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HPF2 Begins |
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Topic: HPF2 Begins (Read 11860 times) |
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From Dr Bonneau at WCG...
HI FROM THE NYU CENTER FOR COMPARATIVE FUNCTIONAL GENOMICS!
ok, i'm a bit excited ...
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.
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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.
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Thanks for the heads up, you sneaky little mouse  |
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Wonderful news, higher resolution is almost always good. And in this case I am certain it will be.
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I can think that than which a greater cannot be thought. Now, if that than which a greater cannot be thought existed only in the intellect, it would not be that than which a greater cannot be thought, since it can be thought to exist in reality which is greater. It follows, then, that that than which a greater cannot be thought exists in reality.  |
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The HPF2 agent is initially a 9+ Mb download and includes a surprize, a cpu throttle that automatically maxes cpu usage @ 60% forthe agent. If you runs any apps, the % will drop even further, even down to 0%. There's more info about this plus a tool download so that you can control cpu usage your self at the WCG forums.
Note: The cpu throttle only applies to those using ud software. BOINC is not affected.
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The Phase 2 units are very fast. All I've had so far finish in around 2 hours. Pretty quick for a 1 meg d/l.
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Some people are reporting inconclusive results and errors with the new work units. I've had 2 out of 3 not complete with a valid result. I'm going to wait on running any more until they get the bugs ironed out. For those running BOINC, keep an eye on your results and be sure you're returning valid ones.
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Is there some way to identify the HPF2 WUs by name? I'm using BOINC client to do my WCG. I'd like to know what type of work I'm doing.
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I can think that than which a greater cannot be thought. Now, if that than which a greater cannot be thought existed only in the intellect, it would not be that than which a greater cannot be thought, since it can be thought to exist in reality which is greater. It follows, then, that that than which a greater cannot be thought exists in reality. |
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If you open your BOINC manager you click on the "work" tab. You'll see under "Application" a listing for hpf2 5.06 if you're running the HPF2 units. Next to that is the name of the work unit itself.
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Some people are reporting inconclusive results and errors with the new work units. I've had 2 out of 3 not complete with a valid result. I'm going to wait on running any more until they get the bugs ironed out. For those running BOINC, keep an eye on your results and be sure you're returning valid ones.
Completed 7 so far and got credit for all. |
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Good to hear you're getting all good results, John. Hopefully the problem work units are a small percentage.
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These units do act a little strange. Just saw one go to 23 minutes with 0%, then suddenly jumped to 16%. The completion comes in chunks.
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Yes, the save points seem to be infrequent as compared to hpf1 units. What version of BOINC are you running?
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I run the ud software. Don't like the idea of waiting days for results to get credited. Also don't entirely trust the boys at Berkeley. SETI has been a mess since switching to that platform and I've heard of other dc projects that use BOINC have had some troubles too.
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Gotcha, John. I think the UD software credits for all work, though, so you can't be sure if they are valid results. Is that right?
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You're probably right but it makes no difference to me. Whether the results are valid or not, I spent the time crunching them. Someone over at WCG said even invalid results are important so even better.  |
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Just had my first uncredited workunit of HPF2. Shades of Grid!!! Apparently, the ud software works the same as BOINC as far as not giving credit for aborts goes. Switched all back to AIDS. This has been very stable and has never had a bogus result. Looks like the guy who wrote HPF2 went to the same school as the idiot who created the train wreck Cancer project over at grid, Clown College.  |
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Say whatcha think, why don'tcha?  |
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I use boinc and the invalid ones I've got I got points for. The others that messed up I didn't.
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This should help. We have released version 5.07 of the code for the Human Proteome Folding - Phase 2 project on BOINC. This version should resolve a number of the problems members have been experiencing. In particular it should significantly reduce the occurance of the exit code 1282 and and exit code -1073741819 errors.
BOINC users will automatically recieve the new version when the client connects to the server to download new workunits. If you wish to get the new version of the application immediately, then you can reset the project (open the BOINC Manager, go to the Projects tab, select 'World Community Grid', and then click on the 'Reset Project' button).
We apologize for these problems and appreciate your patience and support while we resolve them |
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Thanks for the update, phicks. Error 1282 is the one that I got. Nice fast response from WCG.
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I just had one lock up my system and force me to reboot before it would continue. Yesterday I had one turn sour on me on one of my other (non-oc'd) systems. Had to abort it before I could get anything else.
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 "Build a man a fire, and he'll be warm for a day. Set a man on fire, and he'll be warm for the rest of his life." -Terry Pratchett |
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I'm getting all HPF2 via BOINC now. Haven't noticed any issues so far.
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I can think that than which a greater cannot be thought. Now, if that than which a greater cannot be thought existed only in the intellect, it would not be that than which a greater cannot be thought, since it can be thought to exist in reality which is greater. It follows, then, that that than which a greater cannot be thought exists in reality. |
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Personally, I have 20 hours of crunching that have led to: Inconclusive Invalid Other LOL! 18 hours in "Pending Violation, er, Pending Validation" Ehhh, it will show soon. Other?  How is this for more descriptions? "Sorry, we were disenterested" "It seems that you were ticketed for a parking violation". "Really? You expect this to be validated?" "Uh, we were watching NetFlix, sorry!" "Your Results were given a Yellow card". LOL! Ok, more "descriptions" needed here.  |
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"Always try to be modest. And be damn proud of it!".
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