WebInterViewer

WebInterViewer visualizes large-scale molecular interaction networks to enable analysis of protein-protein and protein-DNA interactions.

Key Features:

• Fast-Layout Algorithm: Employs a fast-layout algorithm that provides an order-of-magnitude speedup over classical graph drawing methods and reduces edge crossings in large networks.
• Connected Components Layout: Identifies and arranges connected components within the entire network as an initial layout step.
• Global Node Arrangement: Establishes a global arrangement of nodes relative to pivot nodes within connected components.
• Local Refinement: Refines local layouts by relocating midnodes with respect to cutvertices and direct neighbors and by adjusting nodes based on proximity within distance 2.
• Direct Data Visualization: Visualizes data directly from protein interaction databases without intermediate conversion steps.
• Abstraction and Comparison Operations: Provides operations for abstracting and comparing large-scale biological networks for comparative analyses.

Scientific Applications:

• Protein Interaction Analysis: Analysis of protein-protein and protein-DNA interaction networks.
• Pathway Exploration: Exploration of complex molecular pathways through network visualization.
• Hypothesis Support: Support for hypothesis generation and testing via visual inspection of network structure.
• Comparative Studies: Comparative analysis of different biological datasets and network abstractions.

Methodology:

Computational steps include identifying connected components, establishing global layouts relative to pivot nodes, performing local refinements by relocating midnodes with respect to cutvertices and neighbors and adjusting nodes within distance 2, and applying a fast-layout algorithm faster than classical graph drawing methods.