title: Tools for kinetic modeling of biochemical networks.
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.
authors.affiliation: Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4; 25008 Lleida, Spain. ralves@cmb.udl.es
authors.forename: Rui
authors.initials: R
authors.lastname: Alves
authors.forename: Fernando
authors.initials: F
authors.lastname: Antunes
authors.forename: Armindo
authors.initials: A
authors.lastname: Salvador
mesh_terms: D001671:Biochemistry / Q000379:methods*; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface