COPASI

swMATH12253MaRDI QIDQ24184FDOQ24184

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Cited In (61)

• How Petri nets might enhance your systems biology toolkit
• Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover
• Activation of contact pathway of blood coagulation on the lipopolysaccharide aggregates
• Systems Biology: The Next Frontier for Bioinformatics
• The union between structural and practical identifiability makes strength in reducing oncological model complexity: a case study
• A computational model of auxin and pH dynamics in a single plant cell
• Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration
• Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis
• Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach
• Gene regulatory networks. Methods and protocols
• Distributed computation with continual population growth
• Probabilistic approximations of ODEs based bio-pathway dynamics
• Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA
• HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
• From quantitative SBML models to Boolean networks
• Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease
• Component-based construction of bio-pathway models: the parameter estimation problem
• Computational cell biology. Methods and protocols
• Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
• Springer Handbook of Bio-/Neuroinformatics
• Modeling the effect of Tat inhibitors on HIV latency
• Stochastic modelling of the eukaryotic heat shock response
• A logic of behaviour in context
• Stability and phase transitions in a mathematical model of Duchenne muscular dystrophy
• Computing difference abstractions of linear equation systems
• Analysing biochemical oscillation through probabilistic model checking
• Computational biology analysis of platelet signaling reveals roles of feedbacks through phospholipase C and inositol 1,4,5-trisphosphate 3-kinase in controlling amplitude and duration of calcium oscillations
• Stochastic modelling for systems biology.
• A mathematical model representing cellular immune development and response to \textit{Salmonella} of chicken intestinal tissue
• A geometric method for model reduction of biochemical networks with polynomial rate functions
• The FRiND model: a mathematical model for representing macrophage plasticity in muscular dystrophy pathogenesis
• Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: application to systems biology models
• Methods of model reduction for large-scale biological systems: a survey of current methods and trends
• Nonlinear and temporal multiscale dynamics of gene regulatory networks: a qualitative simulator
• Computational challenges in systems biology
• Modeling non-homologous end joining
• Discrete Modeling of Biochemical Signaling with Memory Enhancement
• Modularized smad-regulated TGF\(\beta \) signaling pathway
• A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity
• The markup is the model: reasoning about systems biology models in the semantic web era
• On the numerical solution of the general kinetic ``\(K\)-angle reaction system
• Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks
• ODE Analysis of Biological Systems
• Reaction network realizations of rational biochemical systems and their structural properties
• Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis
• Reconstructing the hidden states in time course data of stochastic models
• Metabolic rate constants: some computational aspects
• Stochastic rate parameter inference using the cross-entropy method
• Title not available (Why is that?)
• MobsPy: a meta-species language for chemical reaction networks
• Computational software
• Structure exploiting parameter estimation and optimum experimental design methods and applications in microbial enhanced oil recovery
• HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks
• Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
• The Java environment for nature-inspired approaches (JENA): a workbench for biocomputing and biomodelling enthusiasts
• Mathematical models for immunology: current state of the art and future research directions
• Accuracy analysis of hybrid stochastic simulation algorithm on linear chain reaction systems
• Dynamic publication media with the COPASI R connector (CoRC)
• Glycolysis in saccharomyces cerevisiae: algorithmic exploration of robustness and origin of oscillations
• Petri net models for the semi-automatic construction of large scale biological networks
• Computational heuristics for simplifying a biological model

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