Publication details

Formal Biochemical Space with Semantics in Kappa and BNGL

Authors

DĚD Tadeáš ŠAFRÁNEK David TROJÁK Matej KLEMENT Matej ŠALAGOVIČ Jakub BRIM Luboš

Year of publication 2016
Type Article in Proceedings
Conference The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015
MU Faculty or unit

Faculty of Informatics

Citation
Doi http://dx.doi.org/10.1016/j.entcs.2016.09.017
Field Informatics
Keywords Kappa; Biochemical space; CMP; cyanobacteria processes
Description 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.
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