Common ground between modelers and simulation software: the Systems Biology Markup Language (SBML)
TM Common ground between modelers and simulation software: The Systems Biology Markup Language (SBML)SBML Editors SBML Team Mike Hucka California Institute of Technology, Pasadena, CA, US Mike Hucka California Institute of Technology, Pasadena, CA, US Frank Bergmann California Institute of Technology, Pasadena, CA, US Frank Bergmann California Institute of Technology, Pasadena, CA, US Sarah Keating European Bioinformatics Institute, Cambridge, UK Sarah Keating European Bioinformatics Institute, Cambridge, UK Chris Myers University of Utah, Salt Lake City, UT, US James Schaff U. Connecticut Health Center, Farmington, CT, US Lucian Smith University of Washington, Seattle, WA, US Lucian Smith University of Washington, Seattle, WA, US Linda Taddeo California Institute of Technology, Pasadena, CA, US SBML SBO The Systems Biology Markup Language (SBML) is a computer-readable The Systems Biology Ontology (SBO) provides a set of controlled vocabularies format for representing models of biological processes. Its applicable to that can be used to make the mathematical meaning of a model more precise simulations of metabolism, cell-signaling, and many other topics. and machine-readable. Each component of model can be annotated with references to terms from SBO, allowing software to “understand” what kind of Over 230 software systems support SBML today. entities they are. The result: software can work more intelligently with models. See http://sbml.org/SBML_Software_Guide Example components of an SBML model: Today, various software systems use SBO terms to give users impressive new capabilities for working with SBML models. • Compartments: well-stirred containers of finite size where species are located. • Species: pools of entities of the same kind located in a compartment and Find out more about SBO at http://biomodels.net/sbo participating in reactions (processes). • Reactions: statements describing transformation, transport or binding MIRIAM processes that change the amount of one or more species. The guidelines for the Minimum Information Requested in the Annotation of biochemical Models (MIRIAM) define a simple approach for two important • Parameters: quantities with symbolic names, usable in mathematical aspects of reusable models: formulas throughout a model. • Events: statements describing discontinuous, instantaneous changes in • The minimum information a model should contain in order for readers to the values of one or more variables of any type (e.g., species). be able to trace its provenance, and • A simple scheme for encoding both the provenance data as well as SBML Level 3 references to external data sources (such as external databases). Find out more about MIRIAM at http://biomodels.net/miriam SBML Level 3 Core released 6 October 2010 See http://sbml.org/Documents/Specifications SBML Level 3 defines a mechanism whereby packages SED-ML can add syntax and semantics for new features. Reproducing the results of using a model requires having more than just Examples being developed today: the model at hand: it requires knowing such things as the simulation system used, the software settings, the initial and starting conditions for the model • Multicellular/multicomponent species: species with internal execution, the way that the output data was arranged, and so on. state, structure & bonds between individual entities. The Simulation Experiment Description Markup Language (SED-ML) is a • Qualitative models: formalisms such as Boolean networks and Petri Nets. software-independent format for recording such data in a way that can be • Flux balance constraints: steady-state models (e.g., for flux-balance analysis). used and exchanged by many different software systems. Its aim is to answer the question “How was this model used to produce that result?” • Spatial models: models where compartments are spatially inhomogeneous and processes involve spatial variables. Find out more about SED-ML at http://sed-ml.org http://sbml.org Support for SBML infrastructure and software development provided by NIGMS grant GM070923.