The topic of the thesis is motivated by the need to automatically process and analyse existing biological pathways available in graphical form in public repositories, e.g., reactome.org, wikipathways, etc. In particular, this thesis focuses on obtaining a compact and unambiguously interpretable representation of biological pathways represented in the standard visual notation SBGN (Systems Biology Graphical Notation).

The goal of the thesis is to design and implement a software tool that automatically generates for a given SBGN process diagram (SBGN-PD) an executable rule-based model that will be readable (and analysable) by the tool eBCSgen. The targeted rule-based language is Biochemical Space Language (BCSL) developed at the Faculty of Informatics. The tool will be designed to robustly interoperate with the eBCSgen software.

The implementation will be available in a public repository (e.g., github). The preferred programming language is Python but other languages can be used.