Inhalt

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   Deutschsprachige Kurzfassung
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   Preface
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  List of Symbols and Abbreviations
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   Symbols
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   Abbreviations
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   Glossary
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   Contents
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  Introduction
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   The Complexity of Life
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   Systems Biology
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   Benefit of the Holistic Approach
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   ``Ome'' and ``Omics''
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   Biological Processes represented by Networks
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   Multi-Omics Data
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   Visualization of Data
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   Existing Visualization Tools
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   Restrictions of Existing Tools
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   Research Context
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   Contribution of this Thesis
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   Organization of this Thesis
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   Network Drawing
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  Introduction to Network Drawing
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   State-of-the-Art in Network Drawing
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   Tool Survey
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   Proposed Standards
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   Requirements
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  The Network Diagram Editor
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   Ease of Use
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   Network Symbols
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   Network Nodes and Edges
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   Metabolic Pathways
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   Compartments
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   Additional Network Components
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   Network Style
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   Levels of Detail
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   Joining Networks
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   Layout-less Components
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   Example Drawing Process
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   Feature Sheet
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   Network Layout
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  Introduction to Network Layout
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   Layout Conventions
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   Automatic Versus Manual Approaches
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   Circular Arrangements
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   Layout Requirements of Metabolic Networks
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   The Layout Pattern: Shaping the Coarse Network Structure
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   Using the Layout Pattern
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   Challenges and Requirements
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  Semi-automatic Path Search
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   Human-Interactive Path Search
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   Software-Assisted Pre-Selection and Exclusion of Network Paths
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   Pathway-Oriented Layout
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   Motif Stamps: Cloning Small Reaction Patterns
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   Creating Motif Stamps
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   Appending Motifs to Reactions
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  Exemplary Work Flow
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   Metabolic Pathways
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   Using the Layout Pattern
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   Using Motif Stamps
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   Completing the Drawing Process
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   Visualization
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  Introduction to Customizable Visualization
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   State-of-the-Art in Multi-Omics Data Visualization
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   Network-Integrated Visualization of Data
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   Basic Concept of the Visualization Approach
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   Script-based Visualization
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  The Omix Visualization Language
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   Extending Network Components
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   Simplified Access
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   Data Types in OVL
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   Interactive Components
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   Additional Information Carriers
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   Accessory Arrays
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   Meta-Information
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   OVL Development
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   Visualization on Demand
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   Interactive Visualization of Custom Properties
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   Custom Data Types
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   Information Management
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   VoD Example
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   Advantages of OVL
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  Application Examples
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   Comparative Visualization of Metabolome Data
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   Visualization in the Context of Metabolic Flux Analysis
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   Visualization in the Context of Synthetic Biology
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   Visualization of Transcriptome Data
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   Animation of a Pulse Experiment
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   Visualization of Isotopic Mass Distributions
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   Visualization of Enzyme Kinetics
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   Feature Sheet
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   Extensibility
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  Introduction to Extensibility
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   Motivation
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   Differentiation to OVL
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  The Omix API
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   Interface Concept
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   Features of the Omix API
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  Existing Plug-In Solutions
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  Compatibility and External Resources
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   Model Describing Formats
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   Database Connectivity
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   Visualization of Chemical Structures
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  Metabolic Flux Analysis Work Flow
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   Background
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   13C FLUX 2 Modeling Plug-In
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   13C FLUX 2 Launcher Plug-In
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   FWDSim Import Plug-In
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   Network Analysis Plug-Ins
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  3D Visualization of Isotope Labeling Networks
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   Foundations
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   The CumoVis Plug-In
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  3D Visualization of Network Thermodynamics
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   Foundations
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   The ThermoVis Plug-in
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   Further Features
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   Closing
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  Summary and Discussion
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   Aims
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  Results
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   Novel Solutions
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   Extraordinary Achievement
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   Realized Vision
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  Future Perspectives
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   Other Network Layers
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   Network Layout
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   Metabolic Flux Analysis
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   3D Visualization
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   Appendix
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  Drawing Tool Survey
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   Office Software
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   Graphics Software
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   Drawing Software for Biochemical Networks
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   CytoScape
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   Vanted
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   CellDesigner
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  Evaluation of the Semi-Automatic Layout Approach
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   Case Study Design
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   Elaboration
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   Results
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   Conclusion
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  Original Publications
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   Documentations
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   Related Publications
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   Further Publications
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   Bibliography