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The. Community. 7 th International CellML Workshop, 25 March 2013 Auckland, New Zealand. 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:

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Community

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  1. The Community 7th International CellML Workshop, 25 March 2013 Auckland, New Zealand

  2. 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

  3. 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.

  4. The CellML Editorial Board

  5. The CellML Project Team

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

  7. The CellML community • cellml-discussion@cellml.org • The primary medium for information dissemination and community discussion. • 100+ membersspanning academia and industry. • Generally early discussion of issues of interest to the broad community.

  8. 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.

  9. 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.

  10. 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.

  11. Proposed 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.

  12. Proposed 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.

  13. COmputational Modeling in BIologyNEtwork. • 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

  14. Annual COMBINE forums • Workshop style events with presentations, posters, and breakout sessions. • Standards and supporting tools. • September 2013, Paris.

  15. HARMONY hackathons • HAckathon on Resources for MOdellingiNbiologY • 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!)

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