Community7th International CellML Workshop,

25 March 2013Auckland, New Zealand

The

www.cellml.org

What is CellML?

• After the gory details? Stayed tuned for Alan’s talk

• A model exchange standard originating at the ABI, but with contributors from around the globe.

• Broad areas of application:– electrophysiology, constitutive relationships, gene

regulation, PKPD, synthetic biology, etc.– lumped parameter models across all spatial scales

www.cellml.org

But it is more than a standard…

• A focal point for model description, encoding, and exchange within the Physiome / VPH / VPR / VP* communities.

• A world-leading success story from the ABI.• A worldwide community of scientists.

www.cellml.org

The CellML Editorial Board

www.cellml.org

The CellML Project Team

www.cellml.org

The CellML community

• http://www.cellml.org• All the information you might need:– Specifications;– Links to software tools;– Community news;– Documentation and tutorials.

www.cellml.org

The CellML community

• cellml-discussion@cellml.org• The primary medium for information

dissemination and community discussion.• 100+ members spanning academia and

industry.• Generally early discussion of issues of interest

to the broad community.

www.cellml.org

The CellML community

• https://tracker.physiomeproject.org• Detailed issue discussions.• Includes some related software tools (CellML

API, OpenCell, OpenCMISS(Iron, Zinc), FieldML).

• Ability to cross-link discussions to source repositories and related project’s items.

www.cellml.org

The CellML community

• cellml-tool-developers@cellml.org• Aimed at software developers.• General discussion of CellML support and

implementation across a range of software tools.

www.cellml.org

The CellML community

• Coming soon…• https://github.com/cellml• Will be the home of CellML “official”

specification development.• Publicly available (readonly).• Editorial board have write access.• Will ease the development and integration of

new features for future versions of CellML.

www.cellml.orgProposed workflow for adding new features to CellML

• Editorial board has developed guidelines for the addition of new features to CellML.

• Will take effect following CellML 1.2.• Feature requests– Wishes for support from the community.– Submitted via tracker.– Editors will initiate discussion on mailing list if

required.– Solutions can be provided as proposals.

www.cellml.orgProposed workflow for adding new features to CellML

• Proposals– Welcome any time via the tracker.– May originate from a feature request.– Includes detailed description of desired feature,

including XML examples.– Community vote on suitability of proposal.

• Accepted proposals– Support in at least two software tools to demonstrate

exchange.– Example CellML models demonstrating usage.

www.cellml.org

• COmputational Modeling in BIology NEtwork.• Initiative to coordinate the development of

various community standards and formats for computational models.

• To develop a set of interoperable and non-overlapping standards covering all aspects of modelling in biology.

• Provide a recognised voice.• http://co.mbine.org

www.cellml.org

www.cellml.org

• Annual COMBINE forums– Workshop style events with presentations,

posters, and breakout sessions.– Standards and supporting tools.– September 2013, Paris.

www.cellml.org

• HARMONY hackathons– HAckathon on Resources for MOdelling iN biologY– Focus on development of standards,

interoperability, and infrastructure.– Hands on hacking and interaction between people

focused on practical development of standards and supporting software.

– May 2013, Connecticut.– (combined CellML SBGN SBO BioPAX MIASE

meeting in 2009, Waiheke Island!)