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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding
Thread: Progress of WGC |
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Thread Status: Active Total posts in this thread: 10
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barney15c
Advanced Cruncher Joined: Feb 17, 2005 Post Count: 103 Status: Offline Project Badges: 
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Its been a while since the last update on progress of HPF, have we hit 40% yet ?
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nerd01
Cruncher Joined: Mar 19, 2005 Post Count: 41 Status: Offline |
I've found a post by Viktors (WCG Tech):
----------------------------------------We don't have an exact number for how far along the project is because of various factors. However, based on certain assumptions, the Human Proteome Folding Project is at least (about) 45% done, by my estimate. World Community Grid has contributed about 3/4 and grid.org about 1/4 of the completed results so far. Looks like we're doing quite well...  Your team mate, |
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barney15c
Advanced Cruncher Joined: Feb 17, 2005 Post Count: 103 Status: Offline Project Badges:
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I've found a post by Viktors (WCG Tech): We don't have an exact number for how far along the project is because of various factors. However, based on certain assumptions, the Human Proteome Folding Project is at least (about) 45% done, by my estimate. World Community Grid has contributed about 3/4 and grid.org about 1/4 of the completed results so far. Looks like we're doing quite well... Your team mate, Certainly does! I assume that although grid.org has over 3m devices they must be concentrating their effort on the cancer research project - hence them contributing 1/4 of the HPF results. Thanks for this. Your team mate, Barney15c |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
here are the project stats for both grid HPF project:
grid.org 16298 years of total run time 104 years run time a day 22h 35min avg time per result wcg 8341 years of total run time 39 years avgerage run time per day 10h 32 min per result obviously the wcg has faster devices associated with it. This might be due to the fact that thier is more corporate participation in wcg and they tend to refresh computer hardware every 2 to 3 years. grid.org is made up of mostly individuals who tend to dedicate unused older systems they retrieve from attics and basements to donate to the grid 24/7 |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
So what's the total number of years that we are trying to hit?
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Well, years aren't the real measure. Still, current statistics show 8, 518 years of run time. If the guess a while ago was that we were 45% through, then 2 1/4 * 8,000 = 18,000 years might be a ball-park figure. Looking at http://www.systemsbiology.org/symposium2005/schedule.html I see that the closing comments at the Fourth International Symposium at the ISB in Seattle, Washington, USA were scheduled to begin half an hour ago. So hopefully we shall get some additional information during the coming month.
mycrofth |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
It's real open ended as far as any tangible progress towards the end of the project.
You also have to take into account thier wasnt 100,000 devices connected to this grid back in 2004. So the progress is really hard to measure since you have non deterministic workunits and a constantly changing device grid. I guess they (ISB and the other people) wanted to survey the entire human genome of 100,000 protiens. So an educated guess would be 45,000 protien sequences predicted into structure. Going way out on a limb with this one. Suppose I will get spanked for such a macho assertion. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Spanking is not my way, Bruce.
 But if you look at the thread 'Protein Folding Overview - For Those Who Are Curious - A Facinating Read' and move down to the post titled 'Re: Protein Folding and RNA', you will read that several different proteins can be produced from a protein-encoding gene. So we are trying to fold more proteins than there are protein-encoding genes. We will probably end up with at least twice as many proteins folded as you are predicting. I am cheating, incidentally.  David Autumns has found an early newswire from the ISB Symposium announcing that we have already predicted 50,000 protein structures.  mycrofth |
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barney15c
Advanced Cruncher Joined: Feb 17, 2005 Post Count: 103 Status: Offline Project Badges:
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Spanking is not my way, Bruce. But if you look at the thread 'Protein Folding Overview - For Those Who Are Curious - A Facinating Read' and move down to the post titled 'Re: Protein Folding and RNA', you will read that several different proteins can be produced from a protein-encoding gene. So we are trying to fold more proteins than there are protein-encoding genes. We will probably end up with at least twice as many proteins folded as you are predicting. I am cheating, incidentally. David Autumns has found an early newswire from the ISB Symposium announcing that we have already predicted 50,000 protein structures. mycrofth Here is the Link David Autumns found: http://home.businesswire.com/portal/site/goog...425006124&newsLang=en The total number of structures will be between 100000 and 150000 according to the item. [Edit 1 times, last edit by barney15c at Apr 26, 2005 4:13:43 AM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I might owe Bruce an apology. Looking at the abstract for the NYU Seminar that Dr. Bonneau is giving on Wednesday, 27 April 2005, that I have copied to http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2064#16411
Human Proteome Folding Project: It may be that the estimate that 100,00 - 150,000 folded protein predictions will result from our project includes the proteins of some major human pathogens. If so, it's great with me. [Take that, M. falciparium!] But it means that I have more questions for Dr. Bonneau, if he ever gets over his jet lag.Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. I have previously shown that Rosetta de novo structure prediction can be used to predict three-dimensional structures for proteins of unknown function and that those predicted structures can be used in a systems biology context to glean biological insight into protein function. Rosetta de novo structure prediction is quite computationally intensive and we have implemented a distributed computing strategy that currently employs over 3 million devices globally in collaboration with United Devices and IBM. We have begun folding on the grid, using Rosetta, all relevant protein domains in all fully sequenced genomes (including the Human genome and the genomes of all sequenced major Human pathogens). The results from this effort will be publicly available. mycrofth |
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