SBML Level 3: an extensible format for the exchange and reuse of biological models ; Molecular Systems Biology

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 developedSBMLLevel 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 ofSBMLand a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and howSBMLLevel 3 provides the foundation needed to support this evolution. ; National Institute of General Medical Sciences (NIGMS, US) [R01-GM070923]; Bundesministerium fur Bildung und Forschung (BMBF, DE)Federal Ministry of Education & Research (BMBF) [031L0104A]; NIH (US)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [P41-GM103313, R01-GM095485, 5R35-GM119770-03, GM57089]; Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)German Research Foundation (DFG) [EXC 2124]; German Center for Infection Research (DZIF); JSPS KAKENHIMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of ScienceGrants-in-Aid for Scientific Research (KAKENHI) [21700328]; National Institutes of Health (NIH, US)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [P41-GM103712]; ...