Human Proteome Folding Project (HPF2) launched


V_R

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An update from WCG.

header-bonneauLab.jpg


HPF2 is launched. This is very exiting to me and to my lab members. We’ve been working with IBM for a while now and were very excited when they told us that we could put this project on the grid.

HPF2 is different from HPF1, but in a way that might not mean much to those who don’t think about structure prediction. HPF2 is a higher resolution version of HPF1. In HPF1 we modeled the protein at the level of overall shape (each part of the molecule was represented by a few atoms). In HPF2 we try to model all atoms in the protein and use a mode of Rosetta that pays attention to roughly twice the number of atoms modeled in HPF1. This means we have to spend more compute time per protein and that we have to narrow our focus for HPF2.

If you’re new to HPF then check out the FAQ for HPF2 and HPF1. There is a lot of information in the descriptions of HPF2 that refers back to HPF1 so check out the HPF1 faq and description first if your interested.


I’ve also pasted a prior post below:


HPF phase II:

HPF phase-2 will refine, using Rosetta in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the Human Proteome Folding Project (HPF phase1). The project will focus on human secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the pro-teins). The project will also focus on key secreted pathogenic protein. This project dove-tails with efforts at the ISB in Seattle to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future).

This project continues where the Human Proteome Folding Project leaves off. With the Human proteome Folding project we aimed to get protein function. With the second phase we would aim to increase the resolution of a select subset of Human proteins. Better reso-lution is important for a number of applications including but not limited to virtual screening of drug targets with docking procedures and protein design. The second phase of the pro-ject will also serve to improve our understanding of the physics of protein structure and ad-vance the state of the art in protein structure prediction (help us to further develop our program, Rosetta).

The two main objectives are to: 1) obtain higher resolution structures for specific hu-man proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta structure prediction. Thus, the project would ad-dress two very important parallel imperatives, one biological and one biophysical.

The Human Proteome Folding Project Phase-2 will use the computer power of millions of computers to predict the shape of Human proteins for which researchers currently know little. From this detailed shape scientists hope to learn about the function of these proteins, as the shape of proteins is inherently related to how they function in our bodies. This data-base of protein structures and putative functions will let scientists take the next steps un-derstanding how diseases that involve these proteins work. Proteins are the most important molecules in living beings. Just about everything in your body involves or is made out of pro-teins. Protein structure is key to understanding the functions of this diverse class of bio-molecule. Thus we hope that our work on HPF 1 and HPF 2 will contribute to critical pub-lic infrastructure to the biological and biomedical community.

http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=7702

:)
 
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Adywebb

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Keep an eye on these units results....

This is great news - however i would urge eveyone to check their results progress with these work units as a few folks over at WCG are reporting 'inconclusive' results with these units on machines where they had no problems previously.

I have run a check on a couple that I have recently completed and found one where everyone returning the result is 'inconclusive' so far.

This would suggest to me there may be some teething problems with the work being sent out.
 

muckshifter

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Doh ... me Vista is getting No Server access.

:(
 
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whats up

2 out of 4 units crunched so far today have returned as inconclusive:(
The unit i have just started has 3 other users who have crunched this work as being inconclusive. Will this new unit go the same way:confused:
 
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Adywebb

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Heres what one of the CA's has said over at WCG:

Usually the first month of running a new project brings up a few points that need adjusting in the program. I expect the staff will investigate any work units that are inconclusive or error out to try to determine what is happening. I have no idea what is wrong, but I expect this in a new project. My HPF2 units have all gone through. Although I notice there are very few check points. This is a bad project for stop-and-go computing

From that I would suggest we may well have some problems for a while - for those having problems it may be worth selecting (e-mail address removed) units only for a while, especially those who stop/start or don't run 24/7??
 
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muckshifter

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... and I am having all sorts of problems with Vista & Boinc ... I may as well give UD a try out. :rolleyes:

:(
 

Adywebb

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Has this just started then Mucks - was it running OK with Vista before?
 

muckshifter

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Adywebb said:
Has this just started then Mucks - was it running OK with Vista before?
Yes, no, yes, no ... sometimes. :D

Installed TrendMicro AV today, is the only AV that has a beta out for Vista that works ... well err, it don't work ... now it won't un-install either. Bonkit cannot access the server and keeps telling me to set it up ... well, there is no set-up?

I'm a stubborn old bat but this is getting on my tit ... I have been having a laugh at all the idiots that put Vista on their main PCs though. ;)
 
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Adywebb

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Could be Trend blocking access then??

As you say, its good to be able to play with it away from the main machine - wonder how those who put it on their main ones are getting on, lets hope there really frustrated :D
 

muckshifter

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Adywebb said:
Could be Trend blocking access then??

As you say, its good to be able to play with it away from the main machine - wonder how those who put it on their main ones are getting on, lets hope there really frustrated :D
Yep, it is probably Trend that kicked it into touch ... trouble is now, I cannot uninstall Trend, it messed up, and Bonkit still refuses to 'find' the server ... no other problem connecting to the internet though. Well, not too many problems. :D
 
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The Inconclusive is not necessarily an idication of a problem. Just maybe those units are inconclusive. We had that issue way back with HPF1 for a while. Points will be awarded for the inconclusives as usual.
 
