iCAVE

iCAVE visualizes large, complex biomolecular interaction networks in three dimensions to enable exploration and interpretation of systems-level interactions across cellular processes.

Key Features:

• 3D Visualization Modalities: Supports standard desktop 3D, stereoscopic 3D, and immersive CAVE (Cave Automatic Virtual Environment) display modes.
• Advanced Layout Algorithms: Extends 2D network layout, clustering, and edge-bundling algorithms into three dimensions and implements novel 3D-specific network layout algorithms.
• Database Integration and Customization: Enables querying built-in databases to generate networks related to diseases, drugs, proteins, and metabolites, and supports visualization of user-provided networks.
• Modular Architecture: Employs a modular structure that permits adding new algorithms, datasets, or features without modifying core components.

Scientific Applications:

• Cellular process and pathway analysis: Facilitates visualization and interpretation of complex cellular processes and signaling or metabolic pathways.
• Systems-level disease analysis: Supports analysis of disease impacts at the systems level within biomolecular networks.
• Drug-target and metabolic investigations: Enables exploration of drug-target interactions and metabolic pathway relationships.
• Network dynamics insight: Provides three-dimensional representations that can reveal network dynamics and relationships not readily apparent in two-dimensional layouts.

Methodology:

Extends existing 2D network layout, clustering, and edge-bundling algorithms into three dimensions, implements novel 3D-specific network layout algorithms, and supports querying built-in databases for network generation as well as visualization of user-generated networks.