Posts by James Thompson

41) Message boards : Number crunching : Crunching question (non points related!!!) (Message 22765) Posted 17 Aug 2006 by James Thompson Post: I found that computer for $5.95 at a thrift store a month or so ago. It was the property of a local school district but had never been used. The inside of the case was dust-free and the XP installation was untouched. Hi Matt, Great question. I don't think that your computer can run Rosetta with the current requirements. What sort of RAM does it use? If it uses PC100, I have an extra 128MB stick that I could mail to you. Send me an e-mail if you'd like it and I'll get your address. Maybe this will start some sort of spare parts swap that will allow people to upgrade computers with spare parts to be able to better run Rosetta. I know that I have a couple of other parts around the house that would be much better served in all of your computers than sitting in a drawer in my house.
42) Message boards : Rosetta@home Science : Rosetta@home Active WorkUnit(s) Log (Message 22568) Posted 16 Aug 2006 by James Thompson Post: I've added 58 small jobs to the queue named <protein_name>__CASP7_ABINITIO_SAVE_ALL_OUT_flatss0.33_. These jobs are designed to investigate how problems with secondary structure prediction affect our predictions. Secondary structure prediction is an initial step in our methodology that attempts to predict a local arrangements of a small piece of the protein structure, which Rosetta then arranges into an overall tertiary structure. My impression from CASP is that lack of knowledge of secondary structure makes prediction very difficult, and these workunits will give a better idea of the problem's difficulty.
43) Message boards : Number crunching : When are CASP 7 WU's finished? (Message 21674) Posted 2 Aug 2006 by James Thompson Post: OK I apologize. Since CASP 7 ends AUG 7 then feel free on that date to turn your other pojects back on since CASP 7 participation (S.O.S.) won't bee needed after that date. But Dr. Baker would appreciate it if you could clear out your cues instead of abandoning them, if that's possible. No problem, as long as the science is useful all cached WUs will be completed. Thanks Keith is absolutely correct. I've discussed this with several people other scientists in the lab, and we all agree: workunits submitted after the deadline are very useful indeed! While they will not help the accuracy of our submissions to CASP this year, we can still analyze results after the deadline. We are extremely interested in analyzing our results and refining out techniques using all available computational power. Bottom line: if those workunits are returned after the CASP deadline, they are still useful. Thank you all for your help.
44) Message boards : Number crunching : Utilize Ralph During Casp (Message 20659) Posted 19 Jul 2006 by James Thompson Post: As Feet1st says, we are using Ralph to test workunits that we send out to make certain that there are no problems for our larger Rosetta runs. We actually use the results from Ralph workunits in order to estimate some characteristics of the energy landscape for each run. These characteristics are actually included in the later BOINC run, and makes the use of your computer time more efficient by not exploring protein conformations that are obviously incorrect. So, what I do to make BOINC run: 1. Configure my workunits to run on Ralph, and verify that my configuration runs correctly on the machines local to our lab. 2. Send out a run to Ralph to verify that there are no problems with the workunit, and that the workunit generates reasonable results. 3. Use the results from Ralph to quantify characteristics of the energy landscape. 4. Send out a big run on BOINC using settings derived from the earlier Ralph run. The Ralph runs definitely save us some amount of computing power by determining some minimum energy settings for reasonable answers, although I haven't quantified exactly how much the Ralph runs save us in terms of sampling time. The point I'm trying to make is: Ralph definitely helps!
45) Message boards : Rosetta@home Science : Genetic algorithms and rosetta@home (Message 19492) Posted 29 Jun 2006 by James Thompson Post: I've taken a graduate course on GAs and learned how effective they can be for problems with large search spaces, especially those with lots of local minima or maxima. I even participated in a distributed GA search for optimizing electronic hardware design while it lasted. Has any work been done to look at how GAs can help Rosetta@home's goals? Stephen Genetic algorithms are definitely a very powerful idea. We currently have a visiting graduate student who is using a Genetic Algorithm to combine different parts of predicted protein structures. There's short thread about this here. One of the problems with using something like a GA in Rosetta@Home is communication. While it's plausible to have each computing node with an independently evolving population of structures, that process is limited by the number of structures that can be constructed on that single node in a reasonable amount of time. The most straightforward approach to adding this information would be prohibitively expensive in terms of communication, especially when we consider the number of users that we have on intermittently active or slow connections. Hope that this answers your question.

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