Formal biochemical space with semantics in Kappa and BNGL

DOI10.1016/J.ENTCS.2016.09.017MaRDI QIDQ1744366zbMATH OpenOpenAlexWikidataFDO

Authors T. Děd, M. Klement, D. Šafránek, Matej Troják, Jakub Šalagovič, Luboš Brim

Publication date 23 April 2018

Full work available at URL https://doi.org/10.1016/j.entcs.2016.09.017

zbMATH Keywords

CMPbiochemical spacecyanobacteria processesKappa

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Biochemistry, molecular biology (92C40) Semantics in the theory of computing (68Q55)

Recommendations

• Executable biochemical space for specification and analysis of biochemical systems
• A language for biochemical systems: design and formal specification
• Complex functional rates in rule-based languages for biochemistry
• Computational Methods in Systems Biology
• eBCSgen: a software tool for biochemical space language

Cites work

• A language for biochemical systems: design and formal specification
• Abstract Interpretation of Cellular Signalling Networks
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Compact representation of photosynthesis dynamics by rule-based models
• Evolving BlenX programs to simulate the evolution of biological networks
• Formal molecular biology

Cited in

(7)

• Rigid geometric constraints for Kappa models
• Computational Methods in Systems Biology
• eBCSgen: a software tool for biochemical space language
• Executable biochemical space for specification and analysis of biochemical systems
• A language for biochemical systems: design and formal specification
• eBCSgen 2.0: modelling and analysis of regulated rule-based systems
• Complex functional rates in rule-based languages for biochemistry

Describes a project that uses

Uses Software

• Bio-PEPA
• BioNetGen
• LBS
• BlenX
• KEGG

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