Droste, Peter: Customizable visualization in the context of metabolic networksHöchst anpassbare Visualisierung im Kontext von Stoffwechselnetzwerken. 2011
Inhalt
- Deutschsprachige Kurzfassung
- Preface
- List of Symbols and Abbreviations
- Glossary
- Contents
- Introduction
- The Complexity of Life
- Systems Biology
- Benefit of the Holistic Approach
- ``Ome'' and ``Omics''
- Biological Processes represented by Networks
- Multi-Omics Data
- Visualization of Data
- Existing Visualization Tools
- Restrictions of Existing Tools
- Research Context
- Contribution of this Thesis
- Organization of this Thesis
- Network Drawing
- Feature Sheet
- Network Layout
- Introduction to Network Layout
- Layout Conventions
- Automatic Versus Manual Approaches
- Circular Arrangements
- Layout Requirements of Metabolic Networks
- The Layout Pattern: Shaping the Coarse Network Structure
- Motif Stamps: Cloning Small Reaction Patterns
- Exemplary Work Flow
- Visualization
- Introduction to Customizable Visualization
- State-of-the-Art in Multi-Omics Data Visualization
- Network-Integrated Visualization of Data
- Basic Concept of the Visualization Approach
- Script-based Visualization
- The Omix Visualization Language
- Extending Network Components
- Simplified Access
- Data Types in OVL
- Interactive Components
- Additional Information Carriers
- Accessory Arrays
- Meta-Information
- OVL Development
- Visualization on Demand
- Advantages of OVL
- Application Examples
- Feature Sheet
- Extensibility
- Introduction to Extensibility
- The Omix API
- Existing Plug-In Solutions
- Compatibility and External Resources
- Visualization of Chemical Structures
- Metabolic Flux Analysis Work Flow
- Background
- 13C FLUX 2 Modeling Plug-In
- 13C FLUX 2 Launcher Plug-In
- FWDSim Import Plug-In
- Network Analysis Plug-Ins
- 3D Visualization of Isotope Labeling Networks
- 3D Visualization of Network Thermodynamics
- Further Features
- Closing
- Appendix
- Drawing Tool Survey
- Evaluation of the Semi-Automatic Layout Approach
- Original Publications
- Bibliography