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Bioinformatics Advance Access published online on September 9, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti018
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 28, 2004
Revised August 31, 2004
Accepted September 3, 2004

Article

Simulation tools for biochemical networks: evaluation of performance and usability

Antti Pettinen 1*, Tommi Aho 1, Olli-Pekka Smolander 1, Tiina Manninen 1, Antti Saarinen 1, Kaisa-Leena Taattola 1, Olli Yli-Harja 1, and Marja-Leena Linne 1

1 Institute of Signal Processing, Tampere University of Technology P.O.Box 553, 33101 Tampere, Finland

* To whom correspondence should be addressed. E-mail: antti.pettinen{at}tut.fi.


  Abstract

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 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 which are intended for 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 protein kinase C's active form. 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 which need to be emphasized in the future.


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