Dataset Information
MEANS: python package for Moment Expansion Approximation, iNference and Simulation.
Ontology highlight
ABSTRACT: Motivation
Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems.Results
We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis.Availability and implementation
https://github.com/theosysbio/meansContacts
m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.ukSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Fan S
PROVIDER: S-EPMC5018365 | biostudies-literature | 2016 Sep
REPOSITORIES: biostudies-literature
Publications
MEANS: python package for Moment Expansion Approximation, iNference and Simulation.
Bioinformatics (Oxford, England) 20160505 18
<h4>Motivation</h4>Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the mome ...[more]