Osmium: helping PMR support the VPH requirements for identifiable and discoverable computational models Tommy Yu, Peter Hunter, David Nickerson Auckland.

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Presentation transcript:

Osmium: helping PMR support the VPH requirements for identifiable and discoverable computational models Tommy Yu, Peter Hunter, David Nickerson Auckland Bioengineering Institute University of Auckland

CellML Model Repository `95 CellML Model Repository `00 Physiome Model Repository `05 Physiome Model Repository (v2) `10 `15 Osmium

CellML model repository Collection of demonstration, example, and testing CellML 1.0 models. Internal version control system. Static pages generated as part of cellml.org website.

CellML model repository Collection of demonstration, example, and testing CellML 1.0 models. Internal version control system. Static pages generated as part of cellml.org website. Categorised using some kind of “ontology”

CellML model repository Collection of demonstration, example, and testing CellML 1.0 models. Internal version control system. Static pages generated as part of cellml.org website. Categorised using some kind of “ontology” LaTeX documentation source + CellML XML files

CellML Model Repository `95 CellML Model Repository `00 Physiome Model Repository `05 Physiome Model Repository (v2) `10 `15 Osmium

Physiome Model Repository Introduced Zope server with Plone CMS. LaTeX documentation migrated to “tmpDoc” inside the CellML documents. Extended Plone with CellML specific features to provide similar functionality as the CellML model repository.

CellML Model Repository `95 CellML Model Repository `00 Physiome Model Repository `05 Physiome Model Repository (v2) PMR2 launched June 2009. `10 `15 Osmium

PMR2 Facilitated model exchange directly between modellers, without reliance on a central repository. Detailed revision history for each model. User access workflows to control privacy when required. Embedded workspaces to enable model reuse and promote modular model development. File format agnostic. Distributable, installable... https://github.com/pmr2 https://models.physiomeproject.org

Workspaces Each (model | study | assay) stored in a workspace users can create themselves can store any kind of data is a DVCS (Git or Mercurial) full history is available users control access DVCS enhances collaboration. Support for modularity and reuse via embedded workspaces relative references facilitate sharing and archiving

Exposures Presentation view of a workspace. Plugins for various types of data. Indexing of metadata.

CellML Model Repository `95 CellML Model Repository `00 Physiome Model Repository `05 Physiome Model Repository (v2) PMR2 launched June 2009. `10 `15 Osmium

Osmium http://osmium.readthedocs.io/ RepoDono core component refactoring PMR2 remove distinction between workspaces and exposures (dynamic exposures) calmjs Python framework for building toolchains and utilities for working with the JavaScript/Node.js ecosystem from within a Python environment. more to come...

Acknowledgements