The University of Auckland
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CellML, SED-ML, and the Physiome Model Repository

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posted on 2016-09-19, 13:01 authored by David NickersonDavid Nickerson
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 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.