Automated Execution of Simulation Studies in Systems Medicine Using SED-ML and COMBINE Archive

Abstract

In this chapter we present a brief outlook into the automated execution of simulation studies in systems medicine, using Simulation Experiment Description Markup Language (SED-ML) and the Computational Modeling in Biology Network (COMBINE) archive. We describe the challenges faced in the exchanging of model data for reproducing results and briefly describe the efforts to correct these issues. An outline for SED-ML is given and detailed examples are presented, describing the creation and simulation of SED-ML models from existing standards (CellML and SBML specifically). Finally, we describe the creation of the COMBINE archive from the SED-ML files, as well as other community based standards.