Formal Biochemical Space with Semantics in Kappa and BNGL

D 2016

Formal Biochemical Space with Semantics in Kappa and BNGL

DĚD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIČ et. al.

Basic information

Original name

Formal Biochemical Space with Semantics in Kappa and BNGL

Authors

DĚD, Tadeáš (203 Czech Republic, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Matej TROJÁK (703 Slovakia, belonging to the institution), Matej KLEMENT (703 Slovakia, belonging to the institution), Jakub ŠALAGOVIČ (703 Slovakia, belonging to the institution) and Luboš BRIM (203 Czech Republic, belonging to the institution)

Edition

ENTCS 326. Neuveden, The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015, p. 27-49, 23 pp. 2016

Publisher

Elsevier

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

RIV identification code

RIV/00216224:14330/16:00088812

Organization unit

Faculty of Informatics

ISSN

DOI

http://dx.doi.org/10.1016/j.entcs.2016.09.017

UT WoS

000386589900003

Keywords in English

Kappa; Biochemical space; CMP; cyanobacteria processes

Abstract

V originále

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.

Links

GA15-11089S, research and development project

Name: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Czech Science Foundation

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

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. 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.

@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.

Detailed Information on Publication Record