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

T. Yu, J. R. Lawson, R. D. Britten

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contribution

2 Citations (Scopus)

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.

Original languageEnglish
Title of host publication13th International Conference on Biomedical Engineering - ICBME 2008
Place of PublicationBerlin, Germany
PublisherSpringer, Springer Nature
Pages1908-1911
Number of pages4
Volume23
ISBN (Print)9783540928409
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event13th International Conference on Biomedical Engineering, ICBME 2008 - , Singapore
Duration: 3 Dec 20086 Dec 2008

Other

Other13th International Conference on Biomedical Engineering, ICBME 2008
CountrySingapore
Period3/12/086/12/08

Keywords

  • CellML
  • escience
  • quantitative modeling
  • repository

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