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Open Source Malaria
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We're profiled in International Innovation's Parasites of Poverty Issue http://www.research-europe.com/magazine/ISSUE/129/index.html … (p50-51) along with @WHO @MedsforMalaria
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Prof. José Gutiérrez Fernández's profile photoMatthew Todd's profile photo
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Next open online meeting of OSM (http://opensourcemalaria.org/): Thursday March 27th at these times: http://bit.ly/1eTI8vI. All welcome, including anonymous spectators who would just like to know about open source drug discovery. When you want to join, just come in via your web browser by clicking here: http://webconf.ucc.usyd.edu.au/osmmar2014/. The agenda is taking shape over the next 24 hours here: http://malaria.ourexperiment.org/osddmalaria_meeting_/9470
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Matthew Todd's profile photoKatrina Badiola's profile photo
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Awkwardness with using SMILES - could use input from seasoned cheminformatics guys, who may know all about this. If SMILES is ambiguous in this way, why are we still using it so much in medchem? Pinging +Christopher Southan +Egon Willighagen +George Papadatos 
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George Papadatos's profile photoMatthew Todd's profile photoChristopher Southan's profile photoMurray Robertson's profile photo
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One for +Matthew Todd "Building an R&D chemical registration system"  http://www.jcheminf.com/content/4/1/11
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Happy New Year everyone! The team could use some help/advice with this difluoromethylation. Its proving a bit tricky but we really need to synthesise this intermediate and would greatly value the help of the synthetic community. Blog here: http://malaria.ourexperiment.org/uri/49b explains in more detail. Cheers everyone, all ideas welcome and also for trifluoromethylation.
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How do we best view a collection of molecular structures and their biological activities?

This is a central challenge we have in OSM. It would be good if the casual medicinal chemist could simply browse the project's structures.

Contributors are making molecules every day and regularly but less frequently receiving potencies or other bio/chemdata. We need to be able to share the structures and the activities most effectively. We want the data to be easily shared but also easily browsed. So we need a sheet/something with:

1) Structures, i.e. 2D pictures of the molecules that are human-friendly
2) Associated informatics data (e.g. InChI) that are machine-friendly
3) Potencies or other data
4) Any associated ID numbers
5) A weblink or two to where the molecule is featured/made

It's useful I think for the project to have a discrete place where the data are kept, just to maintain identity - i.e. not just to be subsumed by a larger database. Or at least for the project's structures to be group-able if they are part of a larger database. But really this is a problem about human visualization.

The initial solution was a Google sheet, but we found that beyond about 50 structures the sheet didn't handle the images well.

An alternative is a shared Excel sheet, but as I understand it we would need a plugin to handle the chemical structures. That's do-able, but not if we expect all the readers to have the same plugin.

The current solution is an sd file - a succinct and easy-to-update text file that contains all the information:

https://github.com/OpenSourceMalaria/OSM_compounds

HOWEVER, reading the data (i.e. browsing the structures) is not easy to do for the casual observer.

So what is needed? Well, we're batch-uploading data to Chembl (https://www.ebi.ac.uk/chembl/malaria/doc/inspect/CHEMBL2113921). If we could do an auto-upload to Chembl (daily) then this would be problem solved, since Chembl is very cool and are doing cool things with visualization:

http://chembl.blogspot.com.au/2013/10/some-gamification-of-chembl.html
http://chembl.blogspot.ch/2013/10/chembl-web-service-update-3-image.html

But another possible solution is for us to be able to set up a system where: the sd file is displayed on a webpage with a static address (can be bookmarked). When the sd file is updated, that would lead to a new rendering of the webpage when it is loaded. The page would need to have the structures, and be displayed in an active way such that the data can be re-ordered on demand, like in a spreadsheet.

The main sd file has now been joined by an Excel sheet and sd file of lots of exciting new molecules for the latest series the project's looking at:

http://malaria.ourexperiment.org/uri/438

We coincidentally need to combine these two sd files, and we need to browse the new structures because we need to think about which molecules to make next in that new series.

