Physiome Project: About CellML

The CellML language is an open standard based on the XML markup language. CellML is developed by the Auckland Bioengineering Institute at The University of Auckland and affiliated research groups.

Creating clever codes

Just as HTML is the common language for encoding the words on your web browser, CellML is the XML language and software toolkit used to script, store and exchange computer models of biological systems. CellML makes it easy for people to share models, even if they are using different model-building software, and it can easily fit in with models at the tissue and molecular levels. It also lets people build new models and test their models’ reliability against other models using CellML validation tools.

Storing and exchanging computer-based mathematical models

CellML was first developed at the ABI under the leadership of Associate Professor Poul Nielsen to help the VPH/Physiome Project team build a better model of the heart. It was designed to describe the different parts of the heart model and how they relate to one another, and the mathematical equations that underline processes in the heart’s cells. Today, the online CellML repository has cellular-level models for many different parts of the body, not just the heart. There is also a range of tools available for working with CellML, including the modelling and simulation environment OpenCell, developed at the ABI.

Broader application

Although CellML was originally intended for the description of biological models, it has a broader application (for an example, see the classical Mooney-Rivlin Constitutive Material Law). CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository).

A sanctioned model definition standard

CellML is now a sanctioned model definition standard for European Commission and National Institutes of Health-funded research. It is often used in conjunction with FieldML, another XML-based standard language being developed at the ABI.

FieldML

The CellML project is closely affiliated with another XML-based language project developed by The Physiome Project, FieldML. Combined, these languages will provide a complete vocabulary for describing biological information at a range of resolutions from the subcellular to organism level.

Learn more about CellML

Find out more about the development of CellML at the project website. There you can read detailed information on getting started with CellML, the CellML specification and details about the CellML community.