[open-science] Open Source Malaria Paper 1

Matthew Todd matthew.todd at sydney.edu.au
Tue Sep 27 13:32:31 UTC 2016

Dear all,

People here might be interested in the first paper to come from the Open Source Malaria Consortium: http://pubs.acs.org/doi/full/10.1021/acscentsci.6b00086

(There's also a backstory post on who did what: https://intermolecular.wordpress.com/2016/09/14/open-source-malarias-first-paper/

and an explainer of the context re open drug discovery in The Conversation for those interested: https://theconversation.com/making-drug-development-less-secretive-could-lead-to-quicker-cheaper-therapies-64744)

Reason I'm writing: one of the issues in publishing this work was around using-then-publishing open electronic lab notebooks. We used Labtrove, from Jeremy Frey's group in Southampton Uni. The paper contains links to the active pages of the notebook, which are still online, but the information is archived in two ways: i) snapshotting the whole ELN and posting it as a browsable object on a Uni repo, and ii) taking PDF snapshots of individual pages and uploading those to the journal as SI. Hopefully this takes care of permanence. Figshare/Dryad would have been an alternative. Any other/better possibles for archiving all the details of large lab notebooks, forever?

The synergy of research papers and blog discussions was interesting in this paper. Many strategic decisions in the project were taken in light of community discussions (that's part of the point of open source drug discovery, obviously) and it was essential to capture those discussions for the record. Again, offline snapshots of oral/written discussions uploaded to the journal/repos hopefully take care of that. In one case a referee of the final paper asked a question about something that was difficult to answer without community consultation: whether pharma companies allow their staff to work on their own projects some of the time. After I asked this on Twitter, the resulting blog-based community discussion (which answered the question clearly as "yes, kind of") became the final piece of SI.

(Should anyone want to get involved in a new, central part of OSM that involves cheminformatics, there's a live competition to establish the Mechanism of Action for OSM's current set of antimalarials: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/421)

Best wishes everyone,


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

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