Brett and Bas are co-authors on a new paper in Molecular Systems Biology describing the latest developments in model encoding in systems biology. Bas enthusiastically supports the use of standards in systems biology while Brett has been active in the SBML field for 15 years as a community member, specification writer, package coordinator (FBC), libSBML developer, editor and SBML team member.
This paper provides an overview of the modelling frameworks, tools and facilities that are central to the SBML community.
“Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose.
A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models.
The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. “