Minimal mcmc simbio

.gitignore

@@ -26,3 +26,69 @@ octave-workspace
 
 # .DS_store files
 .DS_Store
+
+*.sublime-project
+*.sublime-workspace
+
+*.txt
+*.todo
+
+# Image files
+*.png
+*.tiff
+*.eps
+*.jpg
+*.svg
+*.fig
+# data files
+*.gc
+*.xlsx
+*.csv
+
+# movie files
+*.mp4
+
+youngha_data_conversion/
+html/
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# MATLAB Crash Dumps #
+######################
+Crash_logs_*/

README.md

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+# Introduction
+
+This package contains two related toolboxes that work with MATALB Simbiology models: txtlsim and mcmc_simbio.
+
+The first toolbox is called txtlsim (ref), and can be used to simulate the chemical reations that occur in the Transcription-Translation (TX-TL) cell-free gene expression system developed at the University of Minnesota (Vincent Noireaux) and Caltech (Richard Murray) (refs). The main features of this toolbox are its ability to track the loading of enzymatic machinery, the consumption of resources, the ease of setting up models, the automatic accounting of retroactivity effects, and the extensibility the reaction networks generated. 
+
+The second toolbox is called mcmc_simbio. This is a concurrent Bayesian parameter inference toolbox for MATLAB Simbiology models. The Bayesian parameter inference is performed using a modification of Aslak Grinsted's MATLAB implementation of the affine invariant ensemble Metropolis-Hastings MCMC sampler (ref). We have added support for what we call 'concurrent' parameter inference, which refers to the capability to estimate a common set of parameters that get used simultaneously and in arbitrary combinations in multiple experiments/models. More information can be found below. 
+
+# The Toolboxes
+
+## Getting the toolbox and running some simple examples
+
+Clone the repository using 
+
+```
+git clone https://github.com/BuildACell/txtlsim.git
+```
+
+into a directory you wish to put the toolbox in. Alternatively, if you do not plan to version control the toolbox, you can simply download it as a zip file using the green button on the [main page](https://github.com/BuildACell/txtlsim). 
+
+Lets call the directory where you cloned or downloaded the repository `trunk`, i.e., this is where directories like `core`, `components`, `examples` and `mcmc_simbio` are. Open MATLAB, and set the current working directory to `trunk`. Type in `txtl_init` and `mcmc_init` into the MATLAB command line. This initializes the txtlsim and mcmc_simbio toolboxes. 
+
+Check if both the toolboxes are installed properly by running the follwoing examples:
+
+### txtlsim examples
+Start with typing in `geneexpr` into the command window. This should run a constitutive gene expression example in the toolbox, and you should see a plot with three subplots (protein; mRNA and DNA; and resource usage) appear. There should not be any error messages in the command window. 
+
+Next, run the `negautoreg` example in the command line. Again, you should see a plot of the species in the system, and no errors. This example simulates the negative autoregulation circuit. 
+
+Type in `edit TXTL_tutorial` into the command line to open the tutorial file. You can also use the MATLAB publisher button to publish this file, and look at it in the MATLAB help file markup. We recommend running through the examples in this file, and exploring the reactions, species, etc set up in this file. Familiarity with the MATLAB Simbiology command line is helpful here. To learn more about Simbiology, go to the [Getting Started Using the Simbiology Command Line](https://www.mathworks.com/help/simbio/gs/simbiology-command-line-tutorial.html) page. 
+
+### mcmc_simbio examples
+
+Next, open and explore the mcmc_simbio estimation examples given in the files `proj_mcmc_tutorial`, `proj_mcmc_tutorial_II`, and `proj_mcmc_tutorial_III` in the `trunk\mcmc_simbio\proj\` directory. We strongly recommend you skim through the `mcmc_info.m` and `data_info` files (`trunk\mcmc_simbio\models_and_supporting_files\` or type `help mcmc_info` and `help data_info` into the MATLAB command line) to gain an understanding of some of the key functionalities of the parameter inference toolbox. Along with the three tutorial files, the `mcmc_info.m` and the `data_info.m` files provide an initial idea of the capabilities of the toolbox. 
+
+## References
+
+More information can be found in the following references: 
+
+Z. A. Tuza, V. Singhal, J. Kim and R. M. Murray, "An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system," 52nd IEEE Conference on Decision and Control, Firenze, 2013, pp. 1404-1410.
+doi: 10.1109/CDC.2013.6760079
+
+
+Vipul Singhal, 2018
+California Institute of Technology 

auxiliary/boundedline/.gitignore

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+# MATLAB #
+##########
+# Editor autosave files
+*~
+*.asv
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

