A Distributed Revision Control System for Collaborative Development of Quantitative Biological Models

Abstract

With CellML 1.0, models are encapsulated completely by a single file. CellML 1.1 now allows a model to be decomposed into many smaller files that can represent a single component of a model that can be reused by other related models. Unfortunately, managing even just tens of models with hundreds of shared component files may be a daunting task. For instance, updating a shared component for one model may break another, or it may be difficult to locate the correct component to be included into a model that one may be building. A new version of the CellML Repository software is under development, and seeks to address those issues. This software, the Physiome Model Repository 2 (PMR2) has been prototyped. The PMR2 prototype uses a distributed version control system (DVCS) as the foundation, with a web-based front end that allows annotation of specific models. DVCS will allow a group of modelers to work together to construct models and using multiple versions of shared components with ease without reliance on a centralized server. The web-based front end of the prototype contains exposure pages that highlight a specific revision of a model; those pages contain curation information, various documentation and rendering of annotations (metadata). Simulation results can also be included on the exposure page, giving users a quick overview of what the models are capable of. © 2009 International Federation of Medical and Biological Engineering.