The Physiome Model Repository – PMR

The Physiome Model Repository – PMRDavid Nickerson ([email protected])

Auckland Bioengineering Institute

The University of Auckland

New Zealand

Acknowledgments

• Funding: • Maurice Wilkins Centre for Molecular Biodiscovery (

http://mauricewilkinscentre.org/)• Auckland Bioengineering Institute

(http://www.abi.auckland.ac.nz)• VPH NoE (http://www.vph-noe.eu)

• Hard work: Tommy Yu ([email protected])

The PHYSIOME model repository

• NOT the CellML model repository• NOT the FieldML model repository• IS a convenient repository aimed at improving

collaboration in model development and dissemination amongst the scientific community

• Use of physiome [COMBINE] standards enhances collaboration and and dissemination– but is not required in order to put your work in the

repository!

PMR Glossary

• Workspace – data agnostic mercurial repository• Changeset – a representation of a single revision of the

content of a workspace• Exposure – a permanent link to a specific changeset,

typically with data rendered for the web• Exposure plug-ins – an extensible framework for

rendering workspace content for web presentation• Plone CMS – workflow manager; user access controls;

web presentation; etc.

Data agnostic workspaces

• Generic mercurial repositories• Can contain any format data (currently relatively

unrestricted)– CellML, SBML, FieldML, SED-ML, PDF, .doc, ...– .m .c .cpp .f .f90 .py ...– .com .ipnode .ipelem .ipequa .ipgrid .ipcell ...

• No restriction to models only– experimental data, simulation results, generated

images, ...

A workspace

Workspace provenance

• A changeset is an immutable representation of the contents of the workspace

• Each changeset is a complete and unambiguous record of the workspace evolution – in the repository or outside of it

• Every changeset pushed to the model repository has a unique URL for citation

• Best practice will ensure that changesets are linked to identified authors

A group of modellers can work and exchange their models privately, until they are ready to publicise their work.

Modellers can push their changesets to a centralised repository, if and when they choose to.

Other users, if given permission, can clone the work from the centralised repository.

Each workspace can contain different types of data.

Collaborative model development and facilitated model exchange

Embedded workspaces

• Intended to manage the separation of modules which are integrated to create a model

• Facilitate the sharing and reuse of model components independently from the source model

• Enables the development of the modules to proceed independently, thus the version of the workspaces embedded is also tracked

• Allows authors to make use of relative URIs when linking data resources providing a file system agnostic method to describe complex module relationships in a portable manner

Membrane transporters

Assemble a cell model

Epithelial Cell

Versioning embedded workspaces

• Workspaces can be embedded at a specific revision or set to track the most recent revision of the source workspace

• Changes made to the source workspace will not affect the embedding workspace until the author explicitly chooses to update the embedded workspace

• Provides the author with the opportunity to review the changesets and make an informed decision regarding alterations to embedded revisions

• Alterations in the revision of an embedded workspace is data captured in a changeset – thus providing a clear provenance record of the entire dataset in the workspace

Exposures

• A permanent link to a specific changeset of a workspace• Data rendered in a format suitable for presentation in

the web interface of PMR – currently, but may also provide the trigger for various extra services

• An extensible plug-in based system has been implemented to provide data type specific rendering functionality

• An exposure provides an excellent object for curation as it is an immutable reference to a specific revision of the data contained in a workspace

PMR web interface

• Uses the Plone content management system• Provides the indexing used to power searching

– specific pieces of information are pulled out of certain file types when making exposures and added to the searchable indexes

• User access control for all workspaces in the repository– who can read from and write to a given workspace– controls the visibility of exposure pages

• Manages the interface workflows– state transitions (private to public to published)– allows repository curators some level of oversight

and control

MORRE search

• Ron Henkel and Tommy Yu have implemented a prototype advanced search and ranked retrieval interface for PMR

• http://184.169.251.126/morre_pmr2_search• Indexes workspaces when triggered during exposure

creation via webservices (driving and testing services)• Leverage the power of Apache Lucene – fuzzy searches,

wildcards, …• Prototype for the integration of BudHat services with

PMR data.

Tutorial / documentation

• Some documentation available at https://abibook.readthedocs.org/ (under the PMR section) - please report issues at: https://github.com/nickerso/ABIBook

• See the CellML model repository tutorial for a guided run through some of the features of PMR (with CellML models)

• Testing instance of PMR available at: http://184.169.251.126/• No changes make it back into the actual repository

unless you migrate them• Have a play!