CellML, SED-ML, and the Physiome Model Repository [article]

David Nickerson
2016 Figshare  
Invited presentation delivered at COMBINE 2016.CellML, SED-ML, and the Physiome Model Repository.David Nickerson, Auckland Bioengineering Institute, University of Auckland, New Zealand.CellML is an XML-based protocol for storing and exchanging computer-based mathematical models in an unambiguous, modular, and reusable manner. In addition to introducing CellML, in this presentation I will provide some of physiological examples that have help drive the development and adoption of CellML. I will
more » ... of CellML. I will also present the proposed changes being introduced in the next version of the specification, CellML 2.0.The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation setups to ensure exchangeability and reproducibility of simulation experiments. Here I will present an overview of the current version of SED-ML (Level 1 Version 2) and discuss the additional features introduced in the draft Level 1 Version 3 specification, as well as some of other upcoming features often requested.I will also demonstrate some of the functionality and content being added to the Physiome Model Repository which makes extensive use of both CellML and SED-ML to provide a rich repository of reproducible model descriptions.
doi:10.6084/m9.figshare.3839841.v1 fatcat:swtpo4tfvrgcdpgwn46urnbm6a