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Open Access Highly Accessed Research article

Revision history aware repositories of computational models of biological systems

Andrew K Miller1*, Tommy Yu1, Randall Britten1, Mike T Cooling1, James Lawson1, Dougal Cowan1, Alan Garny2, Matt DB Halstead1, Peter J Hunter1, David P Nickerson1, Geo Nunns13, Sarala M Wimalaratne14 and Poul M F Nielsen15

Author Affiliations

1 Auckland Bioengineering Institute, The University of Auckland, Private Bag 92019, Auckland, NZ

2 Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK

3 Johns Hopkins University, Baltimore, Maryland, USA

4 EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

5 Department of Engineering Science, Faculty of Engineering, The University of Auckland, Private Bag 92019, Auckland, NZ

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BMC Bioinformatics 2011, 12:22  doi:10.1186/1471-2105-12-22

Published: 14 January 2011

Abstract

Background

Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model.

One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file.

The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs) for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems.

Results

We have extended the Physiome Model Repository software to be fully revision history aware, by building it on top of Mercurial, an existing DVCS. We have demonstrated the utility of this approach, when used in conjunction with the model composition facilities in CellML, to build and understand more complex models. We have also demonstrated the ability of the repository software to present version history to casual users over the web, and to highlight specific versions which are likely to be useful to users.

Conclusions

Providing facilities for maintaining and using revision history information is an important part of building a useful repository of computational models, as this information is useful both for understanding the source of and justification for parts of a model, and to facilitate automated processes such as merges. The availability of fully revision history aware repositories, and associated tools, will therefore be of significant benefit to the community.