Merge MCMC parameter estimation toolbox#42

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murrayrm wants to merge 167 commits intoBuildACell:masterfrom vipulsinghal02:master

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Commits on Aug 28, 2017

first draft of the MCMC toolbox

Vipul Singhal
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Vipul Singhal
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Commits on Nov 20, 2017

temp commit before I delete the sysID stuff

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deleted sys ID

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Commits on Nov 22, 2017

changed the ATP deg parameter setup, and named the NTP consumption binding second step parameters differently.

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added the globalize params function

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modified the txtl_init files

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Commits on Nov 23, 2017

fixed globalize params

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Commits on Nov 27, 2017

parameter globalization and rule creation in txtl_transcription and txtl_translation

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added the mcmc config file

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an mcmc toolbox for simbiology and in particular the txtl modeling toolbox

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added a gitignore file for the projects directory

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Commits on Nov 28, 2017

changed the readme file

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changed sbiointegrable to only tolerate 50% non integrability - down from 75%

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Commits on Feb 21, 2018

Massive developments to the MCMC toolbox

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Commits on Feb 26, 2018

added a file on VNPRL2011, and lots of stubs for the calibration correction work

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getting ready to run vnprl on nessa and lambda

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Commits on Apr 1, 2018

added a bunch of project and mcmc_info files for artificial data MCMC

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updates constgfp3ii mcmc info file for running on linux, 200 walkers, 40 iterations, parallel, thinning 10, step size 1.3

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Commits on Apr 2, 2018

updates constgfp3ii apr 1 7 pm PST for running on nessa and lambda

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updates constgfp3ii mcmc_info smaller step size and number of simulation points, apr 2, 3 pm

Vipul Singhal
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turned proj_protein_constgfp3ii_linux into a function so one does not need to do a commit every time.

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optional ability to add a previous run as a starting point

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Commits on Apr 3, 2018

changes to linux file

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changes to file again

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added standard deviation tot he linux file

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Commits on Apr 16, 2018

bugfix in transcription and translation file, some setup of the covariation stuff

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Commits on Apr 18, 2018

an attempt at the new AGTP regenration system

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Commits on Apr 20, 2018

ommit log

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Commits on Apr 22, 2018

fixed a bug in the mcmc_info file. zzz

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Commits on Apr 25, 2018

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…

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made come changed to the explore regen A file

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new gitignore

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gitignore fix

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Commits on Jul 20, 2018

commit of untracked files, getting ready for setting up a minimal working code branch, which we can then merge into BuildACell

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Commits on Jul 28, 2018

Commits on Jul 29, 2018

Added a readme file in markdown format. Not complete yet; Still need to make the mcmc_tutorial and update the TXTL_tutorial file, and update with a link to the thesis for further documentation

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Added a readme file in markdown format. Not complete yet; Still need to make the mcmc_tutorial and update the TXTL_tutorial file, and update with a link to the thesis for further documentation

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try again with the readme file

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Commits on Jul 30, 2018

tutorial files for mcmc_simbio in MATLAB markup
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Commits on Aug 1, 2018

A lot of write up to the mcmc_info.m helpfile. Will point to this file from all other files whenever something is to be explained about the mcmc_info struct. I imagine I will be updating this file …

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Commits on Aug 3, 2018

added tutorials I-III, an mcmc_info help file, a data_info help file, and the mcmc_info constructor files for the three tutorials

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updated the readme file, and deleted some image files

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Commits on Aug 6, 2018

added support functions needed for this toolbox to function (there were in a common directory on my computer)

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Commits on Jan 1, 2019

changes to the source code to add weighting to trajectories, and the tierra data fitting files from Aug 2018. Here we tried to fit the data Abel sent us.

Vipul Singhal
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modified gitignore to include data tiles, png, tiff, graphclick files

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Commits on Jan 29, 2019

testing on aws, first commit

Vipul Singhal
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some changes to source files. refacter i next commit. this is from the aws instance to get things to work. also, need to check if the gen residuals is working properly.
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Commits on Jan 31, 2019

Commits on Feb 1, 2019

Commits on Feb 2, 2019

Commits on Feb 3, 2019

Commits on Feb 4, 2019

Commits on Feb 5, 2019

Fixed a bug in mcmc_get_walkers that was not gerring the walkers for more than the first timestamp when multiple timestamps were specified.
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Commits on Feb 6, 2019

added the ability to specify a particular iteratino ID from a previous simulation.
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Commits on Feb 7, 2019

Commits on Feb 8, 2019

Commits on Feb 9, 2019

Commits on Feb 10, 2019

upweighted the tx and tl experiment relative to the rna deg experiment. (the rna deg exp to tx+tl experiment used to be 1:0.03, now it is 1:0.3)
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Commits on Feb 11, 2019

Commits on Feb 17, 2019

added a vnprl project. It is basically like the ACS 2014 paper, but with the protein expression and mrna levels scaled down to match what is claimed in Vincent Noireaux's PRL paper.
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Commits on Mar 13, 2019

Commits on Mar 14, 2019

Commits on Mar 15, 2019

Commits on Mar 18, 2019

working on figuring out a better scheme for generalization to the test circuit. see analysis corr1_Ffix2
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Commits on Mar 20, 2019

Commits on Apr 19, 2019

Commits on Apr 21, 2019

phase 1b: fixing more parameters, expanding the range for others. also started the stubs for phase 2 and the full IFFL training.
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Commits on Apr 22, 2019

Commits on Apr 24, 2019

further extended the range of parameter values, and fixed a bug in the data info.
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Commits on Apr 26, 2019

SET UP PHASE 2 WITH THE RIGHT PARAMETERS
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Commits on Apr 28, 2019

added trajectory plotting code, and fixed bug in phase 2 mcmc info file where the ranges were not right.
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Commits on Apr 29, 2019

extended the limits of RNAP and the tetR sequestration parameters.
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Commits on May 1, 2019

Commits on May 3, 2019

bugfix in the full iffl training file.
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Commits on May 6, 2019

the plas system was not fitting well enough. there was not enough deGFP protein produced. I relaxed the termination rate for both tx ans tl, and finally got the plots to look somewhat reasonable by…
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Commits on May 7, 2019

made the parameter ranges for the unactivated plas promoter Kd broader. This is to allow weaker association of the RNAP to the unactivated promoter.
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Commits on May 8, 2019

Added full training B files:
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Commits on May 9, 2019

added the file training_fullC, which has expanded parameter ranges, and also estimates many more parameters.
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Commits on May 11, 2019

added training fullD: relative to training fullC, i fixed 3 parameters, after checking restrictions in analysis..training_fullC. The three parameters fixed were:
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Commits on May 12, 2019

Added training E, that differs from training D in that the ktx and ktl are fixed from values found from training D. Note that in training D, we found the ktx and ktl to be exactly inversely proport…
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Commits on Apr 20, 2020

Commits on May 8, 2020

bugfix in RNAP parameter ranges of vnprl F3
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Commits on May 10, 2020

Commits on May 13, 2020

Commits on Jul 26, 2020

Commits on Jul 27, 2020

Merge branch 'minmcmcv5a' of https://github.com/vipulsinghal02/txtlsim into minmcmcv5a
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Commits on Jul 31, 2020

restoring the runsummaries. a complicated thing between dropbox and github happened that caused it to be deleted: Take note.
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Commits on Aug 5, 2020

Commits on Aug 14, 2020

minor changes to geneexpr
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Commits on Dec 16, 2020

updated run summaries file
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Commits on Mar 27, 2022

Commits on May 24, 2022