Posts by Ant Chubb
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1) Message boards : Number crunching : NO new work. (Message 2877)
Posted 9 Jan 2017 by Ant Chubb
Hi Dirk,

The no work part is due to me - I'm setting up new ligands for docking and it's taking a while (after hours only).

The no forum/teams is Rytis's remit - I'm confident he'll get this sorted out soon.

ciao,
Ant
2) Message boards : Number crunching : Very Sloppy (Message 2876)
Posted 9 Jan 2017 by Ant Chubb
Hi Ronald,

Apologies for this. The transfer of the server was supposed to be an easy affair, but clearly there are more teething problems. I've noticed major changes to the forum pages also - not sure why. I'm confident Rytis will fix this over the next few days/weeks.

Some of the delay is due to me holding up the pipeline. I'm trying to get new ligands set up and ready for crunching, but it's a slow manual process that I can only do after hours. Once the ligand libraries are ready there be LOADS of crunching available.

Thanks for your continued patience and support (and sorry to hear about the arthritis).

ciao,
Ant
3) Message boards : Number crunching : NO new work. (Message 2748)
Posted 22 Nov 2016 by Ant Chubb
We are starting to move over to GridRepublic in Boston who will host backend servers for the FiND@H project. In theory this this should happen automatically in the background, so don't be concerned about error notices (you might see in the client log that the new URL is compute.gridrepublic.org).

ciao,
Ant
4) Message boards : Number crunching : NO new work. (Message 2711)
Posted 20 Apr 2016 by Ant Chubb
Hi All,

Here's a brief update. We are finished with the main docking calculations and now need to analyse all the data from the full 19,000 compounds vs 1530 proteins in malaria, AND the TB work that we snuck in also. So loads of analysis needed on this side.

I'm now employed at a different institution - RCSI - but still have a toehold on the project through Ben who is still at UCD and whom I still see occasionally. The servers are all still running well in UCD, thanks to Ben. I have set up a strong collaboration with Matt Blumberg in Boston - a company called GridRepublic which uses BOINC-like computation for charitable work (Charity Engine). Matt has kindly offered to host the FiND@H project on his servers, so we'll find a safe place to keep this work going in the future. There are loads more pathogens out there, and we have a great system in place to identify novel targets, so I'm as keen as ever to keep this going.

We are applying for funding to set up an automated validation pipeline that will take the data from FM@H and send it directly into a robotic in vitro protein expression, purification and testing facility. Well that's the plan at any rate! It'll take us a while to get this set up (funding cycles, programming to connect to APIs, molecular biology protocol set-up and validation, etc.). But I'm very confident that each of these steps is feasible. We just need time and cash!
:-(

So please bear with us. We're trying to validate these virtual results in the laboratory so that we can safely tell the world about them. The initial data is already available here: http://chemware.ucd.ie/FiNDaH/Malaria.php.

But it would be unsafe to declare new targets without real laboratory based validation studies. If we do, we risk sending other scientists off in the wrong direction, which could waste valuable research funding (paid for by taxpayers).

Thanks again for all your help and support. When we transfer over to GridRepublic we'll tell you all about it on this forum.

ciao,
Ant
5) Message boards : News : 5,610,195 WUs (Message 2300)
Posted 30 Apr 2015 by Ant Chubb
Done. Not elegantly... but it's now there.

ciao,
Ant
6) Message boards : Number crunching : Wu last 3 hours instead of 14 min. (Message 2246)
Posted 8 Apr 2015 by Ant Chubb
Please cancel this WU. They should not run for more than 2-3 hours - tops. There is probably something wrong with that ligand file - we'll look into it and remove it from our lists.

Thanks for the feedback.

ciao,
Ant
7) Message boards : Number crunching : Beware of the monster (Message 2245)
Posted 8 Apr 2015 by Ant Chubb
Oh no! That should not be in there. We set a cut-off of 20 torsions. I'll try to remove this, but it may be too late for the WU queue. If you get this please cancel the job and we'll make sure it does not appear in any repeat WUs.

Sorry about that.

ciao,
Ant
8) Message boards : Science : Third WHO report on neglected tropical diseases (Message 2041)
Posted 27 Feb 2015 by Ant Chubb
Thanks Chris. Good point. Will connect in before moving forward on those.

ciao,
Ant
9) Message boards : Science : Third WHO report on neglected tropical diseases (Message 2007)
Posted 24 Feb 2015 by Ant Chubb
Wow! Thanks for that, Crystal. Nice to have a flag to rally behind. Hopefully this project will make some progress towards solving problem of developing novel antimicrobial agents in the 17 NTDs.

ciao,
Ant

Buruli ulcer
Chagas disease
Dengue
Dracunculiasis (guinea-worm disease)
Echinococcosis
Endemic treponematoses
Foodborne trematodiases
Human African trypanosomiasis (sleeping sickness)
Leishmaniases
Leprosy
Lymphatic filariasis
Onchocerciasis (river blindness)
Rabies
Schistosomiasis
Soil-transmitted helminthiases
Taeniasis and (neuro)cysticercosis
Trachoma
10) Message boards : News : FightMalaria@Home data now available online (Message 1680)
Posted 6 Jan 2015 by Ant Chubb
Hi all volunteers,

We have made a results website for easy access to the data we generated using the FM@H BOINC server. The first 400 MMV compounds (MalariaBox) data is available here:
http://chemware.ucd.ie/FiNDaH/Malaria.php

We're still doing the last repeat calculations for the remaining MMV19k and other datasets, the results of which we'll add to this website. We'll also add the TB data to this site, once we've cleaned it up and added orthogonal scoring data.

