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08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
Eric Bonnet1, Laurence Calzone, Daniel Rovera
1Institut Curie, 26 rue d'Ulm, Paris, F-75248, France.
BMC Systems Biology
|March 5, 2013
Summary
Biological Network Manager (BiNoM) simplifies complex biological network analysis. This Cytoscape plugin facilitates data import/export and offers algorithms to reduce network complexity, aiding systems biology research.
Area of Science:
- Systems biology
- Bioinformatics
- Computational biology
Background:
- Biological pathway and network repositories have grown significantly.
- These databases aid in analyzing high-throughput data and forming hypotheses.
- Interpreting large-scale molecular maps remains challenging.
Purpose of the Study:
- To introduce BiNoM (Biological Network Manager), a Cytoscape plugin.
- To provide tools for managing and analyzing biological networks.
- To address the interpretability challenges of large molecular maps.
Main Methods:
- Developed BiNoM as a Cytoscape plugin.
- Implemented import/export functions for standard systems biology file formats (CellDesigner, BioPAX Level 3, CSML, SBML).
- Integrated graph-based algorithms for network analysis and complexity reduction (path analysis, decomposition, clustering).
Main Results:
- BiNoM efficiently imports, searches, and edits BioPAX files, including large databases like Reactome.
- Offers algorithms for network analysis, such as path analysis, decomposition, and modularization.
- Supports multiple standard file formats for broad compatibility.
Conclusions:
- BiNoM enhances the management and analysis of biological networks.
- Novel features include BioPAX Level 3 support and a new pathway quantification algorithm.
- Demonstrated BiNoM's utility with a case study on cell cycle regulation.
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