Posts by bruce boytler

21) Message boards : Number crunching : My PC RAC > 3000 (Message 34276) Posted 7 Jan 2007 by bruce boytler Post: As I understand it rosetta@home is mainly used to develop the software needed. In that case it might be better to optimize the applications which are using the "final versions". WCG uses a rosetta aplication, don't they? Yes, WCG used Rosseta in both HPF and now recently in HPF2. In HPF the WCG tech optimized rosseta with a heuristic which stablized the workunit on my computer to a 6 hour size. Before they did this my computer had sizes ranging from 2 to 96 hours. With HPF2 they were running into a problem with rosseta newest version which stopped the workunit processing but not the hour meter recording the unit proccessing. These same techs fixed that bug too, or at least troubleshot it.
22) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 34155) Posted 5 Jan 2007 by bruce boytler Post: [/quote] Hi, thanks for the report. I am a little puzzled with the "rosetta WCG" part though .. Does is it mean it will describe results obtained from rosetta .. or from HPF2?(WCG). or are they the same thing anyway?..(the science behind them - that is). [/quote] What Dr. Baker is referring to in "Rosetta WCG" is the HPF1 project recently completed on the IBM World Community Grid. It used a version of Baker Labs Rosseta Program that was about 2 years old to survey 150 Genomes (including the Human Genome). This survey was done in low resolution mode and the results were used to create a public database which show the results of the many protien structure predications from the genome sequences. The HPF2 project takes a subset of the most interesting predictions from HPF1 and does a hig resolution prediction on these. HPF2 is using the most current stable version of Rosseta to do the high resolution prediction. I belive the newest version came from the work of rosetta@home. The version used on HPF1 predates the rosseta@home project.
23) Message boards : Cafe Rosetta : When exactly did R@H go live? (Message 33028) Posted 21 Dec 2006 by bruce boytler Post: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=5 whoops ment to post this link guess it was 16 sept. 2005 that the public started showing up.
24) Message boards : Cafe Rosetta : When exactly did R@H go live? (Message 33027) Posted 21 Dec 2006 by bruce boytler Post: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=2288 Might want to check out this linl it goes to thread start sept.15 2005. I think I was the 4 or 5 th reply on sept. 17. Also rosetta was just in beta when I joined. I remeber Dr. Baker announcing rosetta is now out of beta and in full production a few days after I joined. I remember thinking wow! that was a fast BETA. Anyhoo Have a Great Day Ciao.............
25) Message boards : Cafe Rosetta : Hi all (Message 26938) Posted 16 Sep 2006 by bruce boytler Post: Hi David!!!!
26) Message boards : Rosetta@home Science : Solid answer needed, for who do we do this? (Message 25726) Posted 31 Aug 2006 by bruce boytler Post: Nobody is twisting anyones arm to crunch for R@H. If you have significant misgivings about this type of research, then by all means go to another project. The whole DC movement of which I have been apart of since the late 90's has always been based on Voluntary Grass Roots efforts to try and solve problems not readily approchable by standard methods. This is actually one of the better and more pragmatic of the projects I have been apart of. Because it needs such a huge amount of proccesing power to attack the Protien Folding Problem most participants hate to see even one computer leave. David Baker has stated on many occasions from the projects beginings that the Protien Folding Problem is solvable if only the correct amount of proccessing power can be applied to it. THIS IS WHAT THIS PROJECT IS DOING. Once this is done the methods have far reaching implications for many displines beyond Bio Chemistry. See Ya..............
27) Message boards : Cafe Rosetta : Class of 2005 (Message 24680) Posted 24 Aug 2006 by bruce boytler Post: The very begining of R@H was actually extremely stable! I remember being incredably impressed with the ease my computer processed the workunits. No graphics back then though. This initial stability and the very friendly forums was what brought most of the users at the time into the project. So you can imagine the SHOCK we all had that last week of December when we all saw our workunits crash and burn over and over for the next weeks.
