Simulation tools for biochemical networks: evaluation of performance and usability

Bioinformatics
Antti PettinenMarja-Leena Linne

Abstract

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. 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.

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Citations

Sep 23, 2008·Briefings in Bioinformatics·Dong-Yup LeeIftekhar A Karimi
Feb 9, 2008·Annual Review of Plant Biology·Igor G L Libourel, Yair Shachar-Hill
Jul 20, 2006·BMC Bioinformatics·Matti NykterOlli Yli-Harja
Nov 18, 2006·BMC Bioinformatics·Julio Saez-RodriguezMartin Ginkel
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Aug 2, 2006·Computational Biology and Chemistry·Tiina ManninenKeijo Ruohonen
Jun 21, 2018·Basic & Clinical Pharmacology & Toxicology·Marja-Leena Linne
Mar 21, 2007·IET Systems Biology·J J MandelW Dubitzky
Nov 19, 2005·The Biochemical Journal·Richard J OrtonWalter Kolch
Mar 9, 2017·Frontiers in Neuroinformatics·Tiina ManninenMarja-Leena Linne

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