Physiome Model Repository

The Physiome Model Repository is an open source software suite that integrates Mercurial with Plone to provide a facility to store and manage models.

Introduction

The Physiome Model Repository (PMR) was designed to provide model upload, storage, curation and distribution capabilities. It was also the software that drove the official CellML Model Repository. Since it was not possible to extend it to support to more advanced usage requirements, such as proper version control and support for CellML 1.1, a complete rewrite was required, and so Physiome Model Repository 2 (PMR2) was created.

Like PMR, PMR2 is built upon Plone, an open source Content Management System (CMS), with integrated support for Mercurial, a Distributed Version Control System (DVCS). PMR2 is open source software, and is tri-licensed under the terms of GPLLGPL and MPL.

Mercurial is chosen as it enables modellers to collaborate on development without reliance on a central repository, allowing them to keep full control over their data, while tracking the development history in a way that can easily be merged back into a centralised system, such as the CellML Model Repository, which uses this software.

As PMR2 is built on top of Plone, all content management features it provides can be used. PMR2 provides facilities to generate documentation pages (called Exposure Pages) from the metadata presented in a model, which serves as an introduction to the models a modeller might want to present. Along with the curation facilities, which allow grading and categorization of models, this enables PMR2 to be a comprehensive suite of software that stores, tracks and presents models to the world.

If you wish to cite or reference PMR2, please refer to this citation:

Yu, T., Lloyd, C.M., Nickerson, D.P., Cooling, M.T., Miller, A.K., Garny, A., Terkildsen, J.R., Lawson, J., Britten, R.D., Hunter, P.J., Nielsen, P.M., The Physiome Model Repository 2Bioinformatics, (2011) 27(5): 743-744 doi:10.1093/bioinformatics/btq723.

Using PMR2

If you wish to simply use PMR2 to browse CellML models, the CellML Model Repository is the official instance, where you can find hundreds of CellML model workspaces for you to browse or clone with a Mercurial client. If you wish to install the same software locally on your machine, the installation page has details on installing PMR2 onto your machine, either from the current stable branch (v0.5) or the development version.

For any issues dealing with usage of PMR2, please file a tracker item at the Physiome Tracker. You may also be interested at the roadmap, which details the current development plan.