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Nat Biotechnol. 2006 Jun;24(6):667-72.

Tools for kinetic modeling of biochemical networks.

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  • 1Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4; 25008 Lleida, Spain. ralves@cmb.udl.es

Abstract

The number of software packages for kinetic modeling of biochemical networks continues to grow. Although most packages share a common core of functionality, the specific capabilities and user interfaces of different packages mean that choosing the best package for a given task is not trivial. We compare 12 software packages with respect to their functionality, reliability, efficiency, user-friendliness and compatibility. Although most programs performed reliably in all numerical tasks tested, SBML compatibility and the set-up of multicompartmentalization are problematic in many packages. For simple models, GEPASI seems the best choice for non-expert users. For large-scale models, environments such as Jarnac/JDesigner are preferable, because they allow modular implementation of models. Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization.

PMID:
16763599
DOI:
10.1038/nbt0606-667
[PubMed - indexed for MEDLINE]
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