Discrete stochastic simulation of cell signaling: comparison of computational tools.

Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our study, we have chosen to evaluate three stochastic simulation tools: Dizzy, Systems Biology Toolbox, and Copasi, using our own MATLAB implementation as a benchmark. The Gillespie stochastic simulation algorithm is used in all tests. With all the tools, we are able to simulate stochastically the behavior of the selected test case and to produce similar results as our own MATLAB implementation. However, it is not possible to use time-dependent inputs in stochastic simulations in Systems Biology Toolbox and Copasi. The present study is one of the first evaluations of stochastic simulation tools for realistic signal transduction pathways.

Simulation tools for biochemical networks: evaluation of performance and usability.

MOTIVATION: Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions. Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools. Knowledge of the properties and capabilities of the simulation tools would help bioscientists in building models based on experimental data. RESULTS: We examine selected simulation tools that are intended for the simulation of biochemical systems. We choose four of them for more detailed study and perform time series simulations using a specific pathway describing the concentration of the active form of protein kinase C. We conclude that the simulation results are convergent between the chosen simulation tools. However, the tools differ in their usability, support for data transfer to other programs and support for automatic parameter estimation. From the experimentalists' point of view, all these are properties that need to be emphasized in the future.