CellML, OpenCOR, and the Physiome Project Repository David - - PowerPoint PPT Presentation

CellML, OpenCOR, and the Physiome Project Repository

David Nickerson (about.me/david.nickerson) Auckland Bioengineering Institute University of Auckland, New Zealand (CellML editor, past SED-ML editor)

• Store and exchange computer-based mathematical

models.

• Allows for modular encoding of models.
• Provides a method to reuse modules.
• Aim for an unambiguous description of the

mathematical model.

• Biology pushed off into annotations.
• http://cellml.org

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Modularity & reuse in CellML

• CellML provides the framework for encoding

mathematical models in a very modular manner – separation of mathematical model and a specific instance of the model (parameterization). – unambiguous definition of all physical quantities to allow automated translation between units across connections.

• Following some best practice guidelines ensures the

modules are “easily” reusable by the widest possible audience.

• Some examples…

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The Physiome Project Repository

• http://models.physiomeproject.org
• A freely accessible site for researchers to find, store,

and share models and associated data.

• Currently contains over 500 published models encoded

in CellML, and some examples of FieldML models – and many works in-progress!

• Powered by the PMR2 software framework.

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PMR2 Workspaces

• A collection of one or more related resources in the

repository.

• Version controlled, every revision to a workspace is

recorded as a changeset: – is an immutable representation of the contents of the workspace; – is a complete and unambiguous record of the workspace evolution; – has a unique URL for citation; – is linked to authors responsible for changes.

• Enables accurate provenance tracking.
• Can be nested to take advantage of modularity and

reuse

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PMR2 Exposures

• Data in the repository can be presented through

exposures.

• An exposure is a permanent link to a specific workspace

changeset.

• Data are rendered in a format suitable for presentation

in the web interface of the PMR2 instance.

• Rendering of specific data types is managed by an

extensible plug-in based system.

• Exposures are obvious objects for curation as they are

immutable references to specific revisions of the data contained in a workspace.

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http://opencor.ws

OpenCOR

• The combination of OpenCell and COR tools.
• Will be a comprehensive modeling environment, initially

using CellML but extensible to other standards (SED-ML and SBML desirable targets).

• Plugin-based architecture.
• Current capabilities focused on the simulation and

annotation of CellML models.

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eSolv

• A CellML-based simulation front-end for online teaching

– http://www.esolv.nl/

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CSim

• A minimal stand-alone simulation tool for CellML models

that works on Linux, Mac, and Window.

• https://code.google.com/p/cellml-simulator/
• Used by:

– SED-ML Web Tools – eSolv – GET (https://bitbucket.org/get) – Gib’s multi-cell agent-based simulation tool

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Wnt-CyclinD (??)

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Acknowledgements

• Virtual Physiological Rat Project, NIH grant [P50-

GM094503]

• VPH Network of Excellence – Project ID (FP7-

ICT-223920)

• EuHeart
• The Maurice Wilkins Centre for Molecular Biodiscovery
• RICORDO – Project ID (FP7-ICT-248502)
• More information, tutorial up at:

http://vph2014-abi-tutorial.readthedocs.org/en/latest/ (or come along this afternoon to session 1(b))

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