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Tools for kinetic modeling of biochemical networks

Nature Biotechnology volume 24, pages 667–672 (2006)Cite this article

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.

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Acknowledgements

R.A. acknowledges support by a Ramon y Cajal Investigator Award, from the Spanish Ministerio de Educacion y Ciencia. A.S. and F.A. acknowledge fellowships BPD/9457/2002 and BPD/11487/2002, respectively, from FCT-Portugal.

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Authors and Affiliations

  1. Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4,

    Rui Alves

  2. Lleida, 25008, Spain

    Rui Alves

  3. Instituto Rocha Cabral, Cç. Bento da Rocha Cabral 14, Portugal, Center of Chemistry and Biochemistry, University of Lisbon, Lisboa, 1257-047, Portugal

    Fernando Antunes

  4. CBS Computational Biology Services, Av. Do Brasil, No 20, 4o Esq, Lisboa, 1700-069, Portugal

    Fernando Antunes

  5. Center for Neuroscience and Cell Biology, Largo Marquês de Pombal, Coimbra, 3004-517, Portugal

    Armindo Salvador

  6. Department of Chemistry of the Faculty of Science and Technology, University of Coimbra, Coimbra, 3004-535, Portugal

    Armindo Salvador

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  1. Rui Alves
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  3. Armindo Salvador
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Correspondence to Armindo Salvador.

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Alves, R., Antunes, F. & Salvador, A. Tools for kinetic modeling of biochemical networks. Nat Biotechnol 24, 667–672 (2006). https://doi.org/10.1038/nbt0606-667

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