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

By Vipul Singhad, Zoltan A. Tuza, Zachary Z. Sun, Richard M. Murray

Posted 05 Aug 2020
bioRxiv DOI: 10.1101/2020.08.05.237990

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. ### Competing Interest Statement RMM and ZZS declare a conflict of interest: RMM, ZZS hold ownership in Tierra Biosciences (formerly Synvitrobio). The work presented here was funded off of a DARPA SBIR to Synvitrobio, Inc. (ZZS), contract No: W911NF-16-P-0003, and a Caltech Grubstake Grant (RMM, ZZS).

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