Validation tools

These tools focus on the validation of CellML model documents and the models they describe.

XML validation

Standard XML validation of CellML documents provides a good first stop in model validation. There are several choices here:

  • CellML 1.0 DTD (written by Warren Hedley, Auckland Bioengineering Institute)

  • CellML 1.0 XML Schema (written by Autumn Cuellar, Auckland Bioengineering Institute) — This is the simplest version of a CellML Schema possible. It completely leaves out all elements outside the CellML namespace. This is made available only for those who are used to validating XML against an XML Schema.

  • CellML 1.1 XML Schema (written by Andrew Miller, Auckland Bioengineering Institute) — This is a CellML 1.1 Schema. It imports additional W3C defined schema definitions for content MathML and XLink. A Java program which loads the schema and validates a list of documents is also available. This is made available only for those who are used to validating XML against an XML Schema.

  • RELAX NG schema for CellML 1.0 (written by Jonathan Cooper, University of Oxford) — also requires the MathML RELAX NG schema. Jonathan developed these as part of his validation tool suite, PyCml.

PyCml

As part of the Integrative Biology, Chaste and VPH NoE projects, Jonathan Cooper has been working on a validator tool suite for CellML 1.0. It is written in Python, and uses the RELAX NG and Schematron validation languages where appropriate. PyCml can be obtained and there is a web-based validation service available under the CellML page for the Chaste project.