Posts by steveking

1) Message boards : Rosetta@home Science : folding algorithm(s) (Message 93704) Posted 7 Apr 2020 by steveking Post: Thanks. looks like I got some reading to do.
2) Message boards : Rosetta@home Science : folding algorithm(s) (Message 93649) Posted 6 Apr 2020 by steveking Post: Is there a link to an article detailing the algorithms used to perform automated folding? Or is this a lab secret (proprietary and can't be shared)
3) Message boards : Number crunching : Not getting anymore work units (Message 79713) Posted 8 Mar 2016 by steveking Post: Sun Mar 6 03:51:29 2016 \| rosetta@home \| Rosetta Mini for Android is not available for your type of computer. Mine said that too. Can only speculate that there were only Android WUs left in the scheduler cache. And so this is really more an indication of why you got no work, than the server thinking your machine was Android. If I see no "Ready to start" tasks, I simply close BOINC and reboot PC. Then weh BOINC runs again, it loads up a set of tasks read to start. Closing BOINC and restarting without a reboot appears not to work.
4) Message boards : Number crunching : Not getting anymore work units (Message 79698) Posted 7 Mar 2016 by steveking Post: Why am I not getting anymore work units? I exit BOINC then wait a few minutes and then restart BOINC... still no new work units. I had to exit BOINC then reboot my PC and then restart BOINC to get new work units. Does Rosetta@Home have a bug that prevents getting new work units after a certain period of time?
5) Message boards : Number crunching : Not getting anymore work units (Message 79697) Posted 7 Mar 2016 by steveking Post: Why am I not getting anymore work units?
6) Message boards : Rosetta@home Science : zero gravity, hi-magnetisim (Message 79696) Posted 7 Mar 2016 by steveking Post: Does anyone know how zero gravity affects the folding of proteins? Or... how does a high magnetic field affect folding?
7) Message boards : Rosetta@home Science : Genetic Algorithm (Message 79682) Posted 2 Mar 2016 by steveking Post: Yes! On robetta we send off many individual jobs to create a population of models. These models are then recombined to create new population(s) of models iteratively. Not sure this sounds like a "proper" GA. Do you have a paper/documentation on this? Thanks I actually think this is a "proper" GA. Appears they seek a "folding model" and the best way is to create a population of models. Models that perform the best are kept and mutated to see if the mutation is better or worse. Appears the goal is to find a best fit model until near perfection is met. They will probably use it across a set of proteins to determine if the model can reach lowest energy state in every set. Not a bad approach. Happy to be crunching with PhD Baker. Yes, that is a description of how GAs work. However, in the case of Rosetta they use simulated annealing methods (rather than GA methods) to find local (and hopefully global) minima. The end results of all these folds are amalgamated to produce a graph like this:- So it hinges on what is meant by "These models are then recombined to create new population(s) of models iteratively." Like I said, doesn't sound "GA - y" Maybe they should try a real GA rather than simulated annealing. The problem though with GA in this case is the "cost function". How are they going to define a cost function for a model?
8) Message boards : Rosetta@home Science : Genetic Algorithm (Message 79661) Posted 1 Mar 2016 by steveking Post: Does Rosetta use a genetic algorithm to find a lowest energy state? See "Genetic Algorithms in Search, Optimization and Machine Learning". by David E Goldberg. Yes! On robetta we send off many individual jobs to create a population of models. These models are then recombined to create new population(s) of models iteratively. Not sure this sounds like a "proper" GA. Do you have a paper/documentation on this? Thanks I actually think this is a "proper" GA. Appears they seek a "folding model" and the best way is to create a population of models. Models that perform the best are kept and mutated to see if the mutation is better or worse. Appears the goal is to find a best fit model until near perfection is met. They will probably use it across a set of proteins to determine if the model can reach lowest energy state in every set. Not a bad approach. Happy to be crunching with PhD Baker.
9) Message boards : Rosetta@home Science : Genetic Algorithm (Message 79656) Posted 28 Feb 2016 by steveking Post: Does Rosetta use a genetic algorithm to find a lowest energy state? See "Genetic Algorithms in Search, Optimization and Machine Learning". by David E Goldberg. Yes! On robetta we send off many individual jobs to create a population of models. These models are then recombined to create new population(s) of models iteratively. Don't proteins fold as they exit the ribosomal tunnel? If this is the case then the folding algorithm should model the sequence in which Amino acid chains exit. Correct? This should be a huge clue as to how side-chains bend and twist as they interact hydrophobic-ly and hydrophilic-ly. Sort of like strings of play-doh exiting a child's play-doh press.
10) Message boards : Number crunching : laptop CPU suspends tasks (Message 79638) Posted 27 Feb 2016 by steveking Post: I think I discovered the problem and the solution: My desktop has 4 cores and runs at 3.3GHZ, running 4 threads. RAM = 12GB. The setting in BOINC computing preferences for non-BOINC CPU is at 35%. GPU is OFF. All is good and I have never had a problem. My laptop only has 2 cores but is running 4 threads at 1.7GHZ. RAM = 12GB. The setting in BOINC computing preferences is set at 25% for non-BOINC CPU usage. GPU is OFF. Since I have only 2 cores, I set the non-BOINC usgae needed to be raised to 40%. And this my friends has appeared to have solved the problem of my laptop suspending tasks indefinitely. There are other tasks running that need CPU time and raising the non-BOINC usgae from 25% to 40% appears to have fixed my problem.
11) Message boards : Number crunching : laptop CPU suspends tasks (Message 79637) Posted 27 Feb 2016 by steveking Post: my laptop appears to suspend tasks (cpu busy) after about 3 minutes and then I have to move the mouse to get back into running mode. what's up with that? I check my laptop power and sleep settings and they appear to be in high performance mode ---- meaning I am not have the laptop shut anything down or go into some power saver mode. Jedeeze can anybody help on this one? Please. I have a DELL Inspiron 15 3537, dual core with 12GB ram. Usage of ram is only 3.1GB My desktop is cruising along fine. No problems
12) Message boards : Rosetta@home Science : Genetic Algorithm (Message 79623) Posted 25 Feb 2016 by steveking Post: Does Rosetta use a genetic algorithm to find a lowest energy state? See "Genetic Algorithms in Search, Optimization and Machine Learning". by David E Goldberg.