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Exciting news from the FM@H project - first in vitro validation comes up with hits!
Dear all,
We've had our first major success from the FightMalaria@Home project. After analyzing the data generated in the first phase (docking all the 400 MalariaBox compounds against all models), we have ranked lists of potential inhibitors for each receptor. But are these real? This is the kind of question that keeps us up at night.
Now we can rest easy - we've tested the top 20 hits using a model of the Plasmodial form of HDAC (histone deacetylase) in a laboratory (Dr Marian Brennan, RCSI, Dublin), and found THREE new inhibitors! So that's just one of the 1,500 receptors that we're docking, using only the best docking results (i.e. only the 20 best ligands).
It's a fantastic result, giving us hope that there are other gems waiting to be found in the data that you've generated on your home PCs!
Well done everyone!!!!!
ciao,
Ant
ps: We're in the process of writing up a manuscript for publication in an open-access journal, so you'll be able to read about all the details, and download all the data generated from FM@H, once we've survived the peer review process.
16 May 2013, 9:41:49 UTC
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No new tasks for 24 hours
Hi everyone,
We are going to turn off the work generator for 24 hours to clear the backlog of results.
Thanks to everyone who participated in the challenge.
Kevin
2 May 2013, 17:34:49 UTC
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Database Problem
Hi guys,
One of the tables in our task database has been corrupted. As a result we will be down for at least a few hours while we restore from a recent backup and ensure that we aren't missing anything. We will be back up and running soon.
Thanks,
Kevin
10 Apr 2013, 12:50:31 UTC
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Short downtime
Hi everyone,
We found a small bug in the assimilator daemon which prevented assimilation of WUs for about 2.5 days. We are now turning off the work generator to allow the assimilator to catch up. We will likely be up and running again at this time tomorrow.
Thanks,
Kevin
2 Apr 2013, 16:46:33 UTC
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New workunits in 24 hours
We will be deploying new workunits in the next 24 hours. Between now and then you will not be able to receive new WUs.
Kevin
24 Mar 2013, 18:05:44 UTC
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A few broken WUs
Hi guys,
We are cycling through some old WUs some of which contain errors. There only enough for about 12 hours of computation and things will be back to normal thereafter. This is just to finalize a set of completed experiments.
Thanks,
Kevin
9 Jan 2013, 17:25:57 UTC
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Short downtime
Hi Guys,
There will be a short downtime today due to a hardware fault. All currently running tasks will be completed but new tasks will not be issued. I hope to have everything running again in the next few hours.
Thanks for you patience,
Kevin
Edit:
Unfortunately it's going to take a little longer than expected. We will be back up and running in 24 hours.
Kevin
12 Nov 2012, 12:41:49 UTC
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Changes to the credit system
Hi everyone,
We are currently working on a new credit system which will ensure that everyone is awarded a fair amount of credit. The current system is failing as some users are receiving far more credits than others for the same amount of work.
To fix this we will predefine the amount of credit for each workunit. The amount will be based on a multiple regression of previous results from my own trusted hosts. It will likely be ready early next week.
Thanks to everyone who has pointed out these problems.
Kevin
edit:
I have hidden all other posts in this thread. Most posters have not broken any rules so please do not take offence this. We are switching to 1 credit per WU later today while we wait for the new system.
23 Oct 2012, 10:50:09 UTC
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No new jobs for 24 hours
We need to clear out the backlog that has accumulated in the validator, so we've stopped new jobs for a while. As soon as the server has caught up, we'll set new jobs going again. And early next week we'll purge the DB, so the server status should be back up and running again.
Thanks again for all your help and comments.
Ant
5 Oct 2012, 11:03:14 UTC
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Interview with Ant & Kevin
For those of you who want to see whose behind the icons:
http://www.ucd.ie/casl/newsmedia/caslmedia/title,135839,en.html
3 Oct 2012, 14:37:41 UTC
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Progress Report
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.
We have over 4 million results thus far, and % completion is as follows:
Progress has slowed as we're now docking larger molecules with more rotatable bonds.
Back Online
Hi Guys,
We're back online now. ~1.5 million dockings ready to go.
We still have some improvements to make and we will be making these over the coming weeks.
Thanks for your help!
Kevin
24 Aug 2012, 15:40:41 UTC
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Update
Hi everyone,
We're still having problems with the server. However, the good news is research IT have agreed to provide us with two far better servers. We hope to move the project to these over the weekend but it will likely be Wednesday before we are back up and running. We will not be sending new workunits until then.
Thanks for you patience,
Kevin
17 Aug 2012, 17:19:27 UTC
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Downtime
Hi everyone,
We have had some server problems. For this reason, we will not be sending new tasks for a few days.
Sorry for the inconvenience. We will be up and running again soon. New apps and workunits are coming soon too. The new apps should be a bit faster and compatable with a wider range of hosts, while the workunits will be significantly shorter.
Kevin
13 Aug 2012, 15:46:54 UTC
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Test experiment A is finished!
We have the first set of 144000 data points to sift through from our 'control' experiment. The system seems to be working well. The next batch of 1.2 million docking calculations is in the queue and ready to go.
27 Jul 2012, 23:33:07 UTC
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FMaH server will be down for about 12 hours
Sorry for the inconvenience, but we will not be sending out new tasks for the next 12 hours. We're still optimising the system and will need to go off-line occasionally until Monday 30th July.
25 Jul 2012, 15:23:52 UTC
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Update
Hi everyone,
We have a few updates:
1. We have regenerated our signing keys but due to a technical problem they will not be distributed automatically. Please detach and reattach to the project in order to receive new workunits. We apologise for the inconvenience and will ensure that it does not happen again.
2. We are having issues with a small percentage (less than 1%) of Windows computers and a very small percentage of Linux computers. We are working to release new app versions in order to address these problems.
3. We have limited the number of tasks in progress per computer to 20 per CPU core. Although this has not been an issue for some, we have had a large number of aborted tasks as a result of sending too much work to each node.
Thanks for your your help.
Kevin
23 Jul 2012, 17:45:22 UTC
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FM@H up and running
We have just fired off the first 144,000 docking runs.
If you'd like to see the details behind the 1,000,000,000 docking runs planned, please go to the 'Idea' page on our website:
http://www.fight-malaria.org/index.php?option=com_content&view=article&id=99&Itemid=108
After the first 94 million docking runs, we'll have achieved our first major milestone.
We may have a small delay next week between experiments, then it's all systems go.
Thanks again for your your help with this.
ciao,
Ant
20 Jul 2012, 18:08:58 UTC
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