StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes

PLoS One. 2013 Nov 18;8(11):e79345. doi: 10.1371/journal.pone.0079345. eCollection 2013.

Abstract

Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python), which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Theoretical*
  • Software

Grant support

TRM acknowledges funding from the project BioSolar Cells, co-financed by the Dutch Ministry of Economic Affairs. BGO is supported by the ZonMW Genomics-Zenith program, project 93511039. FJB acknowledges funding of NWO-VIDI Project 864.11.011. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.