SBML Level 3: an extensible format for the exchange and reuse of biological models

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. 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 how SBML Level 3 provides the foundation needed to support this evolution

SBML level 3: An extensible format for the exchange and reuse of biological models

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. 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 how SBML Level 3 provides the foundation needed to support this evolution

Integrative models for TGF-β\beta signaling and extracellular matrix

International audienceThe extracellular matrix (ECM) is the most important regulator of cell-cell communication within tissues. ECM is a complex structure, made up of a wide variety of molecules including proteins, proteglycans and glycoaminoglycans. It contributes to cell signaling through the action of both its constituents and their proteolytic cleaved fragments called ma-tricryptins [Hynes and Naba, 2012, Ricard-Blum and Vallet, 2019]. In addition , ECM acts as a "reservoir" of growth factors and cytokines and regulates their bioavailability at the cell surface. By controlling cell signaling inputs, ECM plays a key role in regulating cell phenotype (differentiation, proliferation, migration, etc.). In this context, signaling networks associated with the polypeptide transforming growth factor TGF-β are unique since their activation are controlled by ECM and TGF-$β$ is a major regulator of ECM remodeling in return