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Ant Chubb
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Message 251 - Posted: 2 Oct 2012, 12:54:42 UTC

We have collected the experiments into groups, each aimed at a separate paper to be submitted to an open-access journal in the near future.


  • A - Docking of MalariaBox compounds against the P. fal. proteome (MMV_400) - Exp=A,Ap,1p,2p,4p,6p
  • B - Using vHTS to find the malarial targets of repurposed drugs (NPC) - Exp=8p-11p
  • C - FightMalaria@Home – using vHTS to find targets for hit compounds (MMV_full) - Exp=B,Bp,3p,5p,7p,12p-15p
  • D - FightMalaria@Home update – the effect of flexible active sites on vHTS (all) - Exp=16p-44p
  • E - Using BOINC to identify novel antimalarial compounds (ZINC, CycloPs) - Exp=45p-47p



We have over 4 million results thus far, and % completion is as follows:


  • A - 78%
  • B - 20%
  • C - 1%
  • D - 0%
  • E - 0%



Progress has slowed as we're now docking larger molecules with more rotatable bonds.

Robert7NBI
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Message 256 - Posted: 3 Oct 2012, 16:27:19 UTC - in response to Message 251.

Now no progress...

fightmalaria@home 03-10-2012 18:26:56 Project has no tasks available

Ant Chubb
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Message 259 - Posted: 4 Oct 2012, 10:08:35 UTC - in response to Message 256.

That's odd, as I am getting new jobs on my box:
Thu 04 Oct 2012 11:08:21 IST fightmalaria@home Scheduler request completed: got 5 new tasks
Has this cleared up for you yet?

Robert7NBI
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Message 260 - Posted: 4 Oct 2012, 10:27:45 UTC - in response to Message 259.

I got a job ca. 1:30 UTC nigt, now I have a bufor.

Unfortunately I have 4500 in pending, but 0 in valid (also 0 invalid).
Server status... inaccessible, but I read that we have to wait until next week.

So, we are working blind. ;)

Bel
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Message 433 - Posted: 18 Nov 2012, 19:10:15 UTC

Hi Ant Chubb. I wonder, when we can expect the next update? :)

Ant Chubb
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Message 444 - Posted: 30 Nov 2012, 17:20:39 UTC - in response to Message 433.
Last modified: 30 Nov 2012, 18:07:40 UTC

Progress report - over 20 million results so far:

A - 61% - 1,328,976 results
B - 60% - 9,002,545 results
C - 7% - 10,111,084 results
D - 0%
E - 0%

20,442,605 results in total!

This is lower than previous % completions as we've added 950 models (18% of the proteome) to the list of receptors we're searching against. We now cover 44% of the proteome in 3D, which is quite substantial.

Jack Lightholder
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Message 469 - Posted: 29 Dec 2012, 3:27:29 UTC

Hi Dr. Chubb,

Would it be possible to get another update one day soon?

Or even better yet a script enabled on the site which automatically updates every so often? It would probably be less time for you folks in the long run and closer to real time updates for the users. NumberFields@Home does something similar as an example: http://numberfields.asu.edu/NumberFields/batch_status.html
____________

jovada
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Message 470 - Posted: 30 Dec 2012, 19:57:31 UTC - in response to Message 469.

Or even better yet a script enabled on the site which automatically updates every so often?

*like*

Communicating about the progress of a project is vital for me.
Otherwise it looks endless..

Vegard
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Message 472 - Posted: 1 Jan 2013, 15:10:20 UTC - in response to Message 470.

Absolutely true! BOINC number crunching is very much about seeing the progress to which one contributes and it is a large part of the fun to see that the donation of CPU time is meaningful is some sense and that one approaches towards some sort of final goal. It should be fairly easy to implement a fast feedback system.

Cheers!

Dylan
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Message 473 - Posted: 1 Jan 2013, 21:48:26 UTC

Also see the progress report of the SimOne@Home project.


http://mmgboinc.unimi.it/osmo_progress.php

Kevin
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Message 474 - Posted: 2 Jan 2013, 11:47:29 UTC

Hi Guys,
I agree that we need an automated system for this. I'll look into it over the next few days.
Thanks,
Kevin

Bel
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Message 479 - Posted: 6 Jan 2013, 13:53:02 UTC

Hello. It's me again =)
I want to ask... What different with vina_15988 and vina_27114? And what experiments we crunching now of this table? http://www.fight-malaria.org/index.php?option=com_content&view=article&id=99&Itemid=108

Kevin
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Message 480 - Posted: 8 Jan 2013, 12:23:01 UTC - in response to Message 479.

Hi Bel,
The number after vina is just used to ensure the WU is unique. To be honest there is some redundant data in it too but we have left it there as it's not causing issues.

We are currently running experiment 5 and also some extra WUs from old experiments as we have made some minor changes. I'll update the table when I get back to the compute lab (it has changed a fair bit in the last few weeks - reordered and some additions/removals).

We're not far off our first paper :)
Best Regards,
Kevin

Bel
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Message 483 - Posted: 9 Jan 2013, 21:48:23 UTC - in response to Message 480.

Tnx Kevin.

Jack Lightholder
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Message 523 - Posted: 1 Feb 2013, 16:05:27 UTC

Any luck on developing a project status page? I can likley be of assistance if need be.

Aurel
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Message 545 - Posted: 14 Feb 2013, 20:25:11 UTC

Hi People,

I want to ask, if we project became a better "status-site". I mean, with an window "ready to x%", or xxx/xxx (xxx%) Wu´s have been computed.

Greetings from Germany,
Aurel

jovada
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Message 548 - Posted: 28 Feb 2013, 19:44:03 UTC - in response to Message 545.

Can we ask for a new progress update?

Tom_unoduetre
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Message 551 - Posted: 4 Mar 2013, 10:51:49 UTC

+1 for a status update and progress website

Kevin
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Message 552 - Posted: 7 Mar 2013, 16:36:21 UTC
Last modified: 7 Mar 2013, 16:37:08 UTC

Hi Guys,
We've decided to change the planned experiments. We now have the results required for paper 1 and are close to finishing the results for paper 2. Unfortunately we are lagging behind fmah with the actual analysis of results as there is a phenomenal amount of data.

We are currently docking some high quality protein models against the MMV dataset. After that we will be docking molecules from chembl assays. We haven't fully decided what we will be docking after that. We have a few choices but we need to prioritize the most important ones. I'll keep you posted.
Thanks for your help!
Kevin

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Message 832 - Posted: 26 Jul 2013, 9:43:06 UTC

Hi Kevin,

you wrote in March that you have the results for paper 1. Any update on that? What about the results for paper 2? And what is the overall status of the project? Do you have a % completion list comparable to the one in the beginning of this thread? (Any news on an automated status page? ;-))

Cheers!

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