A MATLAB toolbox for modeling genetic circuits in cell-free systems

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Title A MATLAB toolbox for modeling genetic circuits in cell-free systems
Authors Vipul Singhal, Zoltan A. Tuza, Zachary Z. Sun and Richard M. Murray
Source Synthetic Biology, 6(1):ysab007, 2021
Abstract We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-based Transcription–Translation (TX–TL) system. This toolbox accounts for several cell-free-related phenomena, such as resource loading, consumption and degradation, and in doing so, models the dynamics of TX–TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein-expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.
Type Journal paper
URL https://www.biorxiv.org/content/10.1101/2020.08.05.237990v1
Tag STSM21-oupsynbio
ID 2021a
Funding Synvitrobio SBIR
Flags Biocircuits