Version control of pathway models using XML patches

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.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.The use of computational modelling is becoming widespread within the biological community. Models are applied to a diverse array of problems and are now a standard analysis technique used both in academia and industry.Although modelling is now widely used, the methodology that supports modelling remains underdeveloped. In particular, a model will often develop and change over time, giving rise to many model versions but there is very little published work on model version control. Some aspects of model version control are similar to the established field of software version control. However, there are a number of significant differences that mean a separate treatment is needed.Many of the differences between software and model version control have at their core a difference in aims. The aim of a piece of software is to address a specific problem, described by its requirements. The aim of a model is the far more vague goal of understanding a biological system, sometimes expressed as specific questions (such as "does this set of reactions provoke a sustained or transient response?"), sometimes as how behaviour might change under different conditions and sometimes as a more general exploration of system properties.This contrast between the convergent aims of a software project and the more divergent aims of a modelling project make the version control needs fundamentally different. These differences include the need to manage combinations of model versions, giving rise to a much greater branching factor. There is also a need to maintain a lar