[World Community Grid] NIEUW PROJECT!! HPF2

[priens]

Het langverwachte nieuwe project Human Proteome Folding phase 2 (HPF2) is gestart. Het is eigenlijk een verfijning van het werk dat bij HPF1 gedaan is. De meest interessante en/of belangrijke proteinen zullen nader worden bekeken bij een hogere resolutie. Hiervoor is ook een nieuwe versie van Rosetta ontwikkeld. (Rosetta crunchers, bedankt! ).

- Om je aan te melden voor de World Community Grid, klik hier
- Uiteraard niet vergeten om je aan te melden bij het goeie team (Dutch Power Cows)
- Om meer te lezen over HPF2, deze link, of over FightAIDS@Home dat ook nog steeds draait, hier.
- De dagelijkse DPCH is natuurijk ook in dit forum te vinden. Voor alle vragen kan je natuurlijk ook daar terecht.

Hieronder wat quotes van het forum.


Launch of Human Proteome Folding Phase 2 project

World Community Grid is pleased to launch Human Proteome Folding Phase 2 (HPF2). The goal of HPF2 is to compute higher resolution structures for proteins involved in malaria, recently identified cancer bio-markers, and other key proteins to help better understand their role in living systems and disease processes. For more detailed information and FAQs about HPF2, please press the Research button in the upper navigation bar or click here.

In addition to providing information about this project, we have created a forum for discussions on Human Proteome Folding Phase 2. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Human Proteome Folding Scientist" are authorized to comment as representatives of New York University (NYU).

HPF2 is one of two projects running on World Community Grid. The other project is FightAIDS@Home, which has been running since November of 2005. For more detailed information and FAQs about FightAIDS@Home, please press the Research button in the upper navigation bar or click here.

Because there are two research projects running on World Community Grid, your grid agent could receive work units from either project. You may elect to focus your computer's time on only one of the projects. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here .

HPF2 uses a program called Rosetta, which has been provided to World Community Grid by the project's sponsor, New York University (NYU) through a license with the Rosetta Commons and the University of Washington. Rosetta is a very large computer program and will not run on all PCs or laptops. To see the minimum system requirements for Rosetta, go to Help and search on "System Requirements" or click here . If your PC does not meet the minimum system requirements for HPF2 or FightAIDS@Home, then your agent will show a pause message until a project with smaller work units is available.

If you are already a member of World Community Grid, there's nothing that you have to do to prepare for HPF2. The next time your grid agent communicates with the servers, it will send you either a HPF2 work unit or a FightAIDS@Home work unit. The work unit your computer receives is determined randomly. To know which project you are running, please double-click on World Community Grid's icon in the system tray, and you will see the title of the project on the upper left-hand corner of the agent's homepage.

Members using the UD software will have the standard grid agent graphics showing on their grid agent. Members on the BOINC platforms, including Windows, Linux, and Mac, will not see a graphic on the BOINC Manager. We are working on providing graphics for BOINC and that should be ready soon.

If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the Help section of the website, (2) Review the forums to see if anyone has asked/answered the question that you have, (3) Ask the question in the appropriate member board Forums and a Community Admin or a more experience member will provide an answer, and (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website.

WELCOME FROM SCIENCE TEAM AT NYU ... AND THANKS IN ADVANCE

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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more details:
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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.

[Megaflix]

Ik zie heel vaak het woord Rosetta voorbijkomen. Is dit niet een soort tweede Rosetta@home of zo?

[priens]

Het komt er eigenlijk op neer dat WorldCommunityGrid een bepaalde versie van de Rosetta client (ik meen 5.50) gebruikt voor het HPF2 project. FightAIDS@Home maakt gebruik van Autodock.

Rosetta(@home) ontwikkelt de Rosetta client zodat WCG deze kan gebruiken, daarom krijgen jullie ook om de haverklap een nieuwe versie voor je kiezen. Uiteindelijk komt daar een versie uit die het best bruikbaar is voor WCG en deze wordt gebruikt.
Indirect helpt Rosetta@home eigenlijk dus ook mee aan WCG.
Daarnaast heeft Rosetta@home een aantal eigen projecten lopen die ook op de Rosetta client draaien.

