Formal Biochemical Space with Semantics in Kappa and BNGL

Biochemical Space (BCS) has been introduced as a semi-formal notation for reaction networks of biological processes. It provides a concise mapping of mathematical models to their biological description established at a desired level of abstraction. In this paper, we first turn BCS into a completely formal language with rigorously defined semantics by means of a simplified Kappa calculus. On the practical end, we support BCS with translation to BNGL, a well-known practically used rule-based language. Finally, we show the current status of BCS defined for cyanobacteria processes.