Version control of pathway models using XML patches. Export

@article{citeulike:4208496, 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.}, author = {Saffrey, Peter and Orton, Richard}, citeulike-article-id = {4208496}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-3-34}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19292901}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19292901}, doi = {10.1186/1752-0509-3-34}, issn = {1752-0509}, journal = {BMC systems biology}, keywords = {biocad, kinetic\_modelling, software}, number = {1}, pages = {34+}, posted-at = {2009-03-23 09:05:45}, priority = {5}, title = {Version control of pathway models using XML patches.}, url = {http://dx.doi.org/10.1186/1752-0509-3-34}, volume = {3}, year = {2009} }

TY - JOUR ID - citeulike:4208496 L3 - citeulike-article-id:4208496 N2 - 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. IS - 1 JF - BMC systems biology SN - 1752-0509 TI - Version control of pathway models using XML patches. VL - 3 SP - 34 KW - biocad KW - kinetic_modelling KW - software AU - Saffrey, Peter AU - Orton, Richard PY - 2009/// UR - http://dx.doi.org/10.1186/1752-0509-3-34 ER -