BioNetGen
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Related Items (61)
The interplay of double phosphorylation and scaffolding in MAPK pathways ⋮ Reachability analysis via orthogonal sets of patterns ⋮ Chromar, a rule-based language of parameterised objects ⋮ Nonlinear pattern matching in rule-based modeling languages ⋮ Combining Model Reductions ⋮ Retroactivity effects dependency on the transcription factors binding mechanisms ⋮ Thermodynamic graph-rewriting ⋮ A process algebra framework for multi-scale modelling of biological systems ⋮ A collective interpretation semantics for reversing Petri nets ⋮ Computational modelling of the kinetic tile assembly model using a rule-based approach ⋮ A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity ⋮ Markov chain aggregation and its applications to combinatorial reaction networks ⋮ Comparing chemical reaction networks: a categorical and algorithmic perspective ⋮ Verifying chemical reaction network implementations: a pathway decomposition approach ⋮ Chromar, a language of parameterised agents ⋮ Lumpability abstractions of rule-based 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 ⋮ Unnamed Item ⋮ A predictive mathematical model of the DNA damage G2 checkpoint ⋮ Algebra, Coalgebra, and Minimization in Polynomial Differential Equations ⋮ Incremental Update for Graph Rewriting ⋮ Lifted Bayesian Filtering in Multiset Rewriting Systems ⋮ 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 ⋮ Biochemical Reaction Rules with Constraints ⋮ Formal biochemical space with semantics in Kappa and BNGL ⋮ Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration ⋮ Fragments-based Model Reduction: Some Case Studies ⋮ Containment in Rule-Based Models ⋮ A multiscale multicellular spatiotemporal model of local influenza infection and immune response ⋮ Mathematical models for immunology: current state of the art and future research directions ⋮ A Syntactic Abstraction for Rule-Based Languages with Binding ⋮ 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 ⋮ Formal Reduction for Rule-based Models ⋮ A unified framework for differential aggregations in Markovian process algebra ⋮ Symbolic computation of differential equivalences ⋮ Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon ⋮ Stochastic effects and bistability in T cell receptor signaling ⋮ Efficient Turing-Universal Computation with DNA Polymers ⋮ Mesoscopic Modeling of Stochastic Reaction-Diffusion Kinetics in the Subdiffusive Regime ⋮ 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 ⋮ Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity ⋮ Mechanistic simulations of inflammation: current state and future prospects ⋮ Symbolic computation of differential equivalences ⋮ Quantitative Abstractions for Collective Adaptive Systems ⋮ Analysis of Fn14-NF-\(\kappa\)B signaling response dynamics using a mechanistic model ⋮ Generalizing Gillespie's direct method to enable network-free simulations ⋮ SBML to bond graphs: from conversion to composition ⋮ Labelled port graph -- a formal structure for models and computations ⋮ The inverse problem in mathematical biology ⋮ 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 ⋮ Computational Software ⋮ MobsPy: a meta-species language for chemical reaction networks ⋮ eBCSgen 2.0: modelling and analysis of regulated rule-based systems ⋮ Semantics and Efficient Simulation Algorithms of an Expressive Multilevel Modeling Language
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