| Index | Recent Threads | Unanswered Threads | Who's Active | Guidelines | Search |
 |
World Community Grid Forums
Category: Completed Research
Forum: Discovering Dengue Drugs - Together
Thread: Completion of DDDT? |
| No member browsing this thread |
|
Thread Status: Active Total posts in this thread: 15
|
|
| Author |
|
|
Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hey im new to this project can anyone tell me how close we are to completion?
Thanks |
||
|
|
Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Many months.
Once the project has finished on the grid, it may be a year or two before there are published results. |
||
|
|
Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
ok thanks!
|
|||
|
||||
|
Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Also, we are currently in Phase I of DDDT. Phase II will use CHARMM to evaluate results from Phase I. I believe Phase II will also run on WCG (at least that's what I recall from a post by Sekerob).
----------------------------------------[Edit 1 times, last edit by Former Member at Jan 14, 2008 5:29:49 PM] |
||
|
|
Brecht Crombez
Cruncher Joined: Oct 16, 2006 Post Count: 40 Status: Offline |
hey,
from the official project website: In Phase 1 of this project, AutoDock will fit over six million small molecules to each of the flavivirus NS3 proteases. there are 2 WU send out / molecule if i'm right now we have already 11,748,719 WU's processed so >6,000,000 * 2 = >12,000,000 + some error WU's = maybe around 13,000,000 WU's in phase 1 13,000,000 - 11,750,000 = 1,250,000 still to crunch at a speed of 60,000/day makes still 20 days to crunch on phase 1 that's what i think  greets and keep on doing the good work |
||
|
|
Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
That info is not quite up to date (think it was scaled down to 3 million) plus it does not say how many tests for each and there are many. Phase 1 will run for a longer(?) wile concurrently with phase 2 which will feed off phase one as 'product' becomes available. They developers are going to start working on preparing phase 2 shortly, January designated as bug fixing month.
----------------------------------------Added: See comment by the project scientist on the work: https://secure.worldcommunitygrid.org/forums/...hread=15782&offset=50
WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 1 times, last edit by Sekerob at Jan 20, 2008 12:05:51 PM] |
||
|
|
Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Brecht, you forgot to multiply by the number of targets.
Quoting from the post Sekerob linked: "We expect to screen 3,000,000 ligands against a single protein target every two weeks. " Currently, we are nowhere near that goal. However, I'm not sure how many ligands are contained in the current work units. I recall an estimate of 50 targets, so 3 million * 50 gives 150 million docking attempts. The work unit : dock ratio may vary between 5 and 1/30, depending on the docking parameters chosen. There's a big grey area there! Can someone deconstruct a work unit to find out how many dockings each one contains? |
||
|
|
Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Last counted 22 with a save interval set to 60 seconds minimum.
----------------------------------------
WCG
Please help to make the Forums an enjoyable experience for All! |
||
|
|
JmBoullier
Former Community Advisor Normandy - France Joined: Jan 26, 2007 Post Count: 3715 Status: Offline Project Badges: 
|
Sekerob, I am not sure I understand your comment correctly. Do you mean that there is one docking per checkpoint?
----------------------------------------If so, since it is exceptional that my not-too-fast PC checkpoints in less than 60 seconds, I can write that there is one checkpoint exactly at every round percentage. That would make 100 dockings per WU, which seems much, no? But why not... Cheers. Jean. |
||
|
|
Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Except for GC, i know of no project at WCG where saves are programmed to happen in fixed (wallclock) time spans, usually at a completed docking attempt, step or whatever you'd like to call them.
----------------------------------------The sample below shows what the last one did in the last 10 minutes after setting the 'write to disk' back from the usual 5 or 1o minutes to default 60 seconds. It suggests that the time each step takes is not constant either for dengue (non-deterministic i guess). 20/01/2008 20:29:33|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed 20/01/2008 20:35:42|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed 20/01/2008 20:39:17|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed I read of some devices running dengue jobs in 8 minutes a piece. Time for me to switch off all sub standard devices. The above job took 1:41 CPU hours to complete on a C2D, so i 'desire' one of these QX9650's at 3ghz  Added: The murphy experience just hit: To what have you set the 'write to disk' limitation as the default is minimum 60 seconds, meaning if there was one in the 60 second span, it will be skipped and one will be written on the next chance. On my C2D it writes one about every 2.5 / 3 minutes and on average it takes an hour to complete. Except for GC, i know of no project at WCG where saves are programmed to happen in fixed (wallclock) time spans. As rules of fist, WCG programs checkpoints at convenient points, steps / attempts whatever you like to call them where the dataset is good to kick off the next try (is this rugby ;). Setting the saving rate back to 60 seconds, where normally i have it at 5 or 10 minutes, the present DDDT job does one about every 6 minutes and took 1:41 hours to complete. Still doing 'about' 22 per job.... it's what i see here on the Apennine peninsula. The sample below shows what the last one did in the last 10 minutes and suggests that the time each step takes is not constant either (non-deterministic i guess). 20/01/2008 20:29:33|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed 20/01/2008 20:35:42|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed 20/01/2008 20:39:17|[checkpoint_debug] result dddt0301n0794_ZINC04279095-0000_00_0 checkpointed I read of some devices running one dengue job in 8 minutes a piece. Time for me to switch off all sub standard devices. Added: They ol Murphy experience.... looks like this one does slightly over 60 seconds.... to me overkill. Think 5 minutes or even 10 is more than sufficient like the GC jobs had. 20/01/2008 21:23:08|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:24:11|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:25:22|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:26:23|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:27:27|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:28:44|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:29:49|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:30:51|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:32:02|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed 20/01/2008 21:33:10|[checkpoint_debug] result dddt0301n0794_ZINC04736581-0000_00_1 checkpointed
WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 1 times, last edit by Sekerob at Jan 20, 2008 8:38:48 PM] |
||
|
|
|