Nature Biotechnology 24, 667 - 672 (2006)
doi:10.1038/nbt0606-667
Tools for kinetic modeling of biochemical networksRui Alves1, Fernando Antunes2, 3
& Armindo Salvador4, 51
Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4; 25008 Lleida, Spain ralves@cmb.udl.es
2
Instituto Rocha Cabral, Cç. Bento da Rocha Cabral 14, Portugal, Center of Chemistry and Biochemistry, University of Lisbon, 1257-047 Lisboa, Portugal. 3
CBS Computational Biology Services, Av. Do Brasil, No 20, 4o Esq, 1700-069 Lisboa, Portugal. 4
Center for Neuroscience and Cell Biology, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal. 5
Department of Chemistry of the Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal.
Correspondence should be addressed to Armindo Salvador salvador@cnc.uc.pt 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.
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