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What is BioSimWare

BioSimWare is a free software that allows the mechanistic modelling, stochastic simulation and analysis of complex biological systems.

BioSimWare is based on a simple modelling approach, which consists in describing the system under investigation through “reagents → products” reactions that represent the interactions between molecular species.

Stochastic simulations of emergent dynamics of the model can be easily run by setting the initial conditions, given by the amounts of molecular species and the kinetic constants, or by modulating the model parameters to test the effect of different initial conditions.

BioSimWare implements optimization techniques to carry out parameter estimation, which can be performed by providing an experimental/synthetic time series curve of one or more molecular species.

Statistical analysis and characterization of the dynamical properties of the system can be finally performed.

Computational tools available in BioSimWare

Here is a list of the main tools currently implemented in BioSimWare:

  • a user-friendly interface for the data entry of reactions and of initial conditions, as well as for the setting of stochastic simulations (single volume models);
  • stochastic simulation algorithms for single volume models: SSA, tau leaping, adaptive tau leaping;
  • stochastic simulation algorithms for multivolume models: tauDPP, StauDPP;
  • genetic algorithms and particle swarm optimizers for parameter estimation in single volume models.

Work in progress:

  • Java interface for multivolume models;
  • automatic tools for parameter sweep application;
  • sensitivity analysis tool;
  • tools for statistical analysis of simulation outcomes.
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