Inhalt

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   ABSTRACT
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   TABLE OF CONTENTS
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  1 INTRODUCTION
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   1.1 MOTIVATION
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   1.2 OBJECTIVES
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   1.3 STRUCTURE
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  2 RELATED WORKS
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   2.1 PETRI NET APPROACHES FOR MODELINGBIOLOGICAL PROCESSES
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   2.2 PETRI NET TOOLS
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   2.3 PETRI NETS IN MODELICA
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  3 BASICS
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   3.1 THE MODELICA LANGUAGE
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   3.1.1 VARIABLES
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   3.1.2 EQUATIONS
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   3.1.3 ALGORITHMS
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   3.1.4 SPECIALIZED CLASSES
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   3.1.5 BALANCED MODELS
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   3.1.6 DISCRETE EVENT AND HYBRID MODELING
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   3.1.7 MATHEMATICAL REPRESENTATION OF MODELICA MODELS
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   3.2 OPTIMIZATION METHODS
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   3.2.1 LOCAL OPTIMIZATION METHOD
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   3.2.2 GLOBAL OPTIMIZATION METHODS
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   3.2.3 HYBRID OPTIMIZATION METHODS
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   3.3 SENSITIVITY ANALYSIS METHODS
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   3.3.1 LOCAL APPROACH
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   3.3.2 GLOBAL APPROACH: FOURIER AMPLITUDE SENSITIVITY TEST
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   3.3.3 EXTENDED FOURIER AMPLITUDE SENSITIVITY TE
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  4 PETRI NETS
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   4.1 BASIC CONCEPTS
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  4.2 ABBREVIATIONS AND EXTENSIONS OF THEBASIC CONCEPTS
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   4.2.1 CAPACITIVE PETRI NETS
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   4.2.2 EXTENDED PETRI NETS
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   4.2.3 EXTENDED CAPACITIVE PETRI NETS
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   4.2.4 SELF-MODIFIED PETRI NETS
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   4.2.5 FUNCTIONAL PETRI NETS
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  4.3 NON-AUTONOMOUS PETRI NETS
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   4.3.1 CONDITIONAL PETRI NETS
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   4.3.2 TIMED PETRI NETS
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   4.3.3 STOCHASTIC PETRI NETS
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   4.3.4 CONDITIONAL TIMED PETRI NETS
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   4.4 CONTINUOUS PETRI NETS
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   4.4.1 CONTINUOUS CAPACITIVE PETRI NETS
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   4.4.2 CONTINUOUS EXTENDED PETRI NETS
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   4.4.3 CONTINUOUS EXTENDED CAPACITIVE PETRI NETS
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   4.4.4 CONTINUOUS FUNCTIONAL PETRI NETS
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   4.4.5 CONDITIONAL CONTINUOUS PETRI NETS
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   4.5 HYBRID PETRI NETS
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   4.5.1 VARIATION OF TRANSITIONS
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   4.5.2 ARC WEIGHT AND MAXIMUM SPEED FUNCTIONS DEPENDINGON MARKING/TIME
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   4.5.3 CAPACITIES AND EXTENSIONS
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   4.5.4 EXTENDED HYBRID PETRI NETS
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   5 MODELING PROCESS OF BIOLOGICAL SYSTEMS
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   5.1 PREPROCESSING AND RELATIONSHIP ANALYSIS
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   5.2 MATHEMATICAL MODELING: XHPN FORBIOLOGICAL APPLICATIONS
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   5.3 PARAMETER ESTIMATION
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   5.4 SENSITIVITY ANALYSIS
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   5.5 DETERMINISTIC AND STOCHASTIC HYBRIDSIMULATION
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   5.6 MODEL PREDICTION
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   5.7 PROCESS OPTIMIZATION
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   6 THE PETRI NET LIBRARY
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   6.1 IMPLEMENTATION OF THE PETRI NET ELEMENTS
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   6.1.1 CONNECTORS
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   6.1.2 PLACES
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   6.1.3 TRANSITIONS
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   6.1.4 ARCS
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   6.2 MODELING, SIMULATION, AND ANIMATIONWITH DYMOLA
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   6.3 CONNECTION BETWEEN DYMOLA ANDMATLAB/SIMULINK
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   6.4 PETRI NET LIBRARY FOR PROCESS MODELINGOF BIOLOGICAL SYSTEMS
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   6.5 TOOL FOR THE ANALYSIS OF MODELICA MODELS
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   6.6 COMPARISON TO OTHER PETRI NET TOOLS
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   7 APPLICATION
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   7.1 STEP 1: BIOLOGICAL PHENOMENA
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  7.2 STEP 2: EXPERIMENTAL DATA AND PRIORKNOWLEDGE
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   7.2.1 INFLUENCE FACTORS ON GROWTH AND XANTHANPRODUCTION
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   7.2.2 MODELING OF GROWTH AND XANTHAN PRODUCTION
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   7.3 STEP 3: MODEL HYPOTHESES
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   7.4 STEP 4 AND 5: PREPROCESSING ANDRELATIONSHIP ANALYSIS
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   7.5 STEP 6 UND 8: PARAMETER ESTIMATION ANDSENSITIVITY ANALYSIS
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   7.6 STEP 9: PROCESS OPTIMIZATION
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   7.7 STEP 7: DETERMINISTIC AND STOCHASTICHYBRID SIMULATION
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   8 DISCUSSION AND OUTLOOK
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  APPENDIX
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   A1 ALGORITHMS
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   A2 CONNECTOR VARIABLES OF THE PNLIB
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  A3 SUPPLEMENTS TO THE AMMOD-TOOL
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   A3-1 PRA
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   A3-2 PESA
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  A4 SUPPLEMENTS TO THE APPLICATION
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   A4-1 PSEUDO EXPERIMENTAL DATA
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   A4-2 METHOD-SPECIFIC PARAMETERS
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   A4-3 COMPONENTS AND PARAMETERS OF THE MODELS
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   LIST OF FIGURES
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   LIST OF TABLES
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   LIST OF ABBREVIATIONS
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   LIST OF REFERENCES