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@proceedings{1675419,
author = {Troják, Matej and Šafránek, David and Mertová, Lukrécia and Brim, Luboš},
booktitle = {7th Workshop on Hybrid Systems and Biology},
keywords = {systems biology; rule-based modelling; annotation},
language = {eng},
title = {Executable Biochemical Space for Specification and Analysis of Biochemical Systems},
year = {2020}
}
TY - CONF
ID - 1675419
AU - Troják, Matej - Šafránek, David - Mertová, Lukrécia - Brim, Luboš
PY - 2020
TI - Executable Biochemical Space for Specification and Analysis of Biochemical Systems
KW - systems biology
KW - rule-based modelling
KW - annotation
N2 - We present a rule-based language called Biochemical Space Language (BCSL) as an integral part of a general framework called Comprehensive Modelling Platform, developed for comprehensive modelling in systems biology. The general goal of the platform is to respect the need for maintaining existing ODE models but allows to align them with a mechanistic rule-based description that is understandable by biologists, compact in size, executable in terms of allowing basic analysis tasks ensuring consistency of the description, and provides links to existing bioinformatics annotation databases. Such a comprehensive solution allows to support effort of modellers in building mathematical models that have clear biochemical meaning and can be easily integrated. Moreover, mechanistic descriptions can be later used as computational models having all advantages of rule-based modelling.
ER -
TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. In \textit{7th Workshop on Hybrid Systems and Biology}. 2020.
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