SimBioNeT

SimBioNeT simulates biological network topologies to generate hierarchical, modular networks with controlled degree distributions and clustering coefficients for benchmarking and analysis of biological network structure.

Key Features:

• Modular Structure Replication: Replicates module structures of varying types and sizes across multiple organizational levels to represent hierarchical biological systems.
• Customizable Network Properties: Generates networks with specified degree distributions, including scale-free distributions, while maintaining a clustering coefficient relative to node count.
• Flexibility and Adaptability: Allows adjustment of network parameters to simulate networks for different organisms for comparative studies.

Scientific Applications:

• Assessment of Reverse Engineering Algorithms: Produces synthetic networks with known properties to benchmark and evaluate reverse engineering algorithms.
• Investigation of Topological Properties: Enables exploration of how changes in network parameters affect topological features of biological networks.
• Empirical Validation: Has been compared with transcriptional networks from Escherichia coli and Saccharomyces cerevisiae to assess reproduction of characteristic network properties.

Methodology:

SimBioNeT interconnects module structures at multiple organizational levels to produce networks with specified degree distributions and clustering coefficients.