Abstract
BackgroundComputational 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.ResultsWe 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.ConclusionOur 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.
Highlights
Computational modelling has become an important tool in understanding biological systems such as signalling pathways
Case Study: Epidermal Growth Factor (EGF) pathway To demonstrate our system we have tested it on a suite of models based on the EGFR/Mitogen Activated Protein Kinase (MAPK) system
The Mitogen Activated Protein Kinase (MAPK) pathway is at the heart of a molecular signalling network that governs the growth, proliferation, differentiation and survival of many, if not all, cell types [12,13,14]
Summary
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. The use of computational modelling is becoming widespread within the biological community. Models are applied to a diverse array of problems and are a standard analysis technique used both in academia and industry. Some aspects of model version control are similar to the established field of software version control. There are a number of significant differences that mean a separate treatment is needed
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