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Message boards : Graphics cards (GPUs) : Special request + Ignasi's Masters thesis defense (June 19th)

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ignasi
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Message 10580 - Posted: 15 Jun 2009 | 14:58:13 UTC

Dear crunchers,

I have an unusual request to make you. In a normal situation we would never ask you to manually prioritize one WU versus another, because that's something we can more or less manage with BOINC's priority settings. But this time is different. Let me tell you why.

Since I started to work on this project, I have been working with the SH2/ligand complex system to find a way to be able to systematically calculate accurate binding affinities between proteins (that is how strong they interact with each other) in a semi-automated manner, for many protein pairs at a time. It has been hard to get with proper settings for the approach but finally, we think we are about to have the results that can prove it. Then it will be a matter of reinforcing our statements by adding extra calculations and measurements to the current results.
My Masters thesis was somehow bound to proving that we could calculate these binding affinities for several different configurations of the SH2 protein and ligand (the shorter piece of protein). By the time I had to submit the report we just had one preliminary result to show. But yesterday, I got to submit three more simulations (batches of WUs for you) which would be very cool to show at the thesis defense (if they happen to be correct!).

The actual request is that IF you have the chance of prioritizing any WU over an other, could you please prioritize the following ones ONLY during this week?

*-IBUCH_pYEEI_1406-*
*-IBUCH_pYEpYI_1406-*
*-IBUCH_pYIpYV_1406-*

And if you find two of the same batch, please give priority to those with the lower number following the tag, i.e:
*-IBUCH_pYEEI_1406-0-10-* over *-IBUCH_pYEEI_1406-1-10-*
Which means "current step (0/1) out of total (10)".

(there is no need to cancel anything that is running already!!! Above all, loose NO credits at all)

I would really appreciate it and as always, I'd properly credit you guys for all the effort ;).

Many thanks again and I'll keep you informed,
ignasi

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Message 10581 - Posted: 15 Jun 2009 | 16:16:17 UTC - in response to Message 10580.

Ok, no problem, but I thing only few of crunchers read this forum...
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Message 10587 - Posted: 15 Jun 2009 | 20:16:21 UTC - in response to Message 10581.

Ok, no problem, but I thing only few of crunchers read this forum...


maybe we can quote ignasi message to our team forums ;)

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Message 10588 - Posted: 15 Jun 2009 | 20:23:38 UTC - in response to Message 10587.

maybe we can quote ignasi message to our team forums ;)


That's the way to go. Plus it's got to be short and quickly understandable news on the homepage (and can be removed after Friday).

Good luck, mate!
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Message 10593 - Posted: 16 Jun 2009 | 0:52:30 UTC - in response to Message 10580.

Great idea - I'm up for it, its a small reciprocal for all you do for us - good luck on the Thesis Defence.

I've also posted it to the Team England Board as per [FVG]bax's suggestion, I'm sure the guys will pitch in if they see it.

Regards
Zy

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Message 10600 - Posted: 16 Jun 2009 | 12:47:57 UTC - in response to Message 10580.

I would really appreciate it and as always, I'd properly credit you guys for all the effort ;).

Many thanks again and I'll keep you informed,
ignasi


I bet you say that to all the crunchers :)

I have suspended a couple of KASHIF_HIVPR and Seti cuda tasks so as to get some through sooner for you. I have about 6 cooking at the moment.

Good luck with the thesis defence.
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ignasi
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Message 10605 - Posted: 16 Jun 2009 | 14:28:16 UTC - in response to Message 10600.

Many thanks for your enthusiastic response guys.

I'm already analyzing the first results as they come in... it's too early to say much but at the moment the energies of the interaction seem too high (sigh!) but let's let the ligands cool down a bit with further time (steps X over 10) and see where they head to...
Just in case though, I am already preparing more simulations with some variations that may relax the energy of the interaction although they wouldn't be ready for Friday in any case... but c'est la vie.

Anyhow, let's see how the current ones do.

Salut!
ignasi

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Message 10642 - Posted: 18 Jun 2009 | 10:08:14 UTC - in response to Message 10605.

I finally saw your request, but all my CUDA workunits currently appear to be of this type already.

