Executable biochemical space for specification and analysis of biochemical systems

DOI10.1016/j.entcs.2020.06.006zbMath1458.92038arXiv2002.00731OpenAlexW3080413141WikidataQ113317324 ScholiaQ113317324MaRDI QIDQ2229140

David Šafránek, Jan Červený, Matej Troják, Jakub Šalagovič, Luboš Brim

Publication date: 22 February 2021

Full work available at URL: https://arxiv.org/abs/2002.00731

zbMATH Keywords

formal specificationstatic analysisrule-based modelling

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Uses Software

• Bio-PEPA
• BioNetGen
• BIOCHAM
• LBS
• PySB
• NFsim
• Smoldyn
• rxncon

Cites Work

• Formal biochemical space with semantics in Kappa and BNGL
• Reachability analysis via orthogonal sets of patterns
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• A Language for Biochemical Systems: Design and Formal Specification

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