Download Master Thesis semanticSBML a Tool for Creating, Checking

annotations are added. This makes it the best source for real life examples of
models that use the SBML format. The BioModels database was used not only
in the experiment as a source for models but also during the whole development
of semanticSBML.
Experiments To exemplify the functional efficiency and the potential uses
of the new algorithms three experiments were conducted. In the first experiment a clustering of the BioModels database was performed to exemplify a fully
automated method for finding similar models with the aide of the MIRIAM annotation API. In the second experiment the merging of the previously introduced
glycolysis models using semanticSBMLs new merge algorithm was attempted.
The third experiment consisted of the merging of a single celled model of an
“... autonomous metabolic oscillations in continuous culture of Saccharomyces
cerevisiae” by Wolf et al. [21] into a two celled model.
1.5
Organization of this Document
Special terms that a reader of this thesis should be aware of can be found in the
Appendix A. An overview of the most improtant SBML elements can be found
in the Appendix B. SBML elements play an important role in Sections 3.2, 3.3
and 4. Function and variable names are written in typewriter font.
This thesis describes each of the development steps in detail. Whereas
Section 2 has its main focus on the implementation of a fully functional release of semanticSBML. Section 3 has its main focus on the concepts of the
new annotation and merge algorithm with less focus on the implementational
details. In Section 4 the experiments will be presented. The conclusion in Section 5 is followed by and overview of planed enhancements of semanticSBML in
Section 6.
15