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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 a 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, s.~27-49. ISSN~1571-0661. Dostupné z: https://dx.doi.org/10.1016/j.entcs.2016.09.017.
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