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)

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 > School of Infection & Immunity > Centre for Virus Research; College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary 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