Overview

The Systems Biology Markup Language (SBML) is the de facto standard format to store dynamical models of biological networks. It enables the exchange of models, provides interoperability between simulators and promotes model reproducibility. SBML is often used to store models of biochemical networks that represent intracellular regulatory processes, such as cell cycle models. The EBI BioModels repository contains a vast collection of SBML models, browsable by Gene Ontology annotation.

Using SBML models in multicellular models serves two goals:

  1. To enable researchers of single-cell models to expand into multicellular models to explore inter-cellular interactions and the effect of spatial processes.
  2. To facilitate researchers of multicellular systems to include realistic and validated intracellular regulation models.

Morpheus has supported a subset of SBML models since its inception. In version 2.1, we have greatly improved the support for SBML models to include the almost complete SBML core specification in its lastest version (SBML Level 3 Version 2). Moreover, Morpheus’ SBML support has now been systematically validated using the SBML test suite.

This opens up a bridge to more than 8600 published pathway models openly available from the BioModels repository. Notably, Morpheus is the only one among the 12 tested SBML-simulators that also covers spatial and cell-based models. To closely integrate both worlds, Morpheus now offers a rich SBML model import dialog for selecting any of potentially pre-existing cell types from a Morpheus model or to create new cell-based models on the fly.