Validation and simulation of qualitative models in Java™

A package for logical modeling has been added to the Java library JSBML.

In her bachelor thesis, Lisa Falk extended the widely used library JSBML by a package for the representation of logical models. Now Boolean models, Petri nets and much more can be processed. Lisa Falk implemented the necessary validation rules to ensure the syntactical correctness of the models. In cooperation with Prof. Claudine Chaouiya, it was also possible to automatically derive equations for function terms and integrate them into SBMLsqueezer. This means that logical models can now be created partially automatically. The work was done in close cooperation with Nicolas Rodriguez and builds on the results of Roman Schulte's project in the Google Summer of Code 2016.