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World Community Grid Forums
Category: Completed Research
Forum: Genome Comparison
Thread: 99% for a while now... |
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Thread Status: Active Total posts in this thread: 7
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Has anyone else noticed that the Genome comparison project should have reached and exceeded 100% a while ago? Somewhere around 3.8 million results should have been the limit, and now we're up around 4.2 million. Thanks!
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awpollak
Cruncher United States of America Joined: Jan 25, 2007 Post Count: 45 Status: Offline Project Badges: 
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This project just entered into its second phase.
----------------------------------------In a second phase, the initial dataset is being updated with newly published genomic data, adding 393,999 new protein sequences. Additionally, a fully curated reference dataset was added (SwissProt - 254,609 sequences), contributing to controlled annotation and data cross-referencing. Finally, an experimental dataset of about 3 million potential protein sequences derived from Open Reading Frames (ORFs) lacking a classical computational coding prediction was added, in an attempt to discover additional protein sequences or coding patterns. This second phase of the project is expected to take an additional 4 months of WorldGrid processing. This paragraph was taken from the Genome Comparison status update website. I believe that the old estimates (the pie chart specifically) only were about the first phase, which was scheduled to end in March. Now that we are transitioning into the second phase, we have more than the original 3.8 million comparisons to compute. The scientists on this project have a really good track record of updating their stats. Once the status update is made, the current progress will be more indicative of where we stand currently. [Edit 2 times, last edit by moped12 at Apr 3, 2007 9:27:28 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Well, I had read what you're saying about the second phase, but, other projects (like Human Proteome folding) opened a new project after the first was completed. If what you're saying is the case, I wonder why this project didn't. The fact that these scientists are so good about updating their progress page is the main reason why I'm posting. We were getting weekly updates for a while, and then at the culmination of the entire thing.. nothing. I just thought it was strange.
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
It may or may not have been explained in another post, but its the same science app as before with a small tweak. A new phase has always encompassed a material change on what or how it's processed.
----------------------------------------HPF is actually an exception with phase 2 truely being different and running at atomair level . FAAH went into a second phase (split in multiple experiments), but no new project was opened. Phase 3 AFAIK will be different and based on a new AutoDock and be presented as a separate project.
WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 1 times, last edit by Sekerob at Apr 4, 2007 12:19:16 PM] |
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Zigfried
Senior Cruncher Brazil Joined: Dec 12, 2005 Post Count: 368 Status: Offline Project Badges: 
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It may or may not have been explained in another post, but its the same science app as before with a small tweak. A new phase has always encompassed a material change on what or how it's processed. HPF is actually an exception with phase 2 truely being different and running at atomair level . FAAH went into a second phase (split in multiple experiments), but no new project was opened. Phase 3 AFAIK will be different and based on a new AutoDock and be presented as a separate project. I agree Sekerob. I think that they only start a new project when they will use a new software to perform a diferent kind of test but in this case we are only doing the same kind of test but with new proteins. I only wanna see the new pie to show our progress now. We had crunched 2.8 million in the first part and now we have something close to 3.65 million.  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Dear Colleagues,
When preparing our project we have thought that the computation of the similarity scores between all proteins included in the initial dataset would take longer than it actually has. When we realized that the progress was faster than expected (this happened in the beginning of the project), and after talking with the guys from IBM, we were offered the oportunity to include more material to be processed. This is what we are calling the "second phase", although, as already mentioned, it doesn't actually involves any kind of modification in the program. We included a manually curated dataset, which will be of great help in the validation of the automatic annotation process, and another dataset composed of open reading frames that may or may not be real genes, mainly due to their size. In other words, small genes may be "neglected" by gene prediction programs, but the verification of their presence in different genomes may be a strong argument for the confirmation of their existence as real genes. As for the progress pie, it could (and should) be reset to reflect this "new phase". Cheers, Antonio |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
thank you for the reply. maybe the 'progress pie' should be reset
---------------------------------------- [Edit 1 times, last edit by Former Member at Apr 9, 2007 9:05:33 PM] |
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