Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

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Title Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Authors Ayush Pandey, William Poole, Anandh Swaminathan, Victoria Hsiao and and Richard M. Murray
Source Journal of Open Source Software (JOSS), 2023
Abstract In systems and synthetic biology, it is common to build chemical reaction network (CRN) models of biochemical circuits and networks. Although automation and other high-throughput techniques have led to an abundance of data enabling data-driven quantitative modeling and parameter estimation, the intense amount of simulation needed for these methods still frequently results in a computational bottleneck. Here we present bioscrape (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation of highly customizable chemical reaction networks. Specifically, bioscrape supports deterministic and stochastic simulations, which can incorporate delay, cell growth, and cell division. All functionalities - reaction models, simulation algorithms, cell growth models, partitioning models, and Bayesian inference - are implemented as interfaces in an easily extensible and modular object-oriented framework. Models can be constructed via Systems Biology Markup Language (SBML) or specified programmatically via a Python API. 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 show the package’s simulation capabilities on a variety of example simulations of stochastic gene expression. We also demonstrate the package by using it to do parameter inference on a model of integrase enzyme-mediated DNA recombination dynamics with experimental data. The bioscrape package is publicly available online (Pandey, Poole, et al., 2023) along with more detailed documentation and examples.
Type Journal paper
DOI 10.21105/joss.05057
Tag Pan+23-JOSS
ID 2022k
Funding AFOSR Syn Bio MURI