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@inproceedings{1377771,
author = {Děd, Tadeáš and Šafránek, David and Troják, Matej and Klement, Matej and Šalagovič, Jakub and Brim, Luboš},
address = {Neuveden},
booktitle = {The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015},
doi = {http://dx.doi.org/10.1016/j.entcs.2016.09.017},
edition = {ENTCS 326},
editor = {Loic Pauleve et al.},
keywords = {Kappa; Biochemical space; CMP; cyanobacteria processes},
howpublished = {elektronická verze "online"},
language = {eng},
location = {Neuveden},
pages = {27-49},
publisher = {Elsevier},
title = {Formal Biochemical Space with Semantics in Kappa and BNGL},
year = {2016}
}
TY - JOUR
ID - 1377771
AU - Děd, Tadeáš - Šafránek, David - Troják, Matej - Klement, Matej - Šalagovič, Jakub - Brim, Luboš
PY - 2016
TI - Formal Biochemical Space with Semantics in Kappa and BNGL
PB - Elsevier
CY - Neuveden
KW - Kappa
KW - Biochemical space
KW - CMP
KW - cyanobacteria processes
N2 - 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.
ER -
DĚD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIČ and Luboš BRIM. Formal Biochemical Space with Semantics in Kappa and BNGL. Online. In Loic Pauleve et al. \textit{The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015}. ENTCS 326. Neuveden: Elsevier, 2016, p.~27-49. ISSN~1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2016.09.017.
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