title: Simulation tools for biochemical networks: evaluation of performance and usability.
abstract: BACKGROUND
  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.
authors.affiliation: Institute of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland. antti.pettinen@tut.fi
authors.forename: Antti
authors.initials: A
authors.lastname: Pettinen
authors.forename: Tommi
authors.initials: T
authors.lastname: Aho
authors.forename: Olli-Pekka
authors.initials: OP
authors.lastname: Smolander
authors.forename: Tiina
authors.initials: T
authors.lastname: Manninen
authors.forename: Antti
authors.initials: A
authors.lastname: Saarinen
authors.forename: Kaisa-Leena
authors.initials: KL
authors.lastname: Taattola
authors.forename: Olli
authors.initials: O
authors.lastname: Yli-Harja
authors.forename: Marja-Leena
authors.initials: ML
authors.lastname: Linne
mesh_terms: D000818:Animals; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D012986:Software Validation; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors