This package contains the txtlsim toolbox, which 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). 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.
Clone the repository using
git clone https://github.com/vipulsinghal02/txtlsim_buildacell.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 from 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 into the MATLAB command line, followed by mcmc_init. This initializes the txtlsim toolbox.
Check if the toolbox is installed properly by running the follwoing 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.
We have created a series of tutorials that can be used to gain increasing levels of familiarity with the toolbox:
We recommend running through the examples in these tutorials, and exploring the associated reactions, species, and models. 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.
You can generate the figures in the paper using the scripts in the generate_paper_figs directory.
- A full set of worked examples, including the repressilator, toggle switch, IFFL, linear vs plasmid DNA mechanics, and ClpX mediated protein degradation mechanics.
- Worked examples of how to use the toolbox for Bayesian parameter inference and part characterization.
- A tutorial on how to add your own component files to extend the toolbox.
More information can be found in the following references:
Main paper:
Vipul Singhal, Zoltan A. Tuza, Zachary Sun, Richard M Murray, A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems bioRxiv 2020.08.05.237990; doi: https://doi.org/10.1101/2020.08.05.237990
Related:
V. Singhal, Z. A. Tuza, Z. Z. Sun and R. M. Murray, (2020). A MATLAB Toolbox for Modeling the Behavior of Genetic Circuits in Cell-Free Transcription-Translation Systems. In preparation.
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 # txtlsim_buildacell