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I had the exact same issue as you Muckshifter, although i just reformatted, as Trend just wouldn't budge from Vista.

All the antiviruses are a bit naff and broken for Vista at the moment, regardless of what the supplier tells you.
 

muckshifter

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RapidEight said:
I had the exact same issue as you Muckshifter, although i just reformatted, as Trend just wouldn't budge from Vista.

All the antiviruses are a bit naff and broken for Vista at the moment, regardless of what the supplier tells you.
Very true indeed, but I keep trying ... I'm a glutton for punishment.
laughingsmiley.gif



As it turns out, it was nothing to do with any AV or Firewall blocking ... ALL my damn PC ar now 'backing off' 'cos they cannot find the server.

:mad:

As a side note ... restore works very well.
nod.gif
 
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Adywebb

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muckshifter said:
As it turns out, it was nothing to do with any AV or Firewall blocking ... ALL my damn PC ar now 'backing off' 'cos they cannot find the server.

:mad:
Thats not good :( - just checked at my end and I seem ok - is this BT playing around with you again??
 

muckshifter

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Adywebb said:
Thats not good :( - just checked at my end and I seem ok - is this BT playing around with you again??
Nope ... they all connect, but ...

26/06/2006 5:56:03 am|World Community Grid|Scheduler request failed: a timeout was reached
26/06/2006 5:56:03 am|World Community Grid|Deferring scheduler requests for 2 hours, 10 minutes and 57 seconds
26/06/2006 5:56:04 am||Access to reference site succeeded - project servers may be temporarily down.
Now the 'funny' thing is they now all have got work & crunching ... I cannot find anything at WCG about it, so I'm still not sure if it is a problem at my end or not?????????

This all started last night just before my bedtime ... :rolleyes:
 

Adywebb

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What was the scheduler request for - to report a result or to fetch new work?

I had one at 0538 to fetch new work, and again at 0558 to report a result which both went fine:confused:

What did it say 2 hours 10 minutes later when it tried again?
 
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muckshifter

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Ady ... don't worry about it, I ain't, it's only a few points. ;)

26/06/2006 5:56:04 am||Access to reference site succeeded - project servers may be temporarily down.
26/06/2006 6:39:33 am|World Community Grid|Started upload of file za058_00070_1_0
26/06/2006 6:39:45 am|World Community Grid|Finished upload of file za058_00070_1_0
26/06/2006 6:39:45 am|World Community Grid|Throughput 21188 bytes/sec
26/06/2006 8:07:04 am|World Community Grid|Sending scheduler request to https://secure.worldcommunitygrid.org/boinc/wcg_cgi/fcgi
26/06/2006 8:07:04 am|World Community Grid|Reason: To report completed tasks
26/06/2006 8:07:04 am|World Community Grid|Requesting 432 seconds of new work, and reporting 1 completed tasks
26/06/2006 8:07:09 am|World Community Grid|Scheduler request succeeded
26/06/2006 8:07:11 am|World Community Grid|Started download of file faah0656_d426cb071_x1hpv_00_x1hpv.pdbqt
26/06/2006 8:07:11 am|World Community Grid|Started download of file faah0656_d426cb071_x1hpv_00_d426cb071_x1hpv_00.gpf
26/06/2006 8:07:13 am|World Community Grid|Finished download of file faah0656_d426cb071_x1hpv_00_d426cb071_x1hpv_00.gpf
26/06/2006 8:07:13 am|World Community Grid|Throughput 1015 bytes/sec
26/06/2006 8:07:13 am|World Community Grid|Started download of file faah0656_d426cb071_x1hpv_00_faah0656_d426cb071_x1hpv_00.dpf
26/06/2006 8:07:14 am|World Community Grid|Finished download of file faah0656_d426cb071_x1hpv_00_x1hpv.pdbqt
26/06/2006 8:07:14 am|World Community Grid|Throughput 69486 bytes/sec
26/06/2006 8:07:14 am|World Community Grid|Finished download of file faah0656_d426cb071_x1hpv_00_faah0656_d426cb071_x1hpv_00.dpf
26/06/2006 8:07:14 am|World Community Grid|Throughput 3657 bytes/sec
26/06/2006 8:07:14 am|World Community Grid|Started download of file faah0656_d426cb071_x1hpv_00_AD4_parameters.dat
26/06/2006 8:07:14 am|World Community Grid|Started download of file faah0656_d426cb071_x1hpv_00_d426cb071.pdbqt
26/06/2006 8:07:16 am|World Community Grid|Finished download of file faah0656_d426cb071_x1hpv_00_AD4_parameters.dat
26/06/2006 8:07:16 am|World Community Grid|Throughput 3544 bytes/sec
26/06/2006 8:07:16 am|World Community Grid|Finished download of file faah0656_d426cb071_x1hpv_00_d426cb071.pdbqt
26/06/2006 8:07:16 am|World Community Grid|Throughput 1827 bytes/sec
26/06/2006 8:07:17 am||Rescheduling CPU: files downloaded
26/06/2006 8:07:17 am|World Community Grid|Starting task faah0656_d426cb071_x1hpv_00_2 using faah version 509
as you see ... now all is working, and, on all PCs. :thumb:

:)
 

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