COPASI Documentation i COPASI Documentation Version 4.6 (Build 32) COPASI Development Team on August 3, 2010 COPASI Documentation 2 / 131 COPASI Documentation 3 / 131 Contents 1 Model Creation 1 1.1 Introduction . 1 1.2 Commandline Version and Commandline Options . 1 1.3 COPASI GUI Elements . 3 1.4 General Model Settings . 3 1.5 Compartments . 5 1.6 Species . 10 1.7 Reactions . 13 1.8 Global Quantities . 15 1.9 Events . 17 1.9.1 Trigger . 17 1.9.2 Assignment . 17 1.9.3 Delay . 18 1.10 Annotating Models and Model Elements . 19 1.11 Parameter View . 20 1.12 User Defined Functions . 21 1.12.1 Standard Operators . 23 1.12.2 Miscellaneaous Functions . 23 1.12.3 Trigonometric Functions . 24 1.12.4 Random Distribuitions . 24 1.12.5 Logical Operators . 24 1.12.6 Conditional Statement . 25 1.12.7 Parenthesis . 25 1.12.8 Built-in Constants . 25 1.13 Sliders . 26 1.14 Tutorial Wizard . 28 2 Output 30 2.1 Predefined Reports . 30 2.2 Output Assistant . 30 2.3 Manual Definition . 31 2.3.1 Reports . 31 2.3.2 Plots . 34 COPASI Documentation 4 / 131 3 Tasks 37 3.1 Steady-State Analysis . 37 3.2 Stoichiometric State Analysis . 38 3.2.1 Elementary Flux Modes . 38 3.2.2 Mass Conservations . 39 3.3 Time Course Simulation . 40 3.3.1 Working with Plots . 42 3.4 Metabolic Control Analysis (MCA) . 43 3.5 Lyapunov Exponents . 44 3.6 Time Scale Separation . 45 3.7 Parameter Scan . 46 3.8 Optimization . 52 3.9 Parameter Estimation . 54 3.9.1 Experimental Data . 55 3.9.2 Result . 57 3.10 Sensitivity Analysis . 58 4 Importing and Exporting 60 4.1 Importing and Exporting SBML files . 60 4.2 Exporting C Source files . 61 4.3 Exporting Berkeley Madonna files . 63 4.4 Exporting XPPAUT files . 63 5 Diagrams 64 6 The Model in COPASI 67 6.1 Compartments . 67 6.2 Species . 67 6.3 Global Quantities . 68 6.4 Reactions . 68 6.5 Functions . 69 6.6 Deterministic Interpretation of the Model . 69 6.7 Stochastic Interpretation of the Model . 69 7 Methods 70 7.1 Time Course Calculation . 70 7.1.1 Deterministic Simulation . 70 7.1.1.1 Deterministic (LSODA) . 70 7.1.2 Stochastic Simulation . 71 7.1.2.1 The Next-Reaction-Method . 71 COPASI Documentation 5 / 131 7.1.3 Hybrid Simulation . 71 7.1.3.1 Hybrid (Runge-Kutta) . 71 7.2 Steady State Calculation . 72 7.2.0.2 Options for Steady State Analysis . 72 7.3 Metabolic Control Analysis . 73 7.3.1 Options for MCA . 73 7.3.2 Control Coefficients . 74 7.3.3 Summation Theorem . ..