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OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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Call for Agenda Items for Online Meeting 10 #317

Closed mattodd closed 8 years ago

mattodd commented 9 years ago

Updated due to meeting postponement: Meeting number 10 will happen on Monday July 27th at these times and at this location.

The two main items under discussion will be analog design (also #301 ) and metabolic clearance <-- this is a new post. A more detailed agenda is now needed, and slides will be sent round before the meeting.

Anyone like to suggest items for discussion below? These will then be incorporated.

mattodd commented 9 years ago

Current Composite Agenda:

1) Summary of Potency Data on Recent Sets of Compounds June 2015 May 2015 Edinburgh November 2014 July 2014

2) Analysis of Metabolic Data Recent Summary: http://malaria.ourexperiment.org/biological_data/8225 All current data: http://openwetware.org/wiki/OpenSourceMalaria:Triazolopyrazine_%28TP%29_Series#Physicochem.2Fmetabolism.2FPK

Are there trends in the logD-clearance data - see #333

3) Analog Design for the Next 10 Compounds Main post: http://malaria.ourexperiment.org/the_osm_blog/11565/What_Should_We_Synthesise_Next.html See also issue #301

4) Summary of new Google Sheets, Informatics, Pubchem/Chembl mining of molecules etc (Chris Swain and Chris Southan)

5) Questions

Powerpoint and Other Files

mattodd commented 9 years ago

Hi @wvanhoorn - note the change in day to the 27th. It'd be really great if you could join us and describe the predictive work you've been doing.

wvanhoorn commented 9 years ago

Thanks for the heads up, I will be there on the 27th

mattodd commented 9 years ago

Hi @wvanhoorn great - would you be amenable to talking us through your approach for literally 2 minutes on Monday? All you'd need is a laptop and browser. I will take the last set of compounds you recommended as an image, but it'd be great if you could very quickly speak to the method. It is a tad early UK time.

cdsouthan commented 9 years ago

Extra slide (time permitting natch)

250 InChIs from OSM master sheet > PubChem mapping https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi 167 are CIDs in PubChem http://www.ncbi.nlm.nih.gov/sites/myncbi/christopher.southan.1/collections/48338932/public/ and 155 have a ChEMBL match

Suggestions Optimise sheet (e.g. missing InChIKeys, round tripping between SMILES and InChI, rounding off significant figs) Submit confirmed summary data as a PubChemBioAssay Refresh (latest data) and extend ChEMBL submission Deposit rest of the (73) structures into PubChem, including pending designs, but clearly labelled as transient virtuals (makes everything globally findable by similarity search) Lock down in-house synonym mapping (structure > OSM >other? > MMV > ChEMBL ID > PubChem CID) and choose what you surface to ROW via ChEMBL/ PubChem

mattodd commented 9 years ago

Added - thanks, though we're under major time pressure. A data-focussed meeting later on might be a good idea. Sept?

Quick and basic question. Are the data in the Master sheet visible to Google? If not, do the data only become visible once we submit to a database?

cdsouthan commented 9 years ago

Fine - initial results exposed here anyway. AWK Google indexing is somewhat mysterious but we can of course do check seaches quickly. For exampe UYWFTHNNGLIMAY-UHFFFAOYSA-N seems to be surfacing from OSM instantiations and Chris's blog but not the Google doc directly

wvanhoorn commented 9 years ago

@mattodd I can present something on Monday, two minutes is very brief so it will be a wizz through

mattodd commented 9 years ago

Yes, great. If you're able to send me a slide beforehand for incorporation into the deck that'd be useful, but no pressure.

On 27 July 2015 at 02:57, Willem van Hoorn notifications@github.com wrote:

@mattodd https://github.com/mattodd I can present something on Monday, two minutes is very brief so it will be a wizz through

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mattodd commented 8 years ago

Meeting took place. Closing.