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World Community Grid Forums
Category: Completed Research
Forum: Uncovering Genome Mysteries
Thread: What's the difference to SIMAP? |
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Thread Status: Active Total posts in this thread: 11
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AmigaForever
Cruncher Germany Joined: Aug 25, 2011 Post Count: 13 Status: Offline Project Badges: 
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Hello Torsten,
----------------------------------------hello Wim! When I read your project's description, I was wondering what the difference of your project is compared to the popular SIMAP. SIMAP is comparing protein sequences to find similarities. They already have a huge database which is used by many scientists around the world. I would like to put some computation power into this project, so please, can you point out what is different? Right now it looks to me that you are doing the same, only on a smaller scale.... Thanks!  [Edit 1 times, last edit by AmigaForever at Oct 14, 2014 9:53:31 PM] |
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Speedy51
Veteran Cruncher New Zealand Joined: Nov 4, 2005 Post Count: 1265 Status: Offline Project Badges: 
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I am not sure if you are aware but Simap is leaving Boinc at the end of 2014
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Crystal Pellet
Veteran Cruncher Joined: May 21, 2008 Post Count: 1316 Status: Offline Project Badges: 
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I am not sure if you are aware but Simap is leaving Boinc at the end of 2014 Leaving BOINC doesn't mean that the SIMAP-project will end: "SIMAP is currently moving towards new algorithms for similarity calculations and scoring. After extensive tests and evaluations during the last months it turned out that the best way to continue SIMAP will be to use dedicated local hardware in our institute."  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
The same question was asked when wim degrave's 'fiocruz comparing genomics' was launched, and reverse was also asked at simap. Overlaps and duplication are always a concern, the board who approved the project certainly checked same. It'd be nice though for this concern to be taken away, in a project faq in help if possible.
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Wu Shichao
Cruncher Joined: Jul 2, 2013 Post Count: 1 Status: Offline Project Badges: 
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"To kick off World Community Grid's 10th anniversary celebrations, we're launching Uncovering Genome Mysteries to compare hundreds of millions of genes from many organisms that have never been studied before, helping scientists unearth some of the hidden superpowers of the natural world."https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=385
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nasher
Veteran Cruncher USA Joined: Dec 2, 2005 Post Count: 1422 Status: Offline Project Badges:
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yes there might end up duplication from one project to another... dose not mean it will be useless... lots of good data either way...
----------------------------------------besides there are TONS of organisms... so they probably are starting in a different set.  |
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AmigaForever
Cruncher Germany Joined: Aug 25, 2011 Post Count: 13 Status: Offline Project Badges:
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"To kick off World Community Grid's 10th anniversary celebrations, we're launching Uncovering Genome Mysteries to compare hundreds of millions of genes from many organisms that have never been studied before, helping scientists unearth some of the hidden superpowers of the natural world."https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=385 Thanks for this, the bold sentence should have been included in the project description under https://secure.worldcommunitygrid.org/research/ugm1/overview.do There it is not that clear, it only points out that "most of the organisms in Earth's biosphere have yet to be identified, let alone understood at the genetic level.". I just would have preferred that the project description makes this issue more clear. And yes, I am fully aware of the status of SIMAP; I was just asking because I don't want to donate my computing power to something which has already been computed... anyway, I will give this project a shot. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi AmigaForever,
Simap has indeed the purpose of mapping protein similarities essentially from the public reference protein sequences and especially domains, resulting in a specific database/repository with very valuable research tools. Back in 2006/2007, the Genomecomparison project focussed on protein datasets from whole genomes, and the use of the rigorous ssearch algoritm for enhanced statistical confidence for inter-genome distance calculations and other applications, while Simap ran a much faster (directional hit detection) Blast implementation, in later years redoing the calculations similar to Genome Comparison. In the Uncovering Genome Mysteries project, we are concentrating much more on metagenomic sequences from environmental samples, containing mostly as yet unknown organisms. The project involves a very large dataset and aims at the discovery of new enzymatic functions, unusual metabolic pathways, and also pretends to shed more light on the ecological relationships and interactions between micro-organisms in specific niches. |
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Speedy51
Veteran Cruncher New Zealand Joined: Nov 4, 2005 Post Count: 1265 Status: Offline Project Badges:
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Thank you for the insight to what data we are looking at.
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AmigaForever
Cruncher Germany Joined: Aug 25, 2011 Post Count: 13 Status: Offline Project Badges:
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Hi AmigaForever, Simap has indeed the purpose of mapping protein similarities essentially from the public reference protein sequences and especially domains, resulting in a specific database/repository with very valuable research tools. Back in 2006/2007, the Genomecomparison project focussed on protein datasets from whole genomes, and the use of the rigorous ssearch algoritm for enhanced statistical confidence for inter-genome distance calculations and other applications, while Simap ran a much faster (directional hit detection) Blast implementation, in later years redoing the calculations similar to Genome Comparison. In the Uncovering Genome Mysteries project, we are concentrating much more on metagenomic sequences from environmental samples, containing mostly as yet unknown organisms. The project involves a very large dataset and aims at the discovery of new enzymatic functions, unusual metabolic pathways, and also pretends to shed more light on the ecological relationships and interactions between micro-organisms in specific niches. Hello Wim, first, let me say SORRY for my late response!  Second, thanks very much for the details about this research! You can count on my contribution. Many greetings! [Edit 1 times, last edit by AmigaForever at Jan 23, 2015 1:09:55 AM] |
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