Formal biochemical space with semantics in Kappa and BNGL

DOI10.1016/J.ENTCS.2016.09.017zbMATH Open1401.92076OpenAlexW2532622426WikidataQ113317656 ScholiaQ113317656MaRDI QIDQ1744366FDOQ1744366

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

Publication date: 23 April 2018

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

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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)

Cites Work

• Bio-PEPA: A framework for the modelling and analysis of biological systems
• A Language for Biochemical Systems: Design and Formal Specification
• Formal molecular biology
• Abstract Interpretation of Cellular Signalling Networks
• Evolving BlenX programs to simulate the evolution of biological networks
• Compact representation of photosynthesis dynamics by rule-based models

Cited In (4)

• eBCSgen: a software tool for biochemical space language
• Executable biochemical space for specification and analysis of biochemical systems
• eBCSgen 2.0: modelling and analysis of regulated rule-based systems
• Computational Methods in Systems Biology

Uses Software

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

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