NDEx

NDEx manages storage, sharing, and publication of biological network models to enable exchange, reuse, and reproducibility in network biology and integration with the Cytoscape ecosystem.

Key Features:

• Comprehensive Network Management: Supports finding, storing, sharing, and publishing biological networks of varying size and complexity.
• Integration with Cytoscape: Integrates with the Cytoscape ecosystem to enable exchange of network models between NDEx and Cytoscape.
• Facilitation of Collaborative Research: Enables sharing of network data to support collaborative research and reproducibility of analyses.
• Programmatic Access: Provides programmatic access via the ndex2 Python client and examples for JavaScript and R.

Scientific Applications:

• Network biology workflows: Centralizes management tasks such as storage, retrieval, and publication of biological networks used in network biology analyses.
• Publication and dissemination of network models: Supports publication-oriented workflows to ensure network data accompanies scientific publications.
• Reproducibility and collaboration: Facilitates access and sharing of network data to support reproducibility and collaborative projects.

Methodology:

Basic Protocol 1 (Getting Started); Basic Protocol 2 (publication-oriented workflow with Cytoscape); Basic Protocol 3 (programmatic network manipulation in NDEx using Python).