Formal Biochemical Space with Semantics in Kappa and BNGL

• Autoři: 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: Fakulta informatiky
• 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.

Související projekty

• Získávání parametrů biologických modelů pomocí techniky ověřování modelů
• The national infrastructure C4SYS - Centre for Systems Biology