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Message 10643 - Posted: 18 Jun 2009 | 10:34:46 UTC - in response to Message 10605.

most of my WUs are also types
*-IBUCH_pYEEI_1406-*
*-IBUCH_pYEpYI_1406-*
*-IBUCH_pYIpYV_1406-*
have done 4 and 1 more later tonight.
if you want some more done please direct them to me as will be able to do 6 WUs a day
Cheers
Ross
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Message 10689 - Posted: 19 Jun 2009 | 17:13:25 UTC - in response to Message 10643.
Last modified: 19 Jun 2009 | 18:11:57 UTC

Dear crunchers,

Many thanks to all. We can almost say that WE (you and me) got a Masters degree in Biomedical Informatics. It's not official yet but the defense was quite straightforward :). Next stop, the PhD... (sigh!)

About the results I wanted to fit in a hurry into the presentation, they didn't finally appear due to time constraints. The discussion for these results resulted a bit complex and we had 15' for everything else so it was simply impossible to fit them in.

Regarding these results themselves, the energies of the interactions were too high to use them 'out-of-the-box' and say 'we have the right values, pack and let's go on vacation'. BUT the simulations actually helped us understanding how sensitive it is to play around with the small peptide when being very close to the protein, in the sense that many unspecific interactions will occur leading to an overestimation of their 'total' attraction.
I have already submitted new experiments in this sense. Back to normal priorities now.

I intend to explain in plain words the whole approach for the calculations of binding affinities in the science section soon. Now I'll have more time for it.

By the way, people outside the DC/BOINC world is still amazed that a relationship science/society like this functions at all.
The star question is 'but... what do the volunteers do it for?', 'They do it for love' -I reply-.

happy weekend,
ignasi

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Message 10695 - Posted: 19 Jun 2009 | 19:34:10 UTC - in response to Message 10689.

Congratulations! Now it's time to relax a bit.. the next period of constant stress will come by itself ;) But I think it's a good idea to do the PhD while GPU-Grid and molecular dynamics are still hot.. so good luck with that!

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Message 10714 - Posted: 20 Jun 2009 | 6:35:34 UTC - in response to Message 10689.

Dear crunchers,

Many thanks to all. We can almost say that WE (you and me) got a Masters degree in Biomedical Informatics.


WOW, my 2nd degree... without so much work ! :-D


Congratulations Ignasi !!!!

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Message 10726 - Posted: 20 Jun 2009 | 12:03:33 UTC - in response to Message 10689.

We can almost say that WE (you and me) got a Masters degree in Biomedical Informatics. It's not official yet but the defense was quite straightforward :). Next stop, the PhD... (sigh!)


Congratulations. Hmm a PhD, I can see some more work coming...

By the way, people outside the DC/BOINC world is still amazed that a relationship science/society like this functions at all.
The star question is 'but... what do the volunteers do it for?', 'They do it for love' -I reply


Yes some of us crunchers wonder why too :-)

All the best
MarkJ
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Message 10733 - Posted: 20 Jun 2009 | 20:14:05 UTC - in response to Message 10726.
Last modified: 20 Jun 2009 | 20:15:39 UTC

Hmm a PhD, I can see some more work coming...

oooooh - you mean we get a phd as well? My old maths teacher would never believe it ...... :)

By the way, people outside the DC/BOINC world is still amazed that a relationship science/society like this functions at all.

The star question is 'but... what do the volunteers do it for?', 'They do it for love' -I reply

Yes I do believe many do, people help people, and in that a sense of appreciation goes a long way - the latter is sorely missing in the current world of bonus driven frenetics.

Primarily though, I believe most do it for a sense of achievement, even if they dont initially realise it. In todays world results are all, speed is everything - do it right, do it by yesterday, not being able to read management teams minds is fatal, you made a minor/major mistake - you die :)

yaddie yadda.

To be able to take part in an event that achieves results, helps others achieve what they are searching for, and see the end result knowing "we did that", presses all the buttons most people have - and they are actually the same buttons that those who wonder why Crunchers do it also have, its just ours are pressed in a different way .... outcome is the same.

Regards
Zy

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Message boards : Graphics cards (GPUs) : Special request + Ignasi's Masters thesis defense (June 19th)

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