A landmark new paper about SBML Level 3 has been published in the journal Molecular Systems Biology. Long in the making, the paper is the work of a large community of SBML users and developers who have contributed to the development of SBML Level 3 for over a decade.
The paper reflects many modern realities and the state of SBML. 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. Systems Biology Markup Language (SBML) is a format designed exactly for this purpose. 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. 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. The paper provides the SBML community’s perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.