Rewriting theory for the life sciences: a unifying theory of CTMC semantics

DOI10.1016/j.tcs.2021.07.026OpenAlexW3184630098MaRDI QIDQ2049987

Daniel Merkle, Jakob L. Andersen, Nicolas Behr, Jean Krivine

Publication date: 27 August 2021

Published in: Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2003.09395

zbMATH Keywords

stochastic mechanicsorganic chemistrybiochemistryalgorithmic cheminformaticsdouble-pushout rewritingrule algebra theorysesqui-pushout rewriting

Mathematics Subject Classification ID

Theory of computing (68Qxx)

Related Items (2)

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics ⋮ Unnamed Item

Uses Software

• Boost
• MedOlDatschgerl
• BGL
• KappaTools
• Fragger

Cites Work

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• Computational methods in systems biology. International conference CMSB 2004, Paris, France, May 26--28, 2004. Revised selected papers.
• Formal molecular biology
• Rate equations for graphs
• Fundamentals of algebraic graph transformation
• Moment Semantics for Reversible Rule-Based Systems
• ℳ-Adhesive Transformation Systems with Nested Application Conditions. Part 2: Embedding, Critical Pairs and Local Confluence
• $\mathcal M, \mathcal N$ -Adhesive Transformation Systems
• Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models
• Incremental Update for Graph Rewriting
• A Software Package for Chemically Inspired Graph Transformation
• Transformation and Refinement of Rigid Structures
• Rule Algebras for Adhesive Categories
• Rule-Based Modelling, Symmetries, Refinements
• Resolution-Like Theorem Proving for High-Level Conditions
• Sesqui-Pushout Rewriting
• Quasitoposes, Quasiadhesive Categories and Artin Glueing
• Correctness of high-level transformation systems relative to nested conditions
• Markov Chains
• Stochastic mechanics of graph rewriting
• Compositionality of Rewriting Rules with Conditions
• Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics
• Intrinsic information carriers in combinatorial dynamical systems
• Graph Transformations
• Adhesive and quasiadhesive categories
• A Rewriting Calculus for Multigraphs with Ports
• 50 Shades of Rule Composition
• Finitary -adhesive categories
• -adhesive transformation systems with nested application conditions. Part 1: parallelism, concurrency and amalgamation

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