Date: Apr. 30, 2001
Link: http://www.cds.caltech.edu/erato
Source Author or Organization: Caltech ERATO Kitano Systems Biology Project

Systems Biology Markup Language (SBML) is an XML-based language for describing simulations in systems biology. The language is oriented towards representing biochemical networks common in research on a number of topics, including: cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.

SBML is the product of close collaboration between the teams developing BioSpice, Gepasi , DBSolve, E-Cell, Jarnac, StochSim and Virtual Cell.

The motivations for developing SBML stemmed from the current inability to exchange models between biochemical network simulation/analysis tools. The creators of SBML kept its base definition as simple as possible in order for simulator developers to be able to implement SBML support in their own specialized tools.

This base definition (SBML Level 1) is the result of merging modeling-language features from a number of existing software packages, and was designed to provide an information model able to meet the minimal requirements of most biochemical models. By freezing subsets of features in SBML definitions at incremental levels, we hope to provide the community with stable standards to which software authors can design to, while at the same time allowing the simulation community to gain experience with the language definitions before introducing new elements.

Additional structures and facilities will be added to SBML in subsequent levels. Features planned for SBML Level 2 include the adoption of hierarchical models and spatial characteristics.