RT Journal Article
SR Electronic
T1 Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 121152
DO 10.1101/121152
A1 Anandh Swaminathan
A1 Victoria Hsiao
A1 Richard M. Murray
YR 2017
UL http://biorxiv.org/content/early/2017/03/27/121152.abstract
AB The recent abundance of high-throughput data for biological circuits enables data-driven quantitative modeling and parameter estimation. Common modeling issues include long computational times during parameter estimation, and the need for many iterations of this cycle to match data. Here, we present BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation for biological circuits. The BioSCRAPE package can be used for deterministic or stochastic simulations and can incorporate delayed reactions, cell growth, and cell division. Simulation run times obtained with the package are comparable to those obtained using C code - this is particularly advantageous for computationally expensive applications such as Bayesian inference or simulation of cell lineages. We first show the package’s simulation capabilities on a variety of example simulations of stochastic gene expression. We then further demonstrate the package by using it to do parameter inference for a model of integrase dynamics using experimental data. The BioSCRAPE package is publicly available online along with more detailed documentation and examples.