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razvandrt
Cruncher Joined: Nov 17, 2006 Post Count: 4 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Hey,
Can anyone tell me where I can read about the scientific results of all these projects. What are their output? I would like to see in what way did this grid computing help the fields of the wcg projects. Thanks, Razvan |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Two projects have started publishing based on grid results so far. The others are still collecting data or preparing papers.
Human Proteome Folding Superfamily Assignments for the Yeast Proteom...on with the Gene Ontology Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, et al. PLoS Biology Vol. 5, No. 4, e76 doi:10.1371/journal.pbio.0050076 FightAIDS@Home Analysis of HIV Wild-Type and Mutant Structur... Diverse Ligand Libraries Max W. Chang, William Lindstrom, Arthur J. Olson, and Richard K. Belew J. Chem. Inf. Model.; 2007; 47(3) pp 1258 - 1262; (Article) DOI: 10.1021/ci700044s |
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aBowers
Advanced Cruncher Joined: Jun 14, 2006 Post Count: 54 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Hi all.
----------------------------------------While I'm not quite as paranoid as the joke that started this thread, I do think it's worthwhile to critically consider the end result/impact of the WCG. I have some thoughts on the matter that I’d like to share. First, I just want to clarify that I firmly believe that distributed computing is a fantastic tool in humanity’s battle against disease. As a concept, the WCG is right on the money. Even if a large portion of the research conducted on the WCG ends up being fruitless (hypothetically), the WCG will still have helped bring thousands of people into the world of philanthropic computing. Furthermore, the WCG should be applauded for spreading its resources over several projects, and for insisting that the research be made public. These steps indicate that the WCG is indeed serious about not wasting users’ donations. However, one concern that I have is the relatively limited number of WCG-derived publications. Many thousands of papers are published in peer-reviewed journals every year, and I think it’s fair to say that not all of these papers have had a sizeable impact on humanity/science. Now I haven’t had a chance to fully read the FAAH and other WCG-derived papers, so they very well may contain important scientific findings. Regardless of whether or not this is the case, it seems that a greater effort should be made to increase the number/frequency of publications, as these are the primary “records” of what has actually be accomplished (scientifically) by the WCG. Of course, the scientists using WCG resources would most likely prefer to continue their research over writing paper after paper. But, the papers serve as a yardstick that the worldwide scientific community can use to assess how successful the research is. Without regular publications, it might be harder for WCG officials to get feedback on how successful the various projects are, and whether or not they are heading in a worthwhile direction. Now I understand that some projects are ongoing, long-term endeavors that are not going to yield meaningful results until much computing has been done. However, I’m suggesting that given the nearly 100,000 years of cpu time donated to the WCG, more than two or three papers should have been published by now. It seems like a gamble to trust that projects are making sound scientific progress when there are so few results for the scientific community as a whole to examine. That being said, I’m going to dutifully continue expanding my crunching capabilities on faith. It will be interesting to see in the coming years how often the WCG-derived papers are cited, and what kind of research stems from them. ![]() |
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twilyth
Master Cruncher US Joined: Mar 30, 2007 Post Count: 2130 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
A hundred thousand years of computer time isn't very much - although that sounds hard to believe. At grid.org we devoted over 45 thousand hours (supposedly) just to the HPF1 paper.
----------------------------------------Computational chemistry is still an experimental endeavor. From what I understand, it is virtually impossible to crunch the numbers for even relatively simple quantum calculations so most of the work involves a lot of short cuts that may or may not be on the money. As a result, the product of our calculations are at best a starting point - pointing researchers in the right direction rather than producing new science. Finally, nobody is more interested in publishing than the researchers. If they can squeeze a paper out of any work that they do, you can bet the ranch that they will. In academia the working premise is "publish or perish". No publications means no job and no grant money. WCG is growing and so is there portfolio of projects. More results will come. It will just take time. ![]() ![]() |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
aBowers, it's a pipeline.
