NAViGaTOR

NAViGaTOR visualizes and analyzes protein-protein interaction networks, providing two-dimensional and three-dimensional graphical representations to support biological network exploration and interpretation.

Key Features:

• Visualization Capabilities: Support for rendering large-scale biological networks in both two-dimensional (2D) and three-dimensional (3D) representations.
• Annotation Tools: Includes manual and automated visual mark-up tools for annotation of network elements.
• Layout Algorithms: Implements fast, scalable layout algorithms to organize and present large interaction datasets.
• Hardware Acceleration: Uses OpenGL hardware acceleration to improve visualization performance for extensive graphs.
• Export Options: Produces publication-quality image rendering via SVG export.
• Data Format Support: Parses and supports community formats PSI-XML, BioPax, and GML to ensure interoperability.
• Extensibility: Provides an extensible plug-in architecture for customization and capability expansion.

Scientific Applications:

• Protein-protein interaction analysis: Visualizes and analyzes protein-protein interactions to reveal network relationships and connectivity.
• Signaling pathway elucidation: Maps and interprets signaling pathway structures and interactions.
• Gene regulatory network exploration: Enables visualization and interrogation of gene regulatory networks and their relationships.
• Systems biology and genomics: Supports integration and interpretation of high-throughput datasets in systems biology and genomics to aid hypothesis generation and experimental design.

Methodology:

Uses 2D and 3D graph rendering, fast scalable layout algorithms, manual and automated visual mark-up annotation, OpenGL hardware acceleration, SVG export, and support for PSI-XML, BioPax, and GML formats within an extensible plug-in architecture.