28) Message boards : Cafe Rosetta : Last one to post here wins! (Message 21016) Posted 24 Jul 2006 by bruce boytler Post: My Turn!!!!!!!!!!! See ya...have a great weekend...........
29) Message boards : Number crunching : Top Predictions - what happened to "your prediction"? (Message 20457) Posted 18 Jul 2006 by bruce boytler Post: I liked it to. It really made you feel like you contributed something. Even though you weren't the lowest energy prediction. I believe that it caused to much drain on already limited resources on the server side. I wish Baker Lab would reconsider (after CASP of course) putting this feature back.
30) Message boards : Cafe Rosetta : Old Geezers Club (Message 19684) Posted 2 Jul 2006 by bruce boytler Post: I started out in my freshman year in 100 level BASIC classes then moved on to FORTRAN. I also remember learning JOB CONTROL LANGUAGE and walking around campus with stacks and stacks of computer (do not fold, spindle or mutilate) cards which input my program to an IBM mainframe. The results would printout on a line printer which the computer lab geeks would put neatly in my box a day or two later. I had no idea monitiors were even invented until I passed an Apple Computer store one day in 1979 and wondered what the heck was an Apple Computer. What a shock!! My first computer turned out to be a dual floppy KAYPRO running CPM a very sweet 8 bit system. Have a great day .................
31) Message boards : Cafe Rosetta : Request from a journalist (Message 15562) Posted 5 May 2006 by bruce boytler Post: How did you find out about the project? I was crunching on the World Community Grid for the HPF 1 project. Which used a earlier version of Rosetta. An annoucement was made on the World Community Grid Forums explaining Rosetta@Home and thier need for computing power. Why did you get involved? I am 100 percent assured by my Genetic background of contracting Cancer anytime in the next 10 to 15 years. Did you buy any new equipment to get into the project or did you just use existing computer hardware? I accelerated the purchase of a new computer I was putting off till the Winter. What have you learned about biomedical research? I have lerned all about protien folding prediction and its relationship to Drug Discovery and protien design. What have you learned about computers? Nothing, I didn't already know. What have you gained from your participation in the project? The knowledge that I took ownership of my Cancer propensity and participated in something which may offer hope to myself and others all over the World. Where do you live? Auburn, Washington State, USA What do you do for a living? Computer Maintenace. How old are you? 48 [/quote]
32) Message boards : Rosetta@home Science : Concerns: Will someone (i.e. BigPharma) make money out of my CPU time? (Message 14031) Posted 18 Apr 2006 by bruce boytler Post: Hi All, Philantropy is definitely a hard road to follow. Knowing that you and a few other interested souls are tasked with finding the way to the new 21 century medicine. This being the case because a large potion of the compute power is now in the hands of joe blow. You would actually be very lucky if big pharma actually did take our results seriously. Then you would be assured of having a drug in the system for you to accesses. As the case is now the big drug companies dont even have us on the radar. I know because I asked. Specificaly at one of the companies anual meeting for which I own some stock. Ciao......
33) Message boards : Rosetta@home Science : Information on Rosetta@home for the BBC (Message 13783) Posted 14 Apr 2006 by bruce boytler Post: Hi All, Great News about the PR rosetta is starting to generate. The request for what Rosetta@home does in laymans terms goes to show what I havebeen encountering all along in my pitches to others about DC an R@H in general. Here is my go at trying to explain in a nutshell what R@H is trying to do and why the plea for more compute: "The Protien Folding problem first put forth by Linus Pauling in 1936. Still remains to be solved. The solution will lead scientists to a whole new class of drugs for combating diseases like Cancer, Alziemers, Malaria, HIV and various Viruses. Help us solve this key to treat disease and bring Biological science to new heights. We are only 120 teraflops of computing power away from this goal. With your donation of unused computer cycles we can move one step forward in solving this problem." Hope this helps feel free to make even simpler or more concise. Ciao......
34) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 13139) Posted 6 Apr 2006 by bruce boytler Post: [With our improvements over the past few months and this big increase in sampling, the prediction failures are becoming far fewer, but for the thornier problems it is clear that we are not sampling enough. With the 150 teraflops the project is aiming for, even these should fall into place.[/quote] Considering the implications of solving the problem of protein structure prediction, if the bottleneck is an issue of CPU power, why aren't more public resources being offered? The only ones I have heard about were the ones belonging to someone called Food and Housing Services. In the end the Baker Lab has made it clear since September 2005 that it is up to us the "crunchers" to come up with the cpu to solve this pivotal science problem. Also, what are the world's top 2 supercomputers BlueGene and BlueGene/L, supposedly built to tackle the protein folding problem (see Gene Machine article in Wired 2001) used for nowadays? Blue Gene at Lawrence Livermore is used to predict Nuclear Weapons Bomb yeilds. This is good because if this was not done on Blue Gene they would be exploding them for real. Like in the 1950's and 1960's out in the Nevada deseret. Hope this helps a little.........Bye All!
35) Message boards : Rosetta@home Science : Rosetta@home page at Wikipedia (Message 12929) Posted 2 Apr 2006 by bruce boytler Post: Hello, That was my first read of the old and new rossetta wikki. This statement: "HPF Phase-1 applied Rosetta v4.2x software on the human genome, started in Nov-04 and finished Nov-05." is incorrect. HPF-1 is still going and will continue to process until HPF-2 begins. I have just recently finished a 20 hour HPF-1 work unit on another computer. If further clarification is needed you can go to the HPF-1 forum on WCG and ask your questions thier. Ciao All! have a nice day.......
36) Message boards : Rosetta@home Science : Rosetta video/outreach project (Message 12708) Posted 26 Mar 2006 by bruce boytler Post: Hello All, One thing that has tripped me up many times in my recruitment efforts is the use of jargon. Amazingly enough, people want things explained to them on what amounts to a 9th grade level. The use of anything more technical is a real turn-off. So there lies another challenge. To translate what is going on here to very simple plain english. The analogy of the explorers jumping out of airplanes looking for the dead sea. That was used a while back was excellent. I used this device many times in my own efforts to explain things with much success. Ciao all.......
37) Message boards : Number crunching : Report stuck & aborted WU here please (Message 12522) Posted 22 Mar 2006 by bruce boytler Post: This unit stuck for 9 hours: FA_RLXpt_hom003_1ptq__361_234 Brought up the graphics screen (I dont run any graphics) and it was all froze except for the cpu clock was still counting. Resetting boinc did no good. Ended up aborting it. out of 183 results i have 4 errors of the frozen or 1 to 15 percent type. Cheers all!!!
38) Message boards : Number crunching : Help us solve the 1% bug! (Message 12510) Posted 22 Mar 2006 by bruce boytler Post: Hi All, I experianced the 1 percent bug but not at 1 percent but at 15 percent. It had been spinning its wheels at 15 %for 15 hours before I realized it. Turned BOINC off then back on and roseeta went back to zero and started all over. checked on BOINC 8 hours later and same thing stuck at 15 percent so I just aborted the whole unit. http://boinc.bakerlab.org/rosetta/result.php?resultid=14382390 FA_RLXpt_hom006_1ptq__361_86_0
39) Message boards : Number crunching : Work Units that fail in under one minute - Report HERE (Message 12267) Posted 19 Mar 2006 by bruce boytler Post: HOMSdt_homDB027_1dtj__352_875 HOMSdt_homDB030_1dtj__352_163 HOMSdt_homDB004_1dtj__352_123 HOMSti_homDB025_1tif__346_132 HOMSdt_homDB011_1dtj__340_114 NO_MORE_RELAX_CYCLES_1dtj_214_18
40) Message boards : Number crunching : Any Xtra Credit for Protein of the Day? (Message 12266) Posted 19 Mar 2006 by bruce boytler Post: The mention of the user with the best prediction both in the journal and on the predictions page and maybe also the chance of being citied in an ensuing paper should be reward enough. I know it would be for me. If someone wants more points add a dual core amd to thier arsenal you will be glad you did. Sonara folks..........

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