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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding
Thread: Feedback on how we are doing |
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Thread Status: Active Total posts in this thread: 11
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
It would be nice to know how much has been done on HPF.
Also, if it's not classified information, how many of us are crunching HPF and how many FightAids (in %)? |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
It would be nice to know how much has been done on HPF. Click on 'About Us' - 'News and Media' - 'Newsletter - November 2005'. There is an article about the HPF project in the newsletter. Also, if it's not classified information, how many of us are crunching HPF and how many FightAids (in %)? Click on Statistics - By Projects, and then click on each project. You will probably want a calculator to convert the figures into percentages. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I read through that information as well and now have a question myself. Sorry if this has been mentioned already somewhere but I couldn't find any information about this anywhere. Any idea how many workunits are left for this project or any kind of time frame on how much longer this project will be around? I currently have my preferences set to run both projects but depending on how much is left I'm thinking of changing it to HPF only as the sooner that's completed the sooner that collective information can be of possible benefit to humanity.
----------------------------------------[Edit 1 times, last edit by Former Member at Dec 15, 2005 1:27:30 AM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello jsprague78,
We have finished all the human proteins. As far as I know, we are currently working through the 10 batches from Arabidopsa, a small inedible mustard plant. For some reason, back in 2000 plant biologists settled on Arabidopsa as their preferred plant for genomic studies so they could more easily cooperate (and compete) with each other while studying basic plant processes. Here is Dr. Bonneau's most recent update on 21 Nov 2005: http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=4708#36738 The first paper to come out of the project is in late draft stages. So there is no hold up being caused by the additional genomes, such as Arabidopsa, that we dumped into the hopper for crunching.An old military maxim runs: 'Reinforce success, starve failure.' We regard the HPF project as successful, and have been willing to expand it to a number of other genomes (even though they are not in the title). mycrofth |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
It's my understanding that the 'first phase' of this project is essentially done. Currently they're doing some folding of other proteins, bacteria and such like, but that they will segue into another phase of the Human Proteome Folding. Short answer; we made it, take a bow. Now on to the next phase.
This next phase will be a more detailed analysis of the folding sites found with the first phase of the folding project. I think we might be years from seeing the fruits of this grid project, but we've probably speeded up the research by years, too. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
rbonneau, the HPF scientist, is scheduled to provide a progress update today or tomorrow.
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in memory of Delores
Cruncher Joined: Nov 18, 2004 Post Count: 3 Status: Offline Project Badges: 
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Is it true that although we think we are working on HPF work units, we are no longer folding Human Proteomes?
----------------------------------------If yes, then I feel like we are being mis-led and are owed a huge apology by the folks running this project! If we are folding something other than Human Proteomes, let us know so we can choose to put our computers to work on something we consider meaningful. Our donation of computer time "in Memory of Delores " was given with the understanding that we were helping to fight awful human diseases like cancer (which sadly took Delores' from her children while they were way too young). The significant donation of computer time made "in memory of Delores " was given by those whose hearts broke when she passed away and should not be diminished in purpose! [Edit 3 times, last edit by in memory of Delores at Dec 16, 2005 1:55:56 AM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I hope I haven't caused a misunderstanding. And I hope that the poster who is contributing their CPU time in the memory of Delores will continue to allow computation on their systems.
As I understand it, all of the information that is generated is part of the research into the Human Proteome Folding project, and it is all important work. I won't try to explain how research on other than human proteins would matter to human diseases, but I do believe that it does matter and I have seen why. I have an older brother with a PhD in statistics in biology and I used to work as a research assistant on some of the experiments that they did at the University of Illinois. I came to appreciate how non-human models of biology lead to insights into human biology, so it was no suprise to me when I heard that they were also modeling other proteins. We have done a lot of important work that we can now build on. I don't think they could do this without our help, and I will continue to provide my computers for their research. Thanks to Delores' friends for their contributions. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello in memory of Delores,
----------------------------------------Here is the recent newsletter article on the Human Proteome Folding project: http://www.worldcommunitygrid.org/newsletter/viewActiveResearch.do Here are the status updates, beginning with the most recent: http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=4708#36738 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=4164#33281 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=4080#32557 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3989#31732 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3848#30082 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3757#29262 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3563#26720 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3345#21550 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3206 This May 2005 update is the one you really want to read. It mentions malaria, tuberculosis, plague, pneumonia, etc: http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2885 This project is devoted primarily to the human proteome and understanding the human proteome by predicting the structure of proteins of unknown function in the human proteome. We are also, however, folding the proteins of unknown function in over 60 other complete genomes that we feel have an important impact on human quality of life. I list below a sampling of the other genomes we’re exploring as part of the proteome folding project on the worldcommunitygrid. I’ll give a sentence or two about each of them, but each organism has a lot of reasons for furthor study. I could give you the full list, but these represent a good mix. In general there are 4 categories of proteins we’re folding (all important for improving people’s health and/or quality of life): 1. Human proteins: Priority 1 for this project. Contribute to the understand the human proteome with structure prediction. 2. Human pathogens: understanding these nasty guys contributes to our efforts to knocking them out. 3. Environmental: More and more we are realizing that the living things in any ecosystem have methods for responding to pollution and other human influences in ways that lead us to believe that bioremediation of toxic waste sites is on the horizon. Understanding bugs/bacteria and archeaeon involved in the environment is the first step. 4. Model systems: These are organisms that are studied in the lab because they are safe, easy to work with and easy to manipulate. Much of what we understand about genetics and biology at large comes from studying these organisms. Now for a few examples of non human proteomes on the grid: http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2607 http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2608 Here is the web page describing the Human Proteome Folding project at the ISB: http://www.systemsbiology.org/Scientists_and_..._Proteome_Folding_Project There has been no deliberate deception involved. At the start, the project promised to fold as many of the unknown human proteins as it could. However, there was no numeric goal set - a curious omission. But it is explained if you compare the dates on the status updates with the dates on which the Advisory Board meets to review projects and set priorities. (See http://www.worldcommunitygrid.org/projects_showcase/viewSubmitAProposal.do ) The Advisory Board has been monitoring the progress of the Human Proteome Folding project and authorizing additional genomes to undergo study for the benefit of humanity. Nothing slowed down or delayed our completion of the Human proteome study. But there have been other important genomes added to the tail end of the project, also for the benefit of humanity. The web page at the ISB was modified (?late Spring, early Summer?) to mention non-human species being studied. Everything was considered on a case-by-case basis, with consideration of the computer time involved. In September 2005, scientists began accessing the database holding our protein predictions. It was still in Beta release back in November, but I expect it will soon go to full public release. At the request of plant biologists, we recently added a plant genome (Arabidopsa) to our study and I believe that it is well underway. I am sorry that you were not aware of this, but it is standard in research. When you create an important tool in the laboratory to answer a specific question, if it works successfully then you immediately use it to answer similar slightly less important questions rather than just disassembling it. mycrofth [Edit 1 times, last edit by Former Member at Dec 16, 2005 7:38:16 AM] |
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in memory of Delores
Cruncher Joined: Nov 18, 2004 Post Count: 3 Status: Offline Project Badges:
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Desanex & Mycrofth;
----------------------------------------Those of us crunching "in memory of Delores " appreciate your exellent explainations. It does seem worthwhile to be crunching non-human proteomes after all. Those of us contributing "in memory of Delores " will keep crunching with the hope that someday these results might prevent other children from having to say goodbye to their mom too early in life. [Edit 2 times, last edit by in memory of Delores at Dec 17, 2005 2:47:45 PM] |
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