Chapter

Membrane Computing

Volume 6501 of the series Lecture Notes in Computer Science pp 119-143

BioSimWare: A Software for the Modeling, Simulation and Analysis of Biological Systems

  • Daniela BesozziAffiliated withDipartimento di Informatica e Comunicazione, Università degli Studi di Milano
  • , Paolo CazzanigaAffiliated withDipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca
  • , Giancarlo MauriAffiliated withDipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca
  • , Dario PesciniAffiliated withDipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca

Abstract

BioSimWare is a novel software that provides a user-friendly framework for the modeling and stochastic simulation of complex biological systems, ranging from cellular processes to population phenomena. BioSimWare implements several stochastic algorithms to simulate the dynamics of single or multi-volume models, as well as automatic tools to analyze the effect of variation of the system parameters. BioSimWare supports SBML format, and can automatically convert stochastic models into the corresponding deterministic formulation. The main features of BioSimWare are presented in this paper, together with some applications which highlight the most relevant aspects of the computational tools that it provides.