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Exploring CellML: Standards and Community Engagement for Biological Modeling

The 7th International CellML Workshop, held on March 25, 2013, in Auckland, New Zealand, offered insights into CellML, a globally collaborative model exchange standard originating from the ABI. This workshop focused on the diverse applications of CellML in fields such as electrophysiology, gene regulation, and synthetic biology. Participants engaged in discussions about model description, encoding, and exchange within the PhysioMe/VPH communities. The event fostered connections among over 100 members from academia and industry, facilitating discourse on CellML support, implementation, new feature requests, and future developments.

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Exploring CellML: Standards and Community Engagement for Biological Modeling

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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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