SBEToolbox

SBEToolbox provides MATLAB-based functions for analysis, clustering, layout, and visualization of biological networks to support systems biology and evolutionary studies.

Key Features:

• Network Analysis: Accepts network files as input and computes centralities and topological metrics to characterize network structure and node importance.
• Clustering Algorithms: Includes MCL, mCode, and clusterOne algorithms to detect clusters and modules within networks.
• Graph Layouts: Provides diverse graph layout algorithms for visualization of network topology.
• Random Network Generation: Implements generation of random networks including small-world and ring lattice models.
• Customization and Extensibility: Supports extension via custom plugins or MATLAB scripts to add or modify analytical functionality.

Scientific Applications:

• Network-level analysis: Analysis of protein-protein interaction, gene regulatory, and metabolic pathway networks.
• Functional and pathological inference: Use of centralities and topological metrics to identify important nodes and network features relevant to biological processes and disease mechanisms.

Methodology:

Accepts network files as input; computes centralities and topological metrics; generates random networks (small-world, ring lattice); performs clustering using MCL, mCode, and clusterOne; and applies graph layout algorithms.