Voor zover ik het goed begrepen heb uit posts van David Baker, is het hoofddoel van Rosetta@home het doorontwikkelen van de Rosetta client en daarnaast worden een aantal eigen projecten gedraaid. (correct me if I'm wrong).

[Kristof]

De uitleg van priens klopt inderdaad.
Op het Rosetta-forum loopt er ook een draadje over:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1863

[Verwijderd]

interrante thread met een behoorlijke hang-up aangaande de redundancy. Persoonlijk, zolang als er geen 100% herhaalbaarheids garantie is, sommige hebben 4 5 6 crunches nodig voordat een quorum van 3 gevonden wordt, denk ik dat het nodig is dat het statistische minimum van 3 blijft bestaan. Minder en je kunt gevoeglijk van GIGO spreken aangaande de kwaliteit van de database die nu opgebouwd wordt.

[Verwijderd]

Belangrijke ontwikkeling aangaande diverse fouten met het nieuwe projekt.....zal niet verbaasd zijn als de hele 12mb exe weer gezonden wordt bij eerstvolgende WCG contact van de Agent.

Re: Error this morning - World Community Grid : Unrecoverable error exit 1282 Reply to this Post

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There are a couple of errors in the HPF2 code that we are working on a fix for now and we expect to start development testing within the next hour or two for that fix. We hope to deploy that version to production within 24 to 48 hours. If this fix works as expected it should significantly reduce the errors.

The errors that we hope to reduce are as follows:

On Windows:

Exit Code 1282

Exit Code 10

Exit Code -1073741819

On Linux

Exit Code 1

We will not be able to know how much improvement we see until we have released the code into production and let it run for a couple of days.

We apologize for the error. Although we ran testing for an extended period (about 6 weeks) the fact of the matter is that all of you members processed more work in the first few hours after we launched then we had processed during our entire 6 week testing period. As such there were some conditions that we did not find during our testing.

As always - we thank you for your contribution and appreciate your support. It is your incredible contribution that makes it possible to process more work in a few hours then we can do in 6 weeks!

[Megaflix]

Lol, sommige van die exit-codes komen me bekend voor van R@H, vooral uit de beginfase daarvan

[Verwijderd]

Hier een post van Art Olson, een brein achter de 'modelling' van zoek algoritmes op ziekmakers. Dit is weliswaar op een FAAH draad, maar toch interessant.

Re: FightAIDS@Home performance Reply to this Post

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appreciate all of your thoughts about making our docking computations more efficient. We have been pondering this issue for some time. The problem is that the "search" that we are conducting in a very high dimensional space (in some cases upwards of 20 dimensions!). The process that we use for this search is stochastic -- that is we make random move in this large parameter space. How do we know that we've covered this space effectively? By running many dockings of the same ligand target pair with different random starting positions, and different random seeds for the docking, we can look at all of the results (usuallly 100 dockings) and cluster them to see if we hit the best energy consistently. If we do see significant clustering from the different runs, then we have some confidence that we have found the global optimum.

We have done some experiments to see if during a given docking we can terminate early if the best energy does not change over a number of "generations." We have not found a magic number yet that says that it it no longer useful to continue the docking -- but we are still looking.

Thank you all for your thoughtful remarks.

Art Olson
[Jul 7, 2006 6:22:11 PM]

@DePriens......hoe kreeg je dat bredere blauwe kader om een quote heen? Ziet er gelikt uit.....zeker was CSS code...maar welke.....bvd.....bedankt

[ Voor 13% gewijzigd door Verwijderd op 19-07-2006 18:32 ]

[priens]

Bedoel je dit?

Quote

Da's gewoon {quote} bericht {/quote} eromheen zetten. De "{}" vervangen door een "[]"

[ Voor 58% gewijzigd door priens op 08-07-2006 16:09 ]