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OpenSourceMalaria / OSMSeries4Paper1

Working Repository of Files Related to Open Source Malaria Series 4, Paper 1
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Editing Session: Friday 25/6 #59

Closed danaklug closed 3 years ago

danaklug commented 3 years ago

Hi everyone, next editing session will be Friday, June 25 at 6:00am Boston/11:00am London/8:00pm Sydney.

FYI @mattodd @edwintse @MedChemProf @drc007 @cdsouthan @maratsydney @holeung et al.

Dana Klug is inviting you to a scheduled Zoom meeting.

Topic: OSM Series 4 Paper Editing Time: This is a recurring meeting Meet anytime

Join Zoom Meeting https://ucl.zoom.us/j/94033228077

Meeting ID: 940 3322 8077 One tap mobile +13462487799,,94033228077# US (Houston) +16699006833,,94033228077# US (San Jose)

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mattodd commented 3 years ago

Gah @danaklug @edwintse @MedChemProf I've double booked and I can't make this session, sorry, nor hours either side. Please feel free to connect in any case to run through anything that remains.

Updates from me:

  1. In vivo PK data for MMV639565. I asked about the origins of the data we quote. Mark Gardner said "The rat PK mentioned in David's poster was run at Pfizer by 6th Oct 2011 - I don't have names of the people involved."

Mark's recollection is that MMV639565 (which is also PF-06342505) was first made at GVK Bio in Dec 2010. The structure/design was first entered into Pfizer's database by Ian Marsh in Sept 2010. Mark's guess is Mike Palmer designed it, though Ian may have too. It was then synthesised by GVK Bio & shipped to Pfizer. Pfizer's database system doesn't record the name of the person at GVK Bio who made it. It looks like another batch was made in Sandwich in April 2011. I'm not sure how we act on this, other to consider a mention in the acknowledgements. Action on @mattodd

2) Paul and Mark confirm it was a 160K compound screen. They do not think that the data were ever published (because the Pfizer site closed). I have uploaded another, related, poster to the Github repo, just FYI. No need to link in paper.

3) Liver data/authors, listed in paper comment: need to be added to author list. Data mentioned needs to go into the SI, along with any protocols, as per the comment in the paper. Action on @edwintse

4) Check whether hypnozoite data obtained on compounds mentioned in the paper comment and at https://github.com/OpenSourceMalaria/Series4/issues/4 Action on @edwintse

5) Gametocyte data to be added to the SI. Action on @edwintse

6) Drug resistant cell line data needs to be added to the SI file list. Action on @edwintse . Action on @mattodd to reach out to Sergio Wittlin at Swiss TPH to find out who generated the data.

7) Add COADD data to the SI file list. Action on @edwintse

8) @edwintse was assembling full hERG scheme for SI, to include all compounds evaluated.

9) @mattodd to continue to pursue extraction of all data from Labtrove.

10) @alintheopen and @david1597 to provide data to @edwintse for their compounds for SI (about 10 total?). No compounds in this paper arose from the undergrad lab practicals.

11) Added a couple of tweaks needed to Figure 8, which I think @MedChemProf said he might be able to do?

Please keep a slot in the diary for next time, so we can tick off the above and finalise.

MedChemProf commented 3 years ago

@mattodd @danaklug @edwintse I am fine if we want to postpone the meeting until next Friday, June 25th. I believe I have a way to better plot the data in Figure 8 according to the comments made. I will work to get the updated Figure 8 in place by the 25th. Please let me know if meeting pushed. Thanks! :)

danaklug commented 3 years ago

Yes, let's just postpone to same time next week. I've changed the details accordingly.

mattodd commented 3 years ago

I forgot one other thing: Inherited data for the SI. We had a reply back from Saumitra from TCG. To paraphrase:

1) She sent data-sheets for MMV 669844, 670652 and 669009 which Abhijit was able to pull down from Cloud. @edwintse I assume you're OK to add those in, and to check that everything looks fine?

2) We can't find data on MMV669103. Is this an important compound, and can we remove from the main paper? @MedChemProf opinion?

3) In lieu of authorship (which was declined) Saumitra said it would be nice and appropriate if we would acknowledge the contribution of TCG Life Sciences towards the synthesis of compounds described in the paper. @danaklug could you please ensure that's added in if not already?