The primary goal of this thesis is to develop and formally define a novel rule-based language Biochemical Space Language (BCSL) for description of biochemical processes. BCSL is motivated by practical needs that come from development and usage of the unique online modelling platform e-cyanobacterium.org. The platform is an ongoing project at FI MU realised in cooperation with the international consortium CyanoNetwork and the National Infrastructure for Systems Biology C4SYS.

The language will satisfy the following requirements:

• compact encoding of chemical reactions in terms of context-free rules,
• abstraction from details of chemical bonds,
• hierarchical specification of biological entities and locations,
• executable operational semantics based on (potentially infinite) state-transition structures.

Definition of the syntax and formal semantics will be part of the thesis (in case of a too large range the parts covering language extensions can be placed in appendix).

The secondary goal is to design methods for automatised static and dynamic analysis of BCSL models. Namely, the student will provide a list of typical problems (reachability, consistency, deadlock freedom, etc.) and will give suggestions for efficient solutions at the level of the language (static analysis) and semantics (dynamic analysis). Finally, comparison with existing rule-based languages will be adequately discussed.