OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
82 stars 13 forks source link

OSM Proposal to the Open Science Prize #371

Closed MedChemProf closed 8 years ago

MedChemProf commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

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.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-179200602 .

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 commented 8 years ago

@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 commented 8 years ago

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.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-179217405 .

mattodd commented 8 years ago

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 commented 8 years ago

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: snow1

cdsouthan commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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.

madgpap commented 8 years ago

@mattodd @drc007 re point no 3: indeed UniChem is completely open and ideal for novelty detection and med chem 'due diligence'.

cdsouthan commented 8 years ago

@madgpap no question https://www.ebi.ac.uk/unichem/ucquery/stats is an impressively comprehensive collection at 109 million. But am I correct in assuming its not suitable for similarity searching (e.g. Tanimoto) that can be done in ChEMBL and PubChem?

lpatiny commented 8 years ago

Our goal for the ELN is really to make a tool that organic chemist can use intuitively. This means retrieving chemical structure, density, previous products, ... It will also deal with all the analytical results using perennial formal (jcamp) that can be not only visualise but also in the future assign on-line. We can even think about automatic assignment of NMR spectra directly in javascript and on-line (we just submitted the paper about it). Because we store correctly the information we are able to make substructure search or chemicals, reaction search and similarity search of spectra.

The way I see what you are describing as SCINDR is "just" a webservice that would get information from many databases, one of them being our ELN, but also pubchem, webreactions, chemspider, ... This webservice would generate a kind of compilation of the best results and inject it directly in our ELN. At the "business" point of view we could think about sponsored results (we sell this reagent at a good price, we can make this reaction for you, ... I don't think that you will ever have a company that will store, even in a private way, a reaction in the ELN. It is their core business so they keep it in the company.

Concerning Chrome indeed it is the development browser but normally modern browser that respect the ECMA 6 specifications should work. Safari however is far behind the implementations of the new specifications. Edge is rather on the top on the other end.

cdsouthan commented 8 years ago

OK - were getting some convergence

InChIKeys generated within SCINDR 1) get struture match checked "inside" SCINDR 2) get novelty checked "outside" a) against UniChem web services by exact and/or connectivity layer match (arguably the only database one we would need since it subsumes PubChem and is updated monthly) but b) also Google. You could think about adding a ChemSpider InChIKey webservices call out as c) (because RSC wont allow their loading into UniChem). However, their novel content is probably low and they are fully indexed in Google anyway (wheras PubChem is not yet) 3) SCINDR structures auto-submitted to PubChem as full SID record with url pointing back to SCINDR. This means they then become similarity-findable in PubChem

I would not overdo the compilation of external source polling unless you can parse them cleanly to present "intuative" results to the chemists.

MedChemProf commented 8 years ago

Thank you all for the insightful comments. I am just following up on @mattodd request to schedule another meeting this upcoming week. I am suggesting 5:00PM EST on Tuesday, February 16th (http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=16&hour=22&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291). Hopefully this can work for most. Google Hangout link is https://talkgadget.google.com/hangouts/_/lh7afwttp3ohfcbl3uep35lnqaa

mattodd commented 8 years ago

That Hangout time is good for me, thanks. (Wed morning @alintheopen ;))

alintheopen commented 8 years ago

;) Noted!

On Mon, Feb 15, 2016 at 9:57 AM, Mat Todd notifications@github.com wrote:

That Hangout time is good for me, thanks. (Wed morning @alintheopen https://github.com/alintheopen ;))

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-183998402 .

alintheopen commented 8 years ago

Have added some edits and comments to the google doc.

On Mon, Feb 15, 2016 at 10:16 AM, Alice Williamson < alice.e.williamson@gmail.com> wrote:

;) Noted!

On Mon, Feb 15, 2016 at 9:57 AM, Mat Todd notifications@github.com wrote:

That Hangout time is good for me, thanks. (Wed morning @alintheopen https://github.com/alintheopen ;))

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-183998402 .

madgpap commented 8 years ago

@cdsouthan this is correct. UniChem currently provides exact and connectivity matches - for now.

lpatiny commented 8 years ago

I'm away from the office this week with limited access to internet and will not be able to attend the meeting. I will try to follow however github and my email. The website will be http://eln.cheminfo.org. You can test it but you can not yet save the data. If you create reaction you can copy / paste the JSON that is on the right and send it to me. Like that we will be able to show many examples of reactions. We are currently migrating our system so that authentication and saving will be possible.

drc007 commented 8 years ago

"@madgpap @cdsouthan this is correct. UniChem currently provides exact and connectivity matches - for now" However we know how to add similarity searching of very large databases ;-) http://blog.matt-swain.com/post/104338864527/chemical-structure-handling-in-mongodb

rajarshi commented 8 years ago

Just came across this proposal - nice idea. Once suggestion came to mind that would enable incorporation of links to outside the immediate OSM community. In addition to the background process linking structures deposited into the ELN to other structure repositories, it'd be useful to have the process look at Pubmed abstracts - you could imagine running OPSIN on them to extract chemical structures (as well as other NER methods to pull out say targets, diseases etc). Certainly, this will lead to some level of false positives, especially for non-chemical structures, but may be worth exploring. So in addition to alerts to other OSM research, you could generate alerts to related research being reported in the general literature

mattodd commented 8 years ago

Hi @rajarshi - oh that's absolutely the idea. It was never intended as an OSM-only thing. OSM is the test bed, but the idea is that there will be a simple way to alert anyone using this lab book to similar work (that's the doozy) but also anyone else doing work in the open - lab books being the best resource, since they're current, followed by the published lit. I see the general open web aspect as a soluble problem (big, but not a new problem) whereas the thing that SCINDR is really going after is lab books, anywhere. Real-time discovery, so that people can work together today.