These first papers we are seeing were produced using the earliest results of our first projects. Both projects have several other papers in progress. But academic publishing is a slow business. The scientists can only start writing when they have the results in and analysed; and once the paper is written, there is the considerable delay involved in peer review. Obviously, this means that scientists can only work on publishing results after they have been crunched. The good news is that now papers have started trickling out of the end of the pipeline, we can hopefully expect a steady flow in the future. Sometimes the project scientists update us about the papers they are working on, but that information tends to get buried in the forums. On average, I expect papers to be published about a year after crunching for a particular experiment ended. That's just a guess, based on sketchy information. But check back later, and see if the WCG publication list hasn't grown.... |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Somewhere lead scientist Dr. Richard Bonneau, of HPF1 and 2 mentioned there was a ream of papers to be expected from these projects.... if i stumble the quote, I'll pass it (think it was in one of the Yeast result related posts)
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WCG
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razvandrt
Cruncher Joined: Nov 17, 2006 Post Count: 4 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Hi all. While I'm not quite as paranoid as the joke that started this thread, I do think it's worthwhile to critically consider the end result/impact of the WCG. I have some thoughts on the matter that I’d like to share. First of all thanks for replying and sharing your thoughts aBowers. Second, i am sorry you misinterpreted my question and found it a paranoid joke. The reason i asked for some "results" is that i needed to make a presentation about grid computing and its use for a grid computing initiative my university has, and decided to ask on the forum for quick replies and straight answers about the WCG projects. Well, thank you all for your replies, thanks Didactylos for the links and if the discussion continues, i hope it will be a constructive one and not a paranoid one ;) Take care! |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Yes. If I understand correctly (and since I am not a biologist I probably do NOT understand what I read), the Yeast paper from HPF1 is a follow up on earlier research using the new HPF1 results. Dr. Bonneau said that they were working on a lot more than just 1 yeast species.
http://homepages.nyu.edu/%7erb133/wcg/thread_2007_04_16.html I will quote some of what he writes: HPF1 Results Update HPF1 has been finished for some months and we can now report that the first high profile paper written using grid results is out (Lars' thesis and a few things I've written were out last year, but this is the first paper that anyone will read ;-) ). Lars, David and I wrote the paper many months ago but the many steps to publishing take time. We think this is the first wcgrid paper, and the first of many. Before we get to the paper I wanted to thank the crunchers because this wouldn't have been possible without you. You're cycles are invaluable to us and the scientific community. So far its been a great relationship between crunchers and scientists and we hope it continues. Here are the main points: 1. This paper was about the methods for combining previous functional information (that was incoded in a database called the Gene Ontology database) with our structure predictions. 2. In order to determine the rate of success and develop the method we chose to first apply the method to Yeast, a key model organism. Much of the biology we know today comes from studies carried out in model organisms. 3. Biologists across the world now have access to the data via the yeast resource center. Mike Riffle tells me that the site is widely used (high use stats for this type of resource). Our experience with yeast has been positive, we have a few more algorithmic details to work out (in how we integrate the data from the grid with other bio sources to maximize utility to biologists) and we're on to writing up the Human results. The next paper will detail results from all 150 proteomes (spanning the tree of life). The concluding sentence in the paper alludes to this work : "The information content in the predicted structures may be further leveraged by integration with other data such as global quantitative measurements of mRNA, protein expression levels, DNA-protein, and protein-protein interactions. Such datasets are available for yeast and several other organisms as part of ongoing functional genomics efforts, and integration of these data types with the predicted structures should contribute to the annotation of protein functions." |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello razvandrt,
Second, i am sorry you misinterpreted my question and found it a paranoid joke. The reason i asked for some "results" is that i needed to make a presentation about grid computing and its use for a grid computing initiative my university has, and decided to ask on the forum for quick replies and straight answers about the WCG projects. You posted while I was researching my answer to the previous post. Sorry I missed seeing your post before I made mine. I think that the 'paranoid joke' was a reference to a different thread that has been going on recently. It was probably caused by a mental hiccup which temporarily confused the two threads due to their similarity on some points. I winced when I read a post in your thread that would only be appropriate in the other thread. I hope that you will not be offended. I really do not think that you were the intended target. Lawrence |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
A hundred thousand years of computer time isn't very much - although that sounds hard to believe. At grid.org we devoted over 45 thousand hours (supposedly) just to the HPF1 paper. The grid.org portion was 43,360 CPUyears, about factor 8,440 of the above number and was excluding the Yeast portion that only ran on WCG (in 3 weeks) :P
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