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Formal biochemical space with semantics in Kappa and BNGL. (English) Zbl 1401.92076
Paulevé, Loïc (ed.) et al., Post-proceedings of the 6th international workshop on static analysis and systems biology (SASB 2015), Saint-Malo, France, September 8, 2015. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 326, 27-49 (2016).
Summary: 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.
For the entire collection see [Zbl 1352.92002].
MSC:
92C40 Biochemistry, molecular biology
68Q45 Formal languages and automata
68Q55 Semantics in the theory of computing
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