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.

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 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