MedChemProf commented 8 years ago

@mattodd to the question on overhead, the Open Science Prize now has this on their FAQ: Q: Does the prize cover overheads/indirect costs? A: This is a prize and not a grant. The prize awards are predetermined ($80,000 for Phase I and $230,000 for Phase II) and not based on costs.

cdsouthan commented 8 years ago

Good to hangout yesterday. To follow up I just had a chat with EB from PubChem. He confirmed we can set up web services "triggers" for any similarity threshold (but it probaly needs to be tight to control hit swamping) for anything up to 10000 cpds (I'm guessing SCINDR initial content would be well inside this). They could be run weekly but I guess monthly would be fine (see http://www.ncbi.nlm.nih.gov/pubmed/25934803). He also said they have an automated deposition system in beta that we could volanteer to test out. Here again I guess the initial SCINDR rate of new syntheses would be modest (10-100 month?) but enumerating hypothetical intermediates could increase this. Note @mattodd if you want a letter of recomendation send him your draft thereof. Note also that PubChem is backed up with submissions and is set to go well north of 100 million live CIDs sooner or later.

mattodd commented 8 years ago

Hi @cdsouthan - that's absolutely great, thanks for reaching out. Would you be able to point EB at the latest version, which is here? Comments/suggestions very welcome, as well as separate comments along the lines of "this would be a useful new tool to have in health research".

So just to clarify - we'd be able to set up triggers within Pubchem that would fire off an alert if something else was entered into Pubchem that was similar to molecules that had been deposited into Pubchem by SCINDR? Is that what you mean? Lay it out for me like I'm an idiot. I'm not clear yet how this is better than just having SCINDR itself query Pubchem continuously.

Yes, as a Phase I project we'd be 10-100 molecules over the course of the project, I would imagine. Many more once we roll out a beta.

cdsouthan commented 8 years ago

@mattodd I have forwarded the mail. I'm not au fait with the technicalities of WSs but I am sure we can set up/try out alternative options for the objectives in hand (n.b. EB knows of @lpatiny so that helps). I suggest its essential that all key structures in SCINDR become PubChem SIDs (especially the novel ones, but probably not common reagents). This set should then be easier to set up the "structural proximity allert" inside, rather than pinging in from the outside. This may be too detailed for the application but we should try to plan in that SCINDR uses check PubChem before they start making anything.

mattodd commented 8 years ago

I've reached out to WHO/TDR, the RSC, USAID and DNDi for possible letters/tweets/videos of support for the proposal. There's no implicit criticism if we don't get it. Everyone's busy. If anyone else has suggestions for organisations to contact, they should go right ahead.

lpatiny commented 8 years ago

I added some text in the proposal. Should we organise an hangout meeting for next Tuesday ? I could make you an update on the ELN and will try to get a proof-of-concept of similarity retrieval before the end of next week. http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=21&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291

MedChemProf commented 8 years ago

@lpatiny I can attend. Chase

mattodd commented 8 years ago

I can't make that time, but can do 2 hours earlier or one hour later.

On 18 February 2016 at 23:00, Chase Smith notifications@github.com wrote:

@lpatiny https://github.com/lpatiny I can attend. Chase

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-185683168 .

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 commented 8 years ago

I have a lot of flexibility around the originally suggested time (+ or - several hours), so I can accommodate any agreed upon time.

lpatiny commented 8 years ago

Well 2 hours earlier is perfect for me ... So we way: http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291 ?

drc007 commented 8 years ago

You choose a time and I’ll try to fit in

Chris

On 18 Feb 2016, at 13:13, lpatiny notifications@github.com wrote:

Well 2 hours earlier is perfect for me ... So we way: http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291 http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291 ?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-185712372.

mattodd commented 8 years ago

Any advance on 2 hours earlier?

On 19 February 2016 at 00:27, Chris Swain notifications@github.com wrote:

You choose a time and I’ll try to fit in

Chris

On 18 Feb 2016, at 13:13, lpatiny notifications@github.com wrote:

Well 2 hours earlier is perfect for me ... So we way:

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291

?

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-185712372 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/371#issuecomment-185717545 .

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.

lpatiny commented 8 years ago

Let's fix it at: http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=2&day=23&hour=19&min=0&sec=0&p1=911&p2=240&p3=268&p4=1234&p5=291

Seems the previous hangout link still works (at least now ...) so we may resue it: https://talkgadget.google.com/hangouts/_/lh7afwttp3ohfcbl3uep35lnqaa

cdsouthan commented 8 years ago

Comments and observations related to the proposal http://cdsouthan.blogspot.se/2016/02/open-drug-discovery-chemistry-sharing.html some parts of which could be incorporated if we see fit