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User Manual
This Documentation applies to COPASI 4.28 (Build 226)
Table of contents:
Model Creation
Introduction
Commandline Version and Commandline Options
COPASI GUI Elements
General Model Settings
Compartments
Species
Reactions
Global Quantities
Events
Annotating Models and Model Elements
Parameter View
User Defined Functions
Sliders
Tutorial Wizard
Output
Predefined Reports
Output Assistant
Manual Definition
Reports
Plots
Tasks
Steady-State Analysis
Stoichiometric State Analysis
Elementary Flux Modes
Mass Conservations
Time Course Simulation
Working with Plots
Metabolic Control Analysis (MCA)
Lyapunov Exponents
Time Scale Separation
Cross Section
Parameter Scan
Optimization
Parameter Estimation
Experimental Data
Result
Sensitivity Analysis
Linear Noise Approximation
Importing and Exporting
Importing and Exporting SBML Files
Exporting C Source Files
Exporting Berkeley Madonna Files
Exporting XPPAUT Files
Diagrams
The Model in COPASI
Compartments
Species
Global Quantities
Reactions
Functions
Deterministic Interpretation of the Model
Stochastic Interpretation of the Model
Methods
Time Course Calculation
Deterministic Simulation
Stochastic Simulation
Hybrid Simulation
Steady State Calculation
Metabolic Control Analysis
Control Coefficients
Summation Theorem
Enzyme Kinetics and the Elasticity Coefficients
Connectivity Relations
Scaling
Optimization Methods
Evolutionary Programming
Evolutionary Strategy (SRES)
Genetic Algorithm
Genetic Algorithm SR
Hooke & Jeeves
Levenberg - Marquardt
Nelder - Mead
NL2SOL
Particle Swarm
Praxis
Random Search
Simulated Annealing
Steepest Descent
Truncated Newton
Lyapunov Exponents Calculation
Sensitivities Calculation
Time Scale Separation Methods
ILDM (Deuflhard)
Modified ILDM
CSP
Error Messages
Memory Allocation
Gepasi File Reader
Kinetic Function
Range
COPASI Vector
Function Parameter
Mass Action
COPASI Method
Reaction
Chemical Equation
Method Parameter
Trajectory Method
XML Reader
Message Queue
Configuration File
Optimization Task
SBML
Trajectory Task
Directory Entry
MathML
Function
Evaluation Node
COPASI Task
Steady State Calculation
Parameter Fitting
COPASI Object
Lyapunov Exponent Calculation
ODE Export
Commercial Version
Time Scale Separation Problem
Time Scale Separation Method
Eigen Value
Bibliography
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