I know that there are solutions that are appropriate for cheminformaticians. We need solutions for people who are happy with email and web browsers only.

Any ideas, anyone?

Egon Willighagen spoke about possible solutions using the sd file during the previous OSM project meeting (http://youtu.be/GxJnWg_eR2I)



 

This post at:

ELN: http://malaria.ourexperiment.org/uri/43e

G+:

Github: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/99
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Next meeting is tomorrow - all welcome.
 
Next open online meeting of OSM (http://opensourcemalaria.org/): Thursday March 27th at these times: http://bit.ly/1eTI8vI. All welcome, including anonymous spectators who would just like to know about open source drug discovery. When you want to join, just come in via your web browser by clicking here: http://webconf.ucc.usyd.edu.au/osmmar2014/. The agenda is taking shape over the next 24 hours here: http://malaria.ourexperiment.org/osddmalaria_meeting_/9470
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Web design meeting planning. We need to have a brainstorm of non-science things to do with OSM, mainly of web design and platforms for collaboration. Draft agenda in the link below, plus some possible times. Comment here or there. Lots of important things we need to talk about for reducing barriers to participation by bench scientists who hate passwords.
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Brian Glanz's profile photoFrank Rummel's profile photoMarco Cicconetti's profile photoMatthew Todd's profile photo
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Starting in 40 minutes.
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Carbonylation for the nation...can you help? Do you want to join team OSM? Ah go on!
Here's the blog: http://malaria.ourexperiment.org/uri/49d
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Egon Willighagen's profile photoMatthew Todd's profile photoVadilson Malaquias dos Santos's profile photoMurray Robertson's profile photo
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Calling all medicinal chemists...can you help us to decide on a good synthetic route for the series four amides?
Blog Post here: http://malaria.ourexperiment.org/uri/44b
GitHub thread here: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/101
Thanks a lot!

P.S...if you would like to sign up for GitHub, instructions are here: http://malaria.ourexperiment.org/uri/42b
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Open Online Project Meeting of Open Source Malaria (OSM)
 
Thursday 10th October 2013
6 pm Sydney
8 am London
9 am Geneva
12:30 pm Delhi
3 am New York
midnight in San Francisco
 
Meeting location: http://webconf.ucc.usyd.edu.au/osmoct10/  
Agenda
 
1. Series 3 (Aminothienopyrimidines)
a) Final selection of 10 compounds
Description: http://malaria.ourexperiment.org/uri/40a
Poll: http://115.146.93.123/quiz/quizzes/view/15  
Questions: who is assigned to make them, and by what date?
 
2. Series 4 (New Triazolopyrazines)
a) Which compounds to be sent to Kirk for ion regulation assays?
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/77  
b) Initial compounds being made - OK?
Experimental work to date: http://malaria.ourexperiment.org/triazolopyrazine_se
Background to Series 4: http://openwetware.org/wiki/OpenSourceMalaria:Triazolopyrazine_%28TP%29_Series  
c) Compounds to be made next - main item of business in this meeting
Relevant location of question: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/86
Need for some informatics: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/87  
d) Need raw data from briefing document
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/84  
e) Any other data needed on existing/known compounds, to further understand the series strengths/weaknesses?
 
3. Clerical - general help needed with writing of wiki and paper. How can we recruit?
e.g.:
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/92
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/89
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/85
https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/75  
4. AOB
a) Comments on usability of site(s) - whether scientists find it easy to get up to speed. Whether it is easy to navigate to the right information.
 
Everyone welcome. Be aware the meeting is "live" and a recording will be placed on Youtube.
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Open Source Malaria's profile photoBrian Glanz's profile photoLava Kafle's profile photoMatthew Todd's profile photo
 
Recording of Meeting: http://youtu.be/GxJnWg_eR2I
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Open Source Malaria - join in!
Introduction
This is the Open Source Malaria project. The core is funded by the Medicines for Malaria Venture and the Australian Government.

Anyone can participate at any level. All data and ideas are freely shared. No patents.

Feel free to join in the discussion, make and test compounds or interpret results.

The main project page, for other resources, is here.