Version control of pathway models using XML patches.
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.


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.


CONCLUSIONS
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.
Saffrey
Peter
P
Department of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK. pzs@dcs.gla.ac.uk
Orton
Richard
R
D000818:Animals; D002460:Cell Line; D003198:Computer Simulation; D004815:Epidermal Growth Factor / Q000378:metabolism; D008954:Models, Biological; D011381:Programming Languages; D051381:Rats; D015398:Signal Transduction
D004815:Epidermal Growth Factor