

On 23 Feb 2016, at 19:46, lpatiny notifications@github.com wrote:

Is there a service where we could retrieve the safety information based on a SMILES ?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187870719.

[mattodd]

Sorry to have to leave the call - school run. Good to talk. Will reply later, but thanks for storyboarding, Alice. On 24 Feb 2016 6:47 am, "lpatiny" notifications@github.com wrote:

Is there a service where we could retrieve the safety information based on a SMILES ?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187870719 .

[alintheopen]

Hi all,

I've uploaded a draft of the 'video' to the Google Folder. About to record as video with mock up of the voice over and then I'll send a link. Please excuse low resolution graphics and images that will need to be changed to open clipart. The reaction chosen will also be one for the OSM project and I'd like the image to emphasise that different ELN can be linked using SCINDR. Give me 15-30 to record the video and then I'd be glad of any feedback. Chase could you send the robot image over at some point?

Cheers

Alice

On Wed, Feb 24, 2016 at 6:54 AM, Mat Todd notifications@github.com wrote:

Sorry to have to leave the call - school run. Good to talk. Will reply later, but thanks for storyboarding, Alice. On 24 Feb 2016 6:47 am, "lpatiny" notifications@github.com wrote:

Is there a service where we could retrieve the safety information based on a SMILES ?

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187870719

.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187875541 .

[MedChemProf]

@alintheopen

[MedChemProf]

@alintheopen I loved your storyboard. (Nice touch with your picture being upside down.) I will also get you a better picture of myself. :)

[alintheopen]

https://www.youtube.com/watch?v=ZvhiTHdzo2A

I've uploaded a draft video here - excuse poor timings and pauses just wanted to give a first idea.

Cheers

Alice

On Wed, Feb 24, 2016 at 9:12 AM, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen I loved your storyboard. (Nice touch with your picture being upside down.) I will also get you a better picture of myself. :)

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187939571 .

[alintheopen]

Hi again,

Sorry - I also realise my video has chopped off the top of the presentation

• will sort this out and I added a slide with a SCINDR alert button inspired by FB/G+ (that is cut off the video too, doh) have uploaded a second video draft as a PDF so that you can see what I mean.

Cheers

Alice

On Wed, Feb 24, 2016 at 9:16 AM, Alice Williamson < alice.e.williamson@gmail.com> wrote:

https://www.youtube.com/watch?v=ZvhiTHdzo2A

I've uploaded a draft video here - excuse poor timings and pauses just wanted to give a first idea.

Cheers

Alice

On Wed, Feb 24, 2016 at 9:12 AM, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen I loved your storyboard. (Nice touch with your picture being upside down.) I will also get you a better picture of myself. :)

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187939571 .

[alintheopen]

[mattodd]

It's really good, Alice. I think this is exactly the kind of thing we need. It gives the credit due to Luc's fantastic system while placing the emphasis on SCINDR. Are we thinking we can just make this with a powerpoint deck and a voiceover? That might be simplest. Are you willing to do it..?

Only change I'd make is maybe we can have actual OSM molecules in the screenshots, and that the molecules could be similar but not identical.

And is there a way of conveying that the ELN is able to take what the researcher has recorded and make it understandable by SCINDR? Without going too much into the strings issue, but a visual way of showing that the molecule is converted into something else in the background.

In the proposal we mention that in the future we could extend to e.g. protein similarity. I wonder if we could also throw that in at the end. That a real-time introduction robot would find wide future use in a number of projects relevant to drug discovery, including identifying people working on similar proteins or drug targets.

On 24 February 2016 at 09:18, alintheopen notifications@github.com wrote:

Hi again,

Sorry - I also realise my video has chopped off the top of the presentation

• will sort this out and I added a slide with a SCINDR alert button inspired (that is cut off the video too, doh) have uploaded a second video draft as a PDF so that you can see what I mean.

Cheers

Alice

On Wed, Feb 24, 2016 at 9:16 AM, Alice Williamson < alice.e.williamson@gmail.com> wrote:

https://www.youtube.com/watch?v=ZvhiTHdzo2A

I've uploaded a draft video here - excuse poor timings and pauses just wanted to give a first idea.

Cheers

Alice

On Wed, Feb 24, 2016 at 9:12 AM, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen I loved your storyboard. (Nice touch with your picture being upside down.) I will also get you a better picture of myself. :)

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187939571

.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-187941141 .

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

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[alintheopen]

Hi Mat

Molecules will be changed for sure - this was just a quick screen grab from this morning that Chris and I took. Tomorrow/tonight I'm going to discuss more with Luc and we will generate the appropriate entry in his awesome ELN and then I will do the same with similar structures in Labtrove, LabArchives and a made up ELN.

I will add a slide that doesn't get too string-y but emphasises the human vs computer readable-ness

and yes, can add protein slide just before final slide.

