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ErikaT
Former World Community Grid Admin
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FightAIDS@Home - Phase 2 project update - February 2016

The research team for Phase 2 of FightAIDS@Home is developing and testing new ways to use the vast computing power of World Community Grid. Their goal is to build on the results from Phase 1 while using volunteers' resources as efficiently as possible.

Read the article here.

Thank you,
ErikaT
[Feb 15, 2016 7:39:17 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: FightAIDS@Home - Phase 2 project update - February 2016

It's pleasing to read an update like this, thanks.
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supdood
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Re: FightAIDS@Home - Phase 2 project update - February 2016

Thanks for the update--great to hear how the scientists are using the WUs. Looking forward to returning to this project soon.
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gb009761
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Re: FightAIDS@Home - Phase 2 project update - February 2016

Having just returned to this project - in order to progress to the next level, this update is very timely.

Please keep the information flowing - as it's greatly appreciated by those churning out the WU's.
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[CSF] Thomas H.V. DUPONT
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Re: FightAIDS@Home - Phase 2 project update - February 2016

Thanks for the heads-up my dear Erika ! cool
And thanks to the FightAIDS@Home research team for keep us informed !
For the french community >> WCG - État d'avancement du projet FAHB
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caring1
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Re: FightAIDS@Home - Phase 2 project update - February 2016

"Their goal is to build on the results from Phase 1 while using volunteers' resources as efficiently as possible."
Then surely to achieve this goal the W.U.'s should be split in two, as they are, they are too big to be efficient.
While other tasks complete in general, 5 hours or less:
My main cruncher, an i5 desktop takes 8.5 hours to complete one W.U.
My i7 Laptop takes around 20 hours per W.U.
My AMD E-350 Laptop took 56 hours to complete the last W.U. for Fighting Aids @ Home Phase 2.
That is not efficient at all.
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Rickjb
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Re: FightAIDS@Home - Phase 2 project update - February 2016

+1 vote of thanks for the update on FAHB.
I find that communications from the scientists help a lot in maintaining my interest in keeping my computers on line crunching.
Sports fans often complain that following a cricket match is like watching grass grow, but the longest matches are international "test" matches and they take only 5 days. Positively adrenaline-pumping compared to crunching WCG!

BTW, the link in the update at "the January issue of Protein Science is a special issue in recognition of Ronald Levy's contributions to the field of computational biophysics! The issue is free to read online" does not bring up the journal issue for me.

I am disappointed that even after about 10 years, FAAH has not yet come up with a drug candidate that has reached clinical trials stage. Here's hoping for a breakthrough using FAHB.

I also hope that the experience gained with FAHB can be put to use for other disease targets, including some such as dengue on which AutoDock and VINA have already been tried but have been found to score too many false positives.

@caring1: I don't see how spitting WUs into pieces that have shorter run times can affect crunching efficiency, except that it would waste the resources used to join up the pieces again at the server end when they've all been returned. OTOH, the issues discussed in the article do address crunching efficiency. Note that the FAHB WUs checkpoint often, so you'll lose very little crunching time if you turn off your computers and restart them later.
(I suggest that if you want to continue discussing this that you start a new forum thread as it's a bit off-topic here).
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ErikaT
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Re: FightAIDS@Home - Phase 2 project update - February 2016

BTW, the link in the update at "the January issue of Protein Science is a special issue in recognition of Ronald Levy's contributions to the field of computational biophysics! The issue is free to read online" does not bring up the journal issue for me.
The link has been fixed. Thank you for letting us know!

ErikaT
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Rickjb
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Re: FightAIDS@Home - Phase 2 project update - February 2016

Thanks, Erica.
The parts of the journal that are probably of most interest to us are under Editorial (pages 5–8) and Recollection (pages 9–11) by Ron Levy.
I don't pretend to know the areas of research described in the abstracts presented in the Editorial, but these 2 sections tell us who Ron is and summarise his career.
They also shed light on what BEDAM is:
"The Binding Energy Distribution Analysis Method (BEDAM)[6] is a free energy method Emilio Gallicchio and I developed based on Widom's potential distribution theorem, to predict enrichment factors for focused ligand libraries; it occupies a niche between docking on one hand, and more computationally intensive free energy methods on the other. While in the 2013 SAMPL4 challenge, it proved to be the most successful approach to identifying active compounds, we are well aware of how challenging the problem is and how much room there is for improvement. This is an active area of research in my group."

With the limitations of AutoDock and VINA found in some WCG projects, I've thought for quite a while that we needed better modelling software and that "our" researchers should look to the wider molecular modelling research community. It seems that they have done this, and if they don't have the world's best now, it's pretty xxxx close.
[Feb 25, 2016 8:22:23 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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