Version control of pathway models using XML patches

Saffrey, P. and Orton, R. (2009) Version control of pathway models using XML patches. BMC Systems Biology, 3(34), (doi:10.1186/1752-0509-3-34)

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Abstract

<p>Background: Computational modelling has become an important tool in understanding biological systems such as signalling pathways. With an increase in size complexity of models comes a need for techniques to manage model versions and their relationship to one another. Model version control for pathway models shares some of the features of software version control but has a number of differences that warrant a specific solution.</p> <p>Results: We present a model version control method, along with a prototype implementation, based on XML patches. We show its application to the EGF/RAS/RAF pathway.</p> <p>Conclusion: Our method allows quick and convenient storage of a wide range of model variations and enables a thorough explanation of these variations. Trying to produce these results without such methods results in slow and cumbersome development that is prone to frustration and human error.</p>

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Saffrey, Dr Peter and Orton, Dr Richard
Authors: Saffrey, P., and Orton, R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Journal Name:BMC Systems Biology
Publisher:BioMed Central
ISSN:1752-0509
Published Online:17 March 2009
Copyright Holders:Copyright © 2009 The Authors
First Published:First published in BMC Systems Biology 3(34)
Publisher Policy:Reproduced under a Creative Commons Licence

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