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OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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Publication of OSM Paper 1 #434

Open mattodd opened 7 years ago

mattodd commented 7 years ago

The first paper to arise from the Open Source Malaria Consortium is published today in ACS Central Science, describing Series 1. Congratulations again to all those OSMers who were involved with this one.

This Issue can act as a place to gather together any materials related to this publication that might be of interest to contributors here. Please add any others below. I’ll close the Issue in a couple of weeks and port the resources to the wiki.

  1. Paper (includes links out to all the supporting information etc)
  2. Lay article in The Conversation
  3. Blog Post by Mat about the project
  4. Article in El Mundo.
  5. Blog post on the Series 1 structures by @cdsouthan
  6. Article by The University of Sydney
  7. Article by MMV.
  8. Article in the Sydney Morning Herald.
  9. Article from Griffith University.
  10. Article from the University of Dundee
  11. Article in IFLScience
  12. Part 1 (starts 5:30 in) and Part 2 (starts 9:20 in) of an audio interview about OSM carried out a couple of years ago, which coincidentally went online in the last few days.
  13. Article at Campus Review
  14. Blog Post by Derek Lowe for In The Pipeline.
  15. Slot on ABC National Radio in Australia
  16. Video interview with GSK, coincidentally released at the same time, highlighting the inputs of GSK Tres Cantos into open source projects.
  17. TV slot on Australia's Channel 10 on data sharing in malaria
  18. Slot on Radio Adelaide on Friday Sept 23rd
  19. Slot on 2SER radio on Wed Sept 21st (starts at 1:44:00)
  20. Article on Asian Scientist
  21. Reddit AMA that took place on Tuesday 4th October, with a summary write up here. Published in The Winnower.
cdsouthan commented 7 years ago

Brill, when the paper goes live in PubMed I will briefly point to Mat's and my blogposts as a PubMed Commons entry. I suggest Mat adds any new pointers of significance as updates to his own blog so we knit the commentaries together.

cdsouthan commented 7 years ago

Regardless of being "parked" could we encourage anyone to attempt to identify the Series1 pathway and/or molecular target (including eliminating Pf4ATPase)? This would obviously increase the scientific payoff for the work. Could we even create a spin-off project team?

Cf. https://cdsouthan.blogspot.se/2012/12/antimalarial-target-deconvolution.html

mattodd commented 7 years ago

Absolutely. This is probably the number 1 thing on the Series 1 to do list. In the paper we eliminate a couple of possibilities (DHODH, PfATP4) but Iain Wallace made predictions on others that have not yet been screened: "carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (Q8I3U9), SUMO-activating enzyme subunit 2 (Q8I553) and 1 (Q8IHS2), and cyclin-dependent kinase 1 (P61075)." Are there other targets you were thinking of? The alternative is generating resistant mutants. There are labs that do this, but the work costs.

cdsouthan commented 7 years ago

Good, JFTR I think I covered most of the options in https://cdsouthan.blogspot.se/2012/12/antimalarial-target-deconvolution-part.html

The two main things that have changed in the last 4 years are the falling costs of RNA seq (transcript profiling for comparative mmoa fingerprinting) "deep" modelling target SAR is now more sophisticated (cf. Alex Clark, Sean Ekins et al.) and of course CRISPR can now be used for dialing mutants. Testing the in silico predictions would also depend on finding in vitro assys for those enzymes. Maybe get an informal TC together for interested parties?