A MATLAB toolbox for modeling genetic circuits in cell-free systems†
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 01, 2021
- Source ID
- 10.1093/synbio/ysab007
Entities
People
- Richard M. Murray
- Vipul Singhal
- Zachary Sun
- Zoltán A. Tuza
Organizations
- Air Force Office of Scientific Research
- California Institute of Technology
- Defense Advanced Research Projects Agency
- Imperial College London