Towards a standard exchange format for spatial, multilevel multicellular models


Standardization of model descriptions has boosted the field of systems biology over the last decade. Standard formats such as SBML and CellML have allowed the exchange of models of biochemical reaction networks between users and simulation software, enhanced reproducibility of models and enables the creation of public model repositories. However, the recent shift in systems biology towards spatial multilevel models requires new modeling formalisms and simulation software for which existing exchange formats are not suitable. Here, we discuss the major challenges in defining a standard exchange format for computational models of multilevel and multicellular systems and formulate some suggestions for the establishment of a standard exchange format for such simulation models.

Proceedings of the Dagstuhl Seminar on Multiscale Spatial Computational Systems Biology (14481).