Publication details

Executable Biochemical Space for Specification and Analysis of Biochemical Systems

Authors

TROJÁK Matej ŠAFRÁNEK David MERTOVÁ Lukrécia BRIM Luboš

Year of publication 2020
Type Appeared in Conference without Proceedings
MU Faculty or unit

Faculty of Informatics

Citation
Description 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.
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