Systems Biology Software Resources

Since computational approaches and modelling are so central to systems biology, an important set of resources for the field is software. This includes software for data and model management, model and data analysis, and model simulation. Many of these resources are produced by the European systems biology community for use in the community, and a searchable and browsable collation of these resource will be provided on the community website.

Various aspects of software resources are important to systems biology:

  • Standard data formats, like SBML and SED-ML
  • Metadata formats, like MIRIAM, MIAME or other Minimum Information Models
  • Ontologies, such as the Systems Biology Ontology and the Gene Ontology.
  • Data analysis tools include things like sequence similarity and alignment tools, pathway analysis and data mining applications. These resources have a large overlap with the bioinformatics community and will include many resources developed or maintained by ELIXIR
  • Model manipulation and simulation software are increasingly accessible online, such as JWS Online, and client-side tools, like COPASI and MatLab. As modelling becomes increasingly multi-scale, new modelling tools will be required.
  • Additionally, online repositories for data and models also exist.


The ISBE infrastructure will need to interface with existing repositories, like BioModels and SABIO-RK, as well as identify gaps and requirements for emerging new data and modeling types.