Dataset Information

Version control of pathway models using XML patches.

ABSTRACT:

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.

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.

SUBMITTER: Saffrey P

PROVIDER: S-EPMC2674044 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

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Publications

Version control of pathway models using XML patches.

Saffrey Peter P Orton Richard R

BMC systems biology 20090317

<h4>Background</h4>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.<h4>Results</h4>We present a model version control method, alon ...[more]

PMID: 19292901

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Dataset Information

Version control of pathway models using XML patches.

Background

Results

Conclusion

Publications

Version control of pathway models using XML patches.

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