collaborating with competition

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collaborating with competition

Postby theteofscuba » Sat Apr 26, 2008 10:40 pm

I noticed that the university of washington is doing their own protein folding simulations -- Rosetta@Home. I have to wonder if Stanford collaborates with UWashington. Sharing results? Ensuring no protein simulations will overlap? Sharing source code? Maybe, quite possibly considering a merger?

Just throwing some ideas out there.
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Re: collaborating with competition

Postby toTOW » Sat Apr 26, 2008 11:01 pm

I read somewhere a long time ago that both projects were more complementary than competitives in the way they work, and what they study :)
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Re: collaborating with competition

Postby anandhanju » Sat Apr 26, 2008 11:32 pm

This is what Prof. Pande, Director of the Folding@home project had to say about Rosetta@home:
I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta@home and Folding@Home are addressing very different problems.
Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we're interested in and the diseases we're tackling (Alzheimer's Disease and other aggregation related diseases).
Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (e.g. with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena. While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always choose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized.
So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that's Rosetta's strength) and some think Rosetta is about misfolding related disease (which it's not, that's Folding@Home's strength). Hopefully this post helps straighten some of that out.
Source: Wikipedia article on Rosetta@home.

Prof. Pande has recently posted an article (http://folding.typepad.com/news/2008/04 ... e-and.html) that details some of the collaborative efforts at FAH and making FAH results/techonologies available to other researchers.
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Re: collaborating with competition

Postby theteofscuba » Sun Apr 27, 2008 1:47 am

I took a look at Rosetta@Home and I've developed an opinion that BOINC is far more stable than any of the F@H clients I've used. I think maybe if F@H were to adopt BOINC there would be less problems.
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Re: collaborating with competition

Postby Foxery » Sun Apr 27, 2008 2:47 am

theteofscuba wrote:I took a look at Rosetta@Home and I've developed an opinion that BOINC is far more stable than any of the F@H clients I've used. I think maybe if F@H were to adopt BOINC there would be less problems.


As far as I can tell, F@H came first and is larger. They're not going to just rewrite everything for the hell of it...
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Re: collaborating with competition

Postby toaster8 » Sun Apr 27, 2008 2:58 am

I tried BOINC before and found far too many problems/issues and at the time no real support. FAH has had a few bumps in the road for me but these forums always sorted me out. NOw, after running for a few months I have no issues and run different clients on different machines - most beta some not just to see how they run and so far they all run fine.
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Re: collaborating with competition

Postby VijayPande » Sun Apr 27, 2008 3:03 am

theteofscuba wrote:I took a look at Rosetta@Home and I've developed an opinion that BOINC is far more stable than any of the F@H clients I've used. I think maybe if F@H were to adopt BOINC there would be less problems.


If you'd like a stable FAH client, we'd suggest you run the classic FAH client (the client analogous to what you'd get in other projects). Other distributed computing projects don't have an SMP/MPI, or GPU, or PS3 client, so comparing to FAH is apples to oranges in that case.

We did check out BOINC extensively (with lots of kind help from Dr. David Anderson, Director of BOINC), but in the end found that it wasn't a good match for our needs.
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Re: collaborating with competition

Postby VijayPande » Sun Apr 27, 2008 3:05 am

PS As said by others in the thread above, our work is very complementary, so there isn't always a direct sharing of code, etc.

However, we are looking to see how FAH can help others. One example is the GPU code (most people would love to get a major speed up in their code). Also, thermodynamic sampling is an expertise of ours and we're looking to see how our methods could help calculations performed in Rosetta@home, amongst other projects.
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Re: collaborating with competition

Postby 7im » Sun Apr 27, 2008 5:26 am

Asked and answered. Thread closed.
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