Will circulate new video once I change slides and ask for more input for the final video. Am happy to do if everyone else is also happy.

[cdsouthan]

Good stuff. Couple of points

1) re stating the obvious the SCINDR concept could be extended to "relationship connect" any relevant entites explicitly identified in an ELN (or even not explicit if described in just free text) beyond chemical structures and reaction schema. While protein targets and bioassay ontology descriptions (BAO http://bioassayontology.org/) could come in the frame, in practice however, these would have to come from a Bio-ELN extension. Its a moot point as to wether we want to stretch this far, I'm neutral. However, the implicit assumption behind what we are doing is that chemical similarity implies biological similarity in some sense (e.g. groups that connect via chemistry are probably working in a similar NTD areas)

2) I completely understand we don't want to overstate the position of PubChem (or even Google) in the proposal but we have to aknowledge it is the big wheel and connection broker (<90 mill stuctures and < 50 mill users per day and the entire Entrez system hooked in) against which we need to engage the small cog of SCINDR (5K cpds 100 total users?).

[lpatiny]

@drc007 > ChemSpider might be the best source

I think chemspider is not obvious because you need to start a query and then make continuous check if the result is done. Is there a way to make a sync similarity search ?

[drc007]

I’m not sure why you need a similarity search for safety data?

On 24 Feb 2016, at 08:58, lpatiny notifications@github.com wrote:

@drc007 https://github.com/drc007 > ChemSpider might be the best source

I think chemspider is not obvious because you need to start a query and then make continuous check if the result is done. Is there a way to make a sync similarity search ?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-188146455.

[drc007]

Perhaps simply say that structures are stored as universally recognised machine readable text strings (SMILES, InChi), these can then be used to search other notebooks but also ANY accessible chemistry data source.

Biological entities can also be represented by universally recognised machine readable text strings , either sequence, uniprotID, gene id etc.

On 24 Feb 2016, at 00:40, Mat Todd notifications@github.com wrote:

And is there a way of conveying that the ELN is able to take what the researcher has recorded and make it understandable by SCINDR? Without going too much into the strings issue, but a visual way of showing that the molecule is converted into something else in the background.

[cdsouthan]

@alintheopen super video first version - but suggest drop "competitors" or Elsevier or Thomson will try to buy us .....

[lpatiny]

Alice, really cool what you did ! The ELN should now be working for everybody.

http://eln.cheminfo.org

Please try to add some reactions !

If you have problems or suggestions please use the github issue tracking system:

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

[lpatiny]

@drc007 you are right exact search (based on cas or available information) but I think again this is async no ?

[mattodd]

So we're getting close. Remaining things:

1) I think @alintheopen is going to tweak the powerpoint images and re-record the video over the weekend. 2) @MedChemProf I think you still need to add some personnel stuff? 3) @MedChemProf how are we looking on word counts? And are there any potential SNAFUs in pasting from Google Doc to web form? 4) I will chase RSC, USAID and WHO for letters. 5) Final submission is Monday - @MedChemProf are you OK to wait till nearly the last minute to see whether we can secure those extra letters?

[MedChemProf]

@mattodd Reply to some of your questions. 2) @MedChemProf I think you still need to add some personnel stuff? -I already entered that information in the actual prize site. I can duplicate if needed. 3) @MedChemProf how are we looking on word counts? And are there any potential SNAFUs in pasting from Google Doc to web form? -Word count is within boundaries. The Executive Summary is 276 words out of the maximum 300.The proposal itself is 12,612 characters (without spaces) which is under the 15,000 character (without spaces) limitation. With spaces, the proposal is 14,884 characters (so still under if we are playing it safe.) -I will be downloading the Google Doc into Word format to check formatting and word count when we have the final version. I will then be converting it to pdf for upload to the prize site to preserve formatting. I have already practiced this workflow without issue. 4) I will chase RSC, USAID and WHO for letters. -Thanks. I will ping Northeastern again for that letter. I plan to combine all of the letters into a single pdf for submission as supplementary material. 5) Final submission is Monday - @MedChemProf are you OK to wait till nearly the last minute to see whether we can secure those extra letters? -I would like to target Monday morning EST if possible to upload the proposal and supporting video. The section for uploading the supplementary letters is contained in another area of the grant site. I can delay that to later in the day my time.

[MedChemProf]

@alintheopen @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'?

[mattodd]

Should rhyme with tinder rather than finder. @alintheopen knows this.

On 26 February 2016 at 12:27, 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'?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189071514 .

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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[alintheopen]

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'?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189071514 .

[alintheopen]

@MedChemProf Did you want a different photo to be used on video? just finalising

[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'?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189071514 .

[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'?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189071514 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189614884.

[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'?

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189071514

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189614884 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189615920 .

[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.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189689620 .

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

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[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.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189946000 .

[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

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189871337.

[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

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-189871337 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-190110080 .

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 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.