BioNetGen
From MaRDI portal
Cited in
(only showing first 100 items - show all)- pyModelChecking
- rxncon
- MLSUM
- Rigid geometric constraints for Kappa models
- Dynamical Systems Toolbox
- Containment in Rule-Based Models
- The inverse problem in mathematical biology
- Lifted Bayesian filtering in multiset rewriting systems
- MobsPy: a meta-species language for chemical reaction networks
- Biochemical reaction rules with constraints
- iBioSim
- Computational software
- Modelling patterns of gene regulation in the bond-calculus
- SBML to bond graphs: from conversion to composition
- Mathematical models for immunology: current state of the art and future research directions
- Labelled port graph -- a formal structure for models and computations
- eBCSgen 2.0: modelling and analysis of regulated rule-based systems
- A process algebra framework for multi-scale modelling of biological systems
- SemanticSBML
- BSim
- Chromar
- SummaRuNNer
- 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
- Thermodynamic graph-rewriting
- Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration
- 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
- Modern methods and software systems of molecular modeling and application of behavior algebra
- Analysis of Fn14-NF-B signaling response dynamics using a mechanistic model
- Symbolic computation of differential equivalences
- 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
- 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
- Coarse-graining the dynamics of ideal branched polymers
- Proving the absence of unbounded polymers in rule-based models
- Tropical abstraction of biochemical reaction networks with guarantees
- Quantitative abstractions for collective adaptive systems
- scientific article; zbMATH DE number 7453970 (Why is no real title available?)
- 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
- 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
- Semantics and efficient simulation algorithms of an expressive multilevel modeling language
- Efficient Turing-universal computation with DNA polymers
- Nonlinear pattern matching in rule-based modeling languages
- A predictive mathematical model of the DNA damage G2 checkpoint
- Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity
- Verifying chemical reaction network implementations: a pathway decomposition approach
- Generalizing Gillespie's direct method to enable network-free simulations
- A unified framework for differential aggregations in Markovian process algebra
- Chromar, a language of parameterised agents
- Verification of spatial and temporal modalities in biochemical systems
- Combining model reductions
- APL
- Bio-PEPA
- SNOOPY
- CellML
- BioShape
- MultiVeStA
- Pirlo
- MEIGO
- SYMBA
- BIOCHAM
- PEPA
- AMIGO
- SpiCO
- BioSPI
- COPASI
- BlenX
- LBS
- libSBML
- PySB
- SBMLsimulator
- StochKit2
- MedOlDatschgerl
- CARMA
- ERODE
- PALOMA
- GillespieSSA
- TinkerCell
- kTAM
- NFsim
- Xtile
- AGREE
- Smoldyn
- StochPy
- BioSimulator.jl
- Kappa
- KaSim
- tellurium
- VCell
- STOCHSIM
- MOSBIE
- KappaTools
- Antimony
- libRoadRunner
- PyBioNetFit
This page was built for software: BioNetGen
