BioModels Database: a repository of mathematical models of biological processes

Methods Mol Biol. 2013;1021:189-99. doi: 10.1007/978-1-62703-450-0_10.


BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

MeSH terms

  • Algorithms*
  • Animals
  • Computer Simulation
  • Databases, Factual*
  • Humans
  • Internet
  • Models, Biological*
  • Search Engine*
  • Systems Biology
  • Vocabulary, Controlled