title: MEANS: python package for Moment Expansion Approximation, iNference and Simulation.
abstract: 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.
  
  
  
  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.
  
  
  
  https://github.com/theosysbio/means
  
  
  
  m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Sisi
authors.initials: S
authors.lastname: Fan
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Geissmann
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Eszter
authors.initials: E
authors.lastname: Lakatos
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Saulius
authors.initials: S
authors.lastname: Lukauskas
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Angelique
authors.initials: A
authors.lastname: Ale
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Ann C
authors.initials: AC
authors.lastname: Babtie
authors.affiliation: MRC Biostatistics Unit, Cambridge CB2 0SR, UK.
authors.forename: Paul D W
authors.initials: PD
authors.lastname: Kirk
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Michael P H
authors.initials: MP
authors.lastname: Stumpf
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D015870:Gene Expression; D007700:Kinetics; D015233:Models, Statistical; D012984:Software; D013269:Stochastic Processes