A large-scale assessment of exact lumping of quantitative models in the biomodels repository

DOI10.1016/J.TCS.2021.06.026MaRDI QIDQ2238205zbMATH OpenOpenAlexFDO

Authors Isabel Cristina Perez-Verona, Mirco Tribastone, Andrea Vandin

Publication date 1 November 2021

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

Full work available at URL http://hdl.handle.net/11382/538790

zbMATH Keywords

chemical reaction networksequivalence relationsmodel reduction

Mathematics Subject Classification ID

Theory of computing (68Qxx)

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Cites work

• A large-scale assessment of exact model reduction in the biomodels repository
• A model checking approach to discrete bifurcation analysis
• Analysis of Kinetic Reaction Mechanisms
• Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
• Approximation of Large-Scale Dynamical Systems
• Biochemical systems theory: a review
• Efficient syntax-driven lumping of differential equations
• Exact and ordinary lumpability in finite Markov chains
• Forward and backward bisimulations for chemical reaction networks
• Guaranteed Error Bounds on Approximate Model Abstractions Through Reachability Analysis
• Methods of model reduction for large-scale biological systems: a survey of current methods and trends
• Quantitative abstractions for collective adaptive systems
• Reducing Boolean networks with backward Boolean equivalence
• Symbolic computation of differential equivalences
• Symbolic computation of differential equivalences
• Syntactic Markovian bisimulation for chemical reaction networks
• Three Partition Refinement Algorithms

Cited in

(6)

• Exact linear reduction for rational dynamical systems
• Reducing Boolean networks with backward Boolean equivalence
• Interpretable exact linear reductions via positivity
• A large-scale assessment of exact model reduction in the biomodels repository
• Formal reduction for rule-based models
• Approximate constrained lumping of polynomial differential equations

Describes a project that uses

Uses Software

• ERODE
• KEGG
• JSBML
• z3
• MetaCyc
• UniProt
• CLUE

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