BioNetGen

swMATH9072MaRDI QIDQ21065FDOQ21065

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Official website: http://bionetgen.org/index.php/Main_Page

Cited In (only showing first 100 items - show all)

• Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration
• Symbolic computation of differential equivalences
• Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
• Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime
• Markov chain aggregation and its applications to combinatorial reaction networks
• Lumpability abstractions of rule-based systems
• Coarse-graining the dynamics of ideal branched polymers
• The interplay of double phosphorylation and scaffolding in MAPK pathways
• Formal biochemical space with semantics in Kappa and BNGL
• Mechanistic simulations of inflammation: current state and future prospects
• Efficient Turing-universal computation with DNA polymers
• A predictive mathematical model of the DNA damage G2 checkpoint
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity
• Fragments-based model reduction: some case studies
• A syntactic abstraction for rule-based languages with binding
• Combining model reductions
• Verification of spatial and temporal modalities in biochemical systems
• SNOOPY
• CellML
• BioShape
• MultiVeStA
• Pirlo
• MEIGO
• SYMBA
• BIOCHAM
• PEPA
• AMIGO
• SpiCO
• BioSPI
• COPASI
• BlenX
• LBS
• libSBML
• PySB
• SBMLsimulator
• StochKit2
• MedOlDatschgerl
• Executable biochemical space for specification and analysis of biochemical systems
• Retroactivity effects dependency on the transcription factors binding mechanisms
• CARMA
• ERODE
• PALOMA
• GillespieSSA
• TinkerCell
• kTAM
• NFsim
• Xtile
• AGREE
• Smoldyn
• StochPy
• BioSimulator.jl
• Kappa
• KaSim
• tellurium
• VCell
• STOCHSIM
• MOSBIE
• KappaTools
• Antimony
• libRoadRunner
• PyBioNetFit
• RuleBender
• Spatkin
• TRuML
• SimpleSBML
• Dizzy
• Stochastic effects and bistability in T cell receptor signaling
• GP 2
• BasiCO
• MobsPy
• Computational modelling of the kinetic tile assembly model using a rule-based approach
• Rule-based modeling of transcriptional attenuation at the tryptophan operon
• Symbolic computation of differential equivalences
• eBCSgen
• pyModelChecking
• rxncon
• MLSUM
• Dynamical Systems Toolbox
• The inverse problem in mathematical biology
• iBioSim
• MobsPy: a meta-species language for chemical reaction networks
• Biochemical reaction rules with constraints
• Computational software
• Mathematical models for immunology: current state of the art and future research directions
• eBCSgen 2.0: modelling and analysis of regulated rule-based systems
• A process algebra framework for multi-scale modelling of biological systems
• Computational modeling of synergistic interaction between \(\alpha\)V\(\beta\)3 integrin and VEGFR2 in endothelial cells: implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides
• Thermodynamic graph-rewriting
• Modern methods and software systems of molecular modeling and application of behavior algebra
• Analysis of Fn14-NF-\(\kappa\)B signaling response dynamics using a mechanistic model
• A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: development of an integrated mathematical model and computational experiments
• Chromar, a rule-based language of parameterised objects
• Title not available (Why is that?)
• Proving the absence of unbounded polymers in rule-based models
• Tropical abstraction of biochemical reaction networks with guarantees
• Quantitative abstractions for collective adaptive systems
• Reachability analysis via orthogonal sets of patterns
• Comparing chemical reaction networks: a categorical and algorithmic perspective
• A multiscale multicellular spatiotemporal model of local influenza infection and immune response

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