auxiliary/boundedline/Inpaint_nans/.gitignore

@@ -0,0 +1,37 @@
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

auxiliary/boundedline/Inpaint_nans/demo/html/inpaint_nans_demo.html

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+<html xmlns:mwsh="http://www.mathworks.com/namespace/mcode/v1/syntaxhighlight.dtd">
+   <head>
+      <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+
+      <!--
+This HTML is auto-generated from an M-file.
+To make changes, update the M-file and republish this document.
+      -->
+      <title>inpaint_nans_demo</title>
+      <meta name="generator" content="MATLAB 7.0.1">
+      <meta name="date" content="2006-06-28">
+      <meta name="m-file" content="inpaint_nans_demo"><style>
+body {
+  background-color: white;
+  margin:10px;
+}
+h1 {
+  color: #990000; 
+  font-size: x-large;
+}
+h2 {
+  color: #990000;
+  font-size: medium;
+}
+p.footer {
+  text-align: right;
+  font-size: xx-small;
+  font-weight: lighter;
+  font-style: italic;
+  color: gray;
+}
+
+pre.codeinput {
+  margin-left: 30px;
+}
+
+span.keyword {color: #0000FF}
+span.comment {color: #228B22}
+span.string {color: #A020F0}
+span.untermstring {color: #B20000}
+span.syscmd {color: #B28C00}
+
+pre.showbuttons {
+  margin-left: 30px;
+  border: solid black 2px;
+  padding: 4px;
+  background: #EBEFF3;
+}
+
+pre.codeoutput {
+  color: gray;
+  font-style: italic;
+}
+pre.error {
+  color: red;
+}
+
+/* Make the text shrink to fit narrow windows, but not stretch too far in 
+wide windows.  On Gecko-based browsers, the shrink-to-fit doesn't work. */ 
+p,h1,h2,div {
+  /* for MATLAB's browser */
+  width: 600px;
+  /* for Mozilla, but the "width" tag overrides it anyway */
+  max-width: 600px;
+  /* for IE */
+  width:expression(document.body.clientWidth > 620 ? "600px": "auto" );
+}
+
+    </style></head>
+   <body><pre class="codeinput"><span class="comment">% Surface fit artifact removal</span>
+[x,y] = meshgrid(0:.01:1);
+z0 = exp(x+y);
+
+znan = z0;
+znan(20:50,40:70) = NaN;
+znan(30:90,5:10) = NaN;
+znan(70:75,40:90) = NaN;
+
+z = inpaint_nans(znan,3);
+
+<span class="comment">% Comparison to griddata</span>
+k = isnan(znan);
+zk = griddata(x(~k),y(~k),z(~k),x(k),y(k));
+zg = znan;
+zg(k) = zk;
+
+close <span class="string">all</span>
+figure
+surf(z0)
+title <span class="string">'Original surface'</span>
+
+figure
+surf(znan)
+title <span class="string">'Artifacts (large holes) in surface'</span>
+
+figure
+surf(zg)
+title([<span class="string">'Griddata inpainting ('</span>,num2str(sum(isnan(zg(:)))),<span class="string">' NaNs remain)'</span>])
+
+figure
+surf(z)
+title <span class="string">'Inpainted surface'</span>
+
+figure
+surf(zg-z0)
+title <span class="string">'Griddata error surface'</span>
+
+figure
+surf(z-z0)
+title <span class="string">'Inpainting error surface (Note z-axis scale)'</span>
+</pre><img vspace="5" hspace="5" src="inpaint_nans_demo_01.png"> <img vspace="5" hspace="5" src="inpaint_nans_demo_02.png"> <img vspace="5" hspace="5" src="inpaint_nans_demo_03.png"> <img vspace="5" hspace="5" src="inpaint_nans_demo_04.png"> <img vspace="5" hspace="5" src="inpaint_nans_demo_05.png"> <img vspace="5" hspace="5" src="inpaint_nans_demo_06.png"> <p class="footer"><br>
+         Published with MATLAB&reg; 7.0.1<br></p>
+      <!--
+##### SOURCE BEGIN #####
+% Surface fit artifact removal
+[x,y] = meshgrid(0:.01:1);
+z0 = exp(x+y);
+
+znan = z0;
+znan(20:50,40:70) = NaN;
+znan(30:90,5:10) = NaN;
+znan(70:75,40:90) = NaN;
+
+z = inpaint_nans(znan,3);
+
+% Comparison to griddata
+k = isnan(znan);
+zk = griddata(x(~k),y(~k),z(~k),x(k),y(k));
+zg = znan;
+zg(k) = zk;
+
+close all
+figure
+surf(z0)
+title 'Original surface'
+
+figure
+surf(znan)
+title 'Artifacts (large holes) in surface'
+
+figure
+surf(zg)
+title(['Griddata inpainting (',num2str(sum(isnan(zg(:)))),' NaNs remain)'])
+
+figure
+surf(z)
+title 'Inpainted surface'
+
+figure
+surf(zg-z0)
+title 'Griddata error surface'
+
+figure
+surf(z-z0)
+title 'Inpainting error surface (Note z-axis scale)'
+
+
+##### SOURCE END #####
+-->
+   </body>
+</html>