I had hoped to get the publication out prior to releasing this 'raw' data, but this is taking longer than I'd hoped. Once the paper is submitted I'll add a pre-print to the website also. The scoring functions will then make more sense.

Thanks again for your generous contributions to this project.

We're optimistic that someone, somewhere, will use this data to confirm our findings and provide the world with novel drugs... and new targets for further anti-malarial drug discovery.

ciao,
Ant
11) Message boards : News : FightNeglectedDiseases@Home server is up... and almost running (Message 1438)
Posted 26 Nov 2014 by Ant Chubb
Dear all,

The long awaited revamp of the FM@H server has finally happened - thanks to Benjamin. And thanks to the generous donations that we collected at the http://www.gofundme.com/1l0u2o website we were able to buy another SSD to build the FiND@H server on. This should be super-fast and will allow us to venture into different diseases beyond malaria, using the same 'whole genome docking' approach.

We should have the first work-units ready within a week or two.

Thanks again for your patience.

ciao,
Ant
12) Message boards : News : We're still chipping away at the data... (Message 1430)
Posted 13 Oct 2014 by Ant Chubb
Hi all,

Our project has a new burst of energy with a new PhD student (Ben) who will take over from Kevin. He's learning the ropes, and is the process of build the FiND@H server.

Thanks for your patience.

ciao,
Ant
13) Message boards : News : We're still chipping away at the data... (Message 1410)
Posted 17 Jun 2014 by Ant Chubb
Sorry to hear this. We are dormant, not defunct. A mixture of workload and holidays mean we won't be able to get anything going again before the end of July.
ciao,
Ant
14) Message boards : News : We're still chipping away at the data... (Message 1390)
Posted 15 May 2014 by Ant Chubb
We've just tested the new server with its new HD and it's failed us. PCIe fail. We're going to have to revert to the old machine using a new HD until we can get new hardware. Hopefully a little speed up there.

ciao,
Ant
15) Message boards : News : We're still chipping away at the data... (Message 1380)
Posted 25 Apr 2014 by Ant Chubb
Thanks Leopards!
We have just received the last piece of hardware we needed to revamp the donated servers, and Kevin has already installed a new version of BOINC on our shiny new SSD - all paid for through the generous support of our BOINC community! So thanks again to all those who donated money on top of CPU time.
Ciao,
Ant
16) Message boards : Cafe : FightTB@Home (Message 1370)
Posted 15 Apr 2014 by Ant Chubb
Thanks for that Thyme. Always motivating to know that our work may have a real impact in the future.
ciao,
Ant
17) Message boards : News : We're still chipping away at the data... (Message 1347)
Posted 3 Apr 2014 by Ant Chubb
Small steps...

We have managed to get agreement from the IT department here to host our new (second hand) servers, and have thus purchased an SSD drive today to install in the main node.

So hopefully we'll be up and running again soon.
['soon' being my new least favourite word!]

ciao,
Ant
18) Message boards : News : We're still chipping away at the data... (Message 1342)
Posted 27 Mar 2014 by Ant Chubb
Hi Aurel,

Good news: the FiND@H transfer should be painless and everyone's accounts should move over directly.

And I'll tell people which diseases we're setting up, and will happily accept suggestions also. So far we've only done Malaria work, and have the whole TB genome ready to go.

Bad news: We tried to build a GPU version of Vina, but failed. As far as we know nobody's managed to make one yet. If we get hold of one we'll add that in as an option. Similarly, we could not re-engineer Vina for checkpointing, so that's also reached a dead end.

ciao,
Ant
19) Message boards : News : We're still chipping away at the data... (Message 1335)
Posted 24 Mar 2014 by Ant Chubb
yep - pretty scary that a person gets infected with TB somewhere in the world EVERY TWO SECONDS! Would be fantastic if we could come up with new drugs to combat this horrid disease. Sadly the server install and reconfigure is taking longer than we'd hoped. But it's great that the enthusiasm to help is still strong. Please bear with us for a bit longer, and I can assure you there will be millions of docking calculations to do. They are ready to go... as soon as the server set-up can be finalized.
ciao,
Ant
20) Message boards : News : We're still chipping away at the data... (Message 1328)
Posted 19 Mar 2014 by Ant Chubb
Hi Brian,

Kevin will hopefully be able to change the name of the FM@H server directly, so no one will need to do anything... hopefully!

Thanks,
Ant


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