BioFabric

BioFabric visualizes biological networks by representing nodes as horizontal lines and edges as vertical lines to enable visualization and assessment of global network alignments using the VISNAB plugin.

Key Features:

• VISNAB plugin: Visualizes global network alignments within BioFabric and extends its layout capabilities for alignment analysis.
• Linear node layout: Represents nodes as horizontal lines and edges as vertical lines to produce an alternative network depiction for alignment inspection.
• Automatic layouts: Provides new automatic layout algorithms to arrange aligned networks and expose problematic regions in alignments.
• Node groups and link groups: Derives node groups and link groups from the visualization to categorize structural alignment relationships.
• Novel numeric measures: Computes quantitative measures based on the visualization-derived node and link groups to assess alignment quality.
• Comparison to topological metrics: Supplements traditional topological measures such as Edge Coverage (EC) and Symmetric Substructure Score (S3) by revealing alignment deficiencies those metrics may miss.

Scientific Applications:

• Network alignment evaluation: Evaluates and compares network alignment algorithms by visualizing alignment performance and structure.
• Comparative genomics: Assists comparative genomics studies that rely on global network alignments to compare molecular interaction networks across species.
• Systems biology: Supports systems biology analyses that use global network alignments to investigate conserved network topology and functional correspondence.

Methodology:

Uses BioFabric's layout where nodes are horizontal lines and edges are vertical lines, applies automatic layout generation for aligned networks, derives node groups and link groups from the visualization, and computes novel numeric measures for alignment quality alongside comparisons to Edge Coverage (EC) and Symmetric Substructure Score (S3).