COPASI Documentation VERSION 4.3 (BUILD 25) 1 / 113 COPASI Documentation Version 4.3 (Build 25) COPASI Development Team on April 3, 2008 COPASI Documentation VERSION 4.3 (BUILD 25) 2 / 113 COPASI Documentation VERSION 4.3 (BUILD 25) 3 / 113 Contents 1 Model Creation 8 1.1 Introduction . 8 1.2 Commandline Version and Commandline Options . 8 1.3 COPASI GUI Elements . 9 1.4 General Model Settings . 10 1.5 Compartments . 12 1.6 Species . 16 1.7 Reactions . 20 1.8 Global Quantities . 22 1.9 Parameter View . 24 1.10 User Defined Functions . 25 1.11 Sliders . 29 1.12 Tutorial Wizard . 32 2 Output 33 2.1 Predefined Reports . 33 2.2 Output Assistant . 33 2.3 Manual Definition . 34 2.3.1 Reports . 34 2.3.2 Plots . 37 3 Simple Tasks 40 3.1 Steady-State Analysis . 40 3.2 Stoichiometric State Analysis . 41 3.2.1 Elementary Flux Modes . 41 3.2.2 Mass Conservations . 42 3.3 Time Course Simulation . 43 3.3.1 Working with Plots . 45 3.4 Metabolic Control Analysis (MCA) . 46 3.5 Lyapunov Exponents . 47 COPASI Documentation VERSION 4.3 (BUILD 25) 4 / 113 4 Complex Tasks 49 4.1 Parameter Scan . 49 4.2 Optimization . 55 4.3 Parameter Estimation . 57 4.3.1 Experimental Data . 58 4.3.2 Result . 60 4.4 Sensitivity Analysis . 61 5 Importing and Exporting 62 5.1 Importing and Exporting SBML files . 62 5.2 Exporting C Source files . 63 5.3 Exporting Berkeley Madonna files . 65 5.4 Exporting XPPAUT files . 65 6 The Model in COPASI 66 6.1 Compartments . 66 6.2 Species . 66 6.3 Global Quantities . 66 6.3.1 Fixed Quantities . 67 6.3.2 Quantities with assignment . 67 6.3.3 Quantities with differential equation . 67 6.4 Reactions . 67 6.5 Functions . 67 6.6 Deterministic Interpretation of the Model . 68 6.7 Stochastic Interpretation of the Model . 68 7 Methods 69 7.1 Time Course Calculation . 69 7.1.1 Deterministic Simulation . 69 7.1.1.1 Deterministic (LSODA) . 69 7.1.2 Stochastic Simulation . 70 7.1.2.1 The Next-Reaction-Method . 70 7.1.3 Hybrid Simulation . 70 7.1.3.1 Hybrid (Runge-Kutta) . 70 7.2 Steady State Calculation . 71 7.3 Metabolic Control Analysis . 72 7.3.1 Control Coefficients . 73 7.3.2 Summation Theorem . 73 7.3.3 Enzyme Kinetics and the Elasticity Coefficients . 73 7.3.4 Connectivity Relations . 74 COPASI Documentation VERSION 4.3 (BUILD 25) 5 / 113 7.3.5 Scaling . 74 7.4 Optimization Methods . 74 7.4.1 Evolutionary Programming . 74 7.4.2 Evolutionary Strategy (SRES) . 75 7.4.3 Genetic Algorithm . 75 7.4.4 Genetic Algorithm SR . 76 7.4.5 Hooke & Jeeves . 78 7.4.6 Levenberg - Marquardt . 78 7.4.7 Nelder - Mead . 78 7.4.8 Particle Swarm . 79 7.4.9 Praxis . ..