SBMLmerge, a system for combining biochemical network models.

@article{citeulike:2707735, abstract = {The Systems Biology Markup Language (SBML) is an XML-based format for representing mathematical models of biochemical reaction networks, and it is likely to become a main standard in the systems biology community. As published mathematical models in cell biology are growing in number and size, modular modelling approaches will gain additional importance. The main issue to be addressed in computer-assisted model combination is the specification and handling of model semantics. The software SBMLmerge assists the user in combining models of biological subsystems to larger biochemical networks. First, the program helps the user in annotating all model elements with unique identifiers pointing to databases such as KEGG or Gene Ontology. Second, during merging, SBMLmerge detects and resolves various syntactic and semantic problems. Typical problems are conflicting variable names, elements which appear in more than one input model, and mathematical problems arising from the combination of equations. If the input models make contradicting statements about a biochemical quantity, the user is asked to choose between them. In the end the merging process results in a new, valid SBML model.}, address = {Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. schulzma@molgen.mpg.de}, author = {Schulz, M. and Uhlendorf, J. and Klipp, E. and Liebermeister, W. }, citeulike-article-id = {2707735}, issn = {0919-9454}, journal = {Genome informatics. International Conference on Genome Informatics}, keywords = {model\_components, model\_management, sbmlmerge}, number = {1}, pages = {62--71}, posted-at = {2008-04-23 15:06:51}, priority = {5}, title = {SBMLmerge, a system for combining biochemical network models.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17503356}, volume = {17}, year = {2006} }

TY - JOUR ID - citeulike:2707735 L3 - citeulike-article-id:2707735 TI - SBMLmerge, a system for combining biochemical network models. JF - Genome informatics. International Conference on Genome Informatics VL - 17 IS - 1 SP - 62 EP - 71 AD - Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. schulzma@molgen.mpg.de SN - 0919-9454 N2 - The Systems Biology Markup Language (SBML) is an XML-based format for representing mathematical models of biochemical reaction networks, and it is likely to become a main standard in the systems biology community. As published mathematical models in cell biology are growing in number and size, modular modelling approaches will gain additional importance. The main issue to be addressed in computer-assisted model combination is the specification and handling of model semantics. The software SBMLmerge assists the user in combining models of biological subsystems to larger biochemical networks. First, the program helps the user in annotating all model elements with unique identifiers pointing to databases such as KEGG or Gene Ontology. Second, during merging, SBMLmerge detects and resolves various syntactic and semantic problems. Typical problems are conflicting variable names, elements which appear in more than one input model, and mathematical problems arising from the combination of equations. If the input models make contradicting statements about a biochemical quantity, the user is asked to choose between them. In the end the merging process results in a new, valid SBML model. KW - model_components KW - model_management KW - sbmlmerge AU - Schulz, M AU - Uhlendorf, J AU - Klipp, E AU - Liebermeister, W PY - 2006/// UR - http://view.ncbi.nlm.nih.gov/pubmed/17503356 ER -