Informace o publikaci

Formal Biochemical Space with Semantics in Kappa and BNGL

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

Rok publikování 2016
Druh Článek ve sborníku
Konference The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015
Fakulta / Pracoviště MU

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Citace
Doi http://dx.doi.org/10.1016/j.entcs.2016.09.017
Obor Informatika
Klíčová slova Kappa; Biochemical space; CMP; cyanobacteria processes
Popis 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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