RT Journal Article
SR Electronic
T1 A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.08.05.237990
DO 10.1101/2020.08.05.237990
A1 Vipul Singhal
A1 Zoltan A. Tuza
A1 Zachary Z. Sun
A1 Richard M. Murray
YR 2020
UL http://biorxiv.org/content/early/2020/08/05/2020.08.05.237990.abstract
AB 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 StatementRMM 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).