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COPASI Documentation
Chapter 1. Model Creation >>

COPASI Documentation

Version 4.3 (Build 25)

COPASI Development Team

Version 4.3 (Build 25)

Table of Contents

1. Model Creation
1. Introduction
2. Commandline Version and Commandline Options
3. COPASI GUI Elements
4. General Model Settings
5. Compartments
6. Species
7. Reactions
8. Global Quantities
9. Parameter View
10. User Defined Functions
11. Sliders
12. Tutorial Wizard
2. Output
1. Predefined Reports
2. Output Assistant
3. Manual Definition
3.1. Reports
3.2. Plots
3. Simple Tasks
1. Steady-State Analysis
2. Stoichiometric State Analysis
2.1. Elementary Flux Modes
2.2. Mass Conservations
3. Time Course Simulation
3.1. Working with Plots
4. Metabolic Control Analysis (MCA)
5. Lyapunov Exponents
4. Complex Tasks
1. Parameter Scan
2. Optimization
3. Parameter Estimation
3.1. Experimental Data
3.2. Result
4. Sensitivity Analysis
5. Importing and Exporting
1. Importing and Exporting SBML files
2. Exporting C Source files
3. Exporting Berkeley Madonna files
4. Exporting XPPAUT files
6. The Model in COPASI
1. Compartments
2. Species
3. Global Quantities
3.1. Fixed Quantities
3.2. Quantities with assignment
3.3. Quantities with differential equation
4. Reactions
5. Functions
6. Deterministic Interpretation of the Model
7. Stochastic Interpretation of the Model
7. Methods
1. Time Course Calculation
1.1. Deterministic Simulation
1.2. Stochastic Simulation
1.3. Hybrid Simulation
2. Steady State Calculation
3. Metabolic Control Analysis
3.1. Control Coefficients
3.2. Summation Theorem
3.3. Enzyme Kinetics and the Elasticity Coefficients
3.4. Connectivity Relations
3.5. Scaling
4. Optimization Methods
4.1. Evolutionary Programming
4.2. Evolutionary Strategy (SRES)
4.3. Genetic Algorithm
4.4. Genetic Algorithm SR
4.5. Hooke & Jeeves
4.6. Levenberg - Marquardt
4.7. Nelder - Mead
4.8. Particle Swarm
4.9. Praxis
4.10. Random Search
4.11. Simulated Annealing
4.12. Steepest Descent
4.13. Truncated Newton
5. Lyapunov Exponents Calculation
6. Sensitivities Calculation
6.1. The "unscaled" result matrix
A. Error Messages
1. Memory Allocation Error Messages
2. Gepasi File Reader Error Messages
3. Kinetic Function Error Messages
4. Range Error Message
5. COPASI Vector Error Messages
6. Function Parameter Error Messages
7. Mass Action Error Messages
8. COPASI Method Error Messages
9. Reaction Error Messages
10. Chemical Equation Error Messages
11. Method Parameter Error Messages
12. Trajectory Method Error Messages
13. XML Reader Error Messages
14. Error Messages
15. Configuration File Error Messages
16. Optimization Task Error Messages
17. SBML Error Messages
18. Trajectory Task Error Messages
19. Directory Entry Error Messages
20. MathML Error Messages
21. Function Error Messages
22. Evaluation Node Error Messages
23. COPASI Task Error Messages
24. Steady State Calculation Error Messages
25. Parameter Fitting Error Messages
26. COPASI Object Error Messages
27. Lyapunov Exponent Calculation Error Messages
28. ODE Export Error Messages
29. Commercial Version Error Messages
30. Timescale Separation Analysis Error Messages
30.1. Errors from the timescale separation analysis method.
30.2. Errors from the timescale separation analysis problem
31. Eigen value Error Messages
Bibliography

List of Tables

1.1. Compartments Simulation Types
1.2. Species Simulation Types
1.3. Global Quantities Simulation Types
1.4. Standard Operators
1.5. Miscellaneous Functions
1.6. Trigonometric Functions
1.7. Logical Functions
1.8. Miscellaneous
1.9. Built-in Constants
4.1. Weight Calculation Methods
5.1. Preprocessor Defines
COPASI Documentation
Chapter 1. Model Creation >>
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