BioNetGen
From MaRDI portal
Cited in
(only showing first 100 items - show all)- Mechanistic simulations of inflammation: current state and future prospects
- BasiCO
- MobsPy
- rxncon
- pyModelChecking
- eBCSgen
- MLSUM
- Dynamical Systems Toolbox
- APL
- Bio-PEPA
- SNOOPY
- Computational modelling of the kinetic tile assembly model using a rule-based approach
- Computational modeling of synergistic interaction between V3 integrin and VEGFR2 in endothelial cells: implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides
- A predictive mathematical model of the DNA damage G2 checkpoint
- Formal biochemical space with semantics in Kappa and BNGL
- CellML
- Stochastic effects and bistability in T cell receptor signaling
- Pirlo
- MultiVeStA
- MEIGO
- BioShape
- SYMBA
- SBML to bond graphs: from conversion to composition
- Modern methods and software systems of molecular modeling and application of behavior algebra
- A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: development of an integrated mathematical model and computational experiments
- MobsPy: a meta-species language for chemical reaction networks
- eBCSgen 2.0: modelling and analysis of regulated rule-based systems
- Reachability analysis via orthogonal sets of patterns
- Chromar, a rule-based language of parameterised objects
- Nonlinear pattern matching in rule-based modeling languages
- BIOCHAM
- Tropical abstraction of biochemical reaction networks with guarantees
- Proving the absence of unbounded polymers in rule-based models
- Executable biochemical space for specification and analysis of biochemical systems
- Modelling patterns of gene regulation in the bond-calculus
- A multiscale multicellular spatiotemporal model of local influenza infection and immune response
- A unified framework for differential aggregations in Markovian process algebra
- SpiCO
- PEPA
- Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity
- Analysis of Fn14-NF-B signaling response dynamics using a mechanistic model
- Generalizing Gillespie's direct method to enable network-free simulations
- Labelled port graph -- a formal structure for models and computations
- The inverse problem in mathematical biology
- BioSPI
- A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity
- COPASI
- Comparing chemical reaction networks: a categorical and algorithmic perspective
- Verifying chemical reaction network implementations: a pathway decomposition approach
- Chromar, a language of parameterised agents
- LBS
- BlenX
- libSBML
- Rigid geometric constraints for Kappa models
- Coarse-graining the dynamics of ideal branched polymers
- Verification of spatial and temporal modalities in biochemical systems
- An algebraic approach for inferring and using symmetries in rule-based models
- SBMLsimulator
- PySB
- StochKit2
- A collective interpretation semantics for reversing Petri nets
- AMIGO
- Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime
- Quantitative abstractions for collective adaptive systems
- The interplay of double phosphorylation and scaffolding in MAPK pathways
- MedOlDatschgerl
- Thermodynamic graph-rewriting
- Incremental update for graph rewriting
- Biochemical reaction rules with constraints
- Rule-based modeling of transcriptional attenuation at the tryptophan operon
- Efficient Turing-universal computation with DNA polymers
- Combining model reductions
- ERODE
- CARMA
- PALOMA
- TinkerCell
- GillespieSSA
- Retroactivity effects dependency on the transcription factors binding mechanisms
- NFsim
- kTAM
- Xtile
- AGREE
- Smoldyn
- A process algebra framework for multi-scale modelling of biological systems
- StochPy
- BioSimulator.jl
- Markov chain aggregation and its applications to combinatorial reaction networks
- Kappa
- KaSim
- tellurium
- VCell
- Lumpability abstractions of rule-based systems
- STOCHSIM
- TRuML
- Spatkin
- MOSBIE
- PyBioNetFit
- libRoadRunner
- RuleBender
- KappaTools
This page was built for software: BioNetGen
