The thesis topic is the development of a programming library that will support the XML-based standard markup language SBML, which is commonly used in computational systems biology. The library will be implemented in Rust and allow users to read, write, manipulate, translate, and validate SBML files and data streams.

The goal of the theoretical part is to become familiar with the Systems Biology Markup Language (level 3) and its external packages, i.e., qualitative and logical models (SBML Qual), constrained-based models, and rule-based models (SBML multi). The student will also discuss the features of the library LibSBML created by the SBML.org consortium.

In the practical part, the student will implement the Rust library of classes for handling all necessary manipulation tasks with SBML files and data structures related to a selected set of SBML Level 3 packages. The implemented library is aimed to be used in the context of the Biodivine toolset developed in the Sybila laboratory. The library needs to be well-documented. The implementation will be available in GitHub and distributed under a suitable open-source license.