COMODI: COmputational MOdels DIffer - a hands-on-poster

Models are regularly updated, even after publication. The BiVeS library [3, 4, 5] offers comparison of versions of SBML [6] and CellML [7] encoded models. The result of such a comparison is a list of changes, based on the differences in both XML files. While it is now easy to see the differences in a network, it is still not possible to provide - or retrieve - information about the causes and effects of these changes. For example, together with a model update it should be possible to provide information on the characteristics of a change, e.g. stating that the changes remove an error in the kinetics.<br>We manually analysed hundreds of model versions and their differences from the BioModels Database [9] and the CellML Model Repository [8] to study the evolution of computational<br>models. We then derived a vocabulary to describe the differences and implemented it in the COMODI ontology. The OWL encoding and a documentation are available from our website [1]. A Java library [2] allows for easy integration in software projects.<br>We envision to use COMODI for automatic annotation of differences generated in BiVeS, and we like to provide it to modellers who wish to document<br>the evolution of their models.<br><br>[1] http://purl.org/net/comodi<br>[2] https://github.com/binfalse/jCOMODI<br>[3] https://sems.uni-rostock.de/bives/<br>[4] Scharm et al.: An algorithm to detect and communicate the differences in computational models describing biological systems Bioinformatics, 2015<br>[5] Waltemath et al.: Improving the reuse of computational models through version control Bioinformatics, 2013<br>[6] Hucka et al.: The Systems Biology Markup Language(SBML): A medium for representation and exchange of biochemical network models Bioinformatics, 2003<br>[7] Lloyd et al.: CellML: its future, presentand past Progress in Biophysicsand Molecular Biology, 2004<br>[8] Lloyd et al.: The CellML ModelRepository Bioinformatics, 2008<br>[9] Liet al.: BioModels Database: An enhanced, curated and annotated resourcefor published quantitative kinetic models BMC Systems Biology, 2010<br><br>