BiNoM

BiNoM enables Cytoscape to import, export, analyze, and decompose biological networks in SBML, SBGN, BioPAX Level 3, CellDesigner, and CSML formats to support systems biology and pathway analysis.

Key Features:

• File Format Support: Import and export of standard systems-biology formats including SBML, SBGN, BioPAX Level 3, CellDesigner and CSML to enable interoperability with existing tools and databases.
• Network Analysis Tools: A suite of algorithms for path analysis, entity involvement decomposition, cyclic decomposition, subnetwork clustering, and modular network decomposition.
• BioPAX Management: Parsing, searching, and editing of extensive BioPAX Level 3 files, enabling the handling of whole pathway databases such as Reactome.
• Graph-Based Functions: Graph-based algorithms for quantifying pathways within influence networks.
• Case Study Application: Demonstrated analysis of the G1/S transition of the cell cycle to study processes frequently disrupted in human tumors.

Scientific Applications:

• Systems Biology Network Analysis: Decomposition and algorithmic analysis of large-scale molecular interaction maps for systems-level investigations.
• High-Throughput Data Interpretation: Support for integrating and interpreting high-throughput experimental data to aid hypothesis generation.
• Pathway Database Curation: Management and simplification of large pathway repositories to derive insights from resources such as Reactome.
• Cell Cycle and Cancer Pathway Analysis: Analysis of cell cycle transitions (e.g., G1/S) and their perturbations in human tumors.

Methodology:

Parsing and import/export of SBML, SBGN, BioPAX Level 3, CellDesigner and CSML files; algorithms for path analysis, entity involvement decomposition, cyclic decomposition, subnetwork clustering and modular decomposition; BioPAX parsing, searching and editing; graph-based quantification of pathways within influence networks.