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bioRxiv · 10.1101/2020.08.05.237990

A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems

Singhal, V.·Tuza, Z. A.·Sun, Z.·Murray, R. M.
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Abstract

We introduce a MATLAB based simulation toolbox, called txtlsim, for an E. 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 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 protien expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

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Singhal, V., Tuza, Z. A., Sun, Z., Murray, R. M.. 2020-08-05. A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems. https://doi.org/10.1101/2020.08.05.237990

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