Minimal mcmc simbio #43
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added 30 commits
August 27, 2017 20:59
…nding second step parameters differently.
… 40 iterations, parallel, thinning 10, step size 1.3
…ion points, apr 2, 3 pm
… need to do a commit every time.
…anges of the tx elongation, agtp regeneration system turnoff time, AA_F, UTRKd parameters. Going to initialize with the previous distributions and rerun at a much larger step size, and a much higher standard deviation (so that there is more mixing. only doing 20 iterations. going to analyze results. then rerun on new step sizes and standard deviations. eventually want to have a small SD and a small SS. This is the cooling effect. Simulated annealing. it should not violate detailed balance since eventually we will still to one set of conditioned, and this initial phase can just be thought of as a randomization phase where we try to find some initial distribution of points. This randomization is not totally random, indeed we are messily searching a distribution of parameters that fit the data, albeit poorly. " git commit -m "first set of nessa and lambda runs done. Now extended the parameter ranges of the tx elongation, agtp regeneration system turnoff time, AA_F, UTRKd parameters. Going to initialize with the previous distributions and rerun at a much larger step size, and a much higher standard deviation. so that there is more mixing. only doing 20 iterations. going to analyze results. then rerun on new step sizes and standard deviations. eventually want to have a small SD and a small SS. This is the cooling effect. Simulated annealing. it should not violate detailed balance since eventually we will still to one set of conditioned, and this initial phase can just be thought of as a randomization phase where we try to find some initial distribution of points. This randomization is not totally random, indeed we are messily searching a distribution of parameters that fit the data, albeit poorly. " "
I am trying a git commit --amend to see if I can get it to work without a problem. Had conflicts in the past. Not sure what is going on.
…e from all other files whenever something is to be explained about the mcmc_info struct. I imagine I will be updating this file with more info as I write the demo examples.
… and the mcmc_info constructor files for the three tutorials
…re in a common directory on my computer)
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Thanks Richard, I will have a look at these and respond with changes / edits soon. |
…tierra data fitting files from Aug 2018. Here we tried to fit the data Abel sent us.
…e aws instance to get things to work. also, need to check if the gen residuals is working properly.
… both spot instances with hibernation, and on demand pricing. Next step is to get some project files set up, and have everything bug free and tested locally or on small aws instances. Then we can run things on large c5.8xlarge type instances either spot or on demand.
…tignore? more importantly, why did the files VNPRL etc show up in the minimal mcmc simbio branch? very confusing, will investigate
…ng and pushing between the master and minimal_mcmc_simbio branches... sigh. need to go over things later and fix manually.
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Here is a minimal_mcmc_simbio branch that we can merge into a branch of the same name in the BuildACell/txtlsim repository. We can then test that separately from my copy to see if things work / people can read the README.md file and get an idea of how to use the mcmc_simbio capabilities (and to see if I haven't introduces bugs into the main txtlsim code while I was adding the ATP regeneration system)