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

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

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

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

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

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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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

Dear crunchers,

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

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