COPASI
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Cited in
(only showing first 100 items - show all)- 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
- Computational heuristics for simplifying a biological model
- Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis
- Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration
- Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach
- Gene regulatory networks. Methods and protocols
- Probabilistic approximations of ODEs based bio-pathway dynamics
- Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA
- Distributed computation with continual population growth
- HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
- Component-based construction of bio-pathway models: the parameter estimation problem
- From quantitative SBML models to Boolean networks
- Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease
- Computational cell biology. Methods and protocols
- Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
- Springer Handbook of Bio-/Neuroinformatics
- Stochastic modelling of the eukaryotic heat shock response
- Modeling the effect of Tat inhibitors on HIV latency
- 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
- 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
- Analysing biochemical oscillation through probabilistic model checking
- Stochastic modelling for systems biology.
- A mathematical model representing cellular immune development and response to \textit{Salmonella} of chicken intestinal tissue
- The FRiND model: a mathematical model for representing macrophage plasticity in muscular dystrophy pathogenesis
- A geometric method for model reduction of biochemical networks with polynomial rate functions
- 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
- Bio-PEPA
- DSSZ-MC
- SCAMP
- CellML
- PoCaB
- PySCeS
- StochKit
- WGCNA
- sbtoolbox
- Stella
- BioStream
- E-CELL
- GEPASI
- MetaCyc
- MEIGO
- BioNetGen
- DAISY
- DBSolve
- BIOCHAM
- Celldesigner
- Casaal
- MoMo
- AMIGO
- BlenX
- PAREMERA
- LBS
- SynTReN
- libSBML
- BioGRID
- BioModels
- PySB
- StochSens
- BiNGO
- KEGG
- StochKit2
- ENZPACK
- K-angle
- SigrafW
- StochDynTools
- sglasso
- Bio-SPICE
- SIRENE
- iNA
- HRSSA
- CERENA
- pnea
- SensSB
- GillespieSSA
- IntAct
- SBML-SAT
- HSimulator
- Hy3S
- Virtual Cell
- Data2Dynamics
- StochSS
- JSim
- RegulonDB
- CaliBayes
- JENA
- MetaPlab
- MEANS
- ConvAn
- StochPy
- BioSimulator.jl
- PESTO
- BioPreDyn-bench
- TaylorSeries.jl
- SOSlib
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