Tools for kinetic modeling of biochemical networks

Nat Biotechnol. 2006 Jun;24(6):667-72. doi: 10.1038/nbt0606-667.


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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biochemistry / methods*
  • Cell Physiological Phenomena*
  • Computer Simulation
  • Kinetics
  • Models, Biological*
  • Programming Languages*
  • Signal Transduction / physiology*
  • Software Validation
  • Software*
  • User-Computer Interface*