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Related Experiment Video

Updated: Oct 19, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

NDEx: Accessing Network Models and Streamlining Network Biology Workflows.

Rudolf T Pillich¹, Jing Chen¹, Christopher Churas¹

¹School of Medicine, University of California San Diego, La Jolla, California.

Current Protocols

|September 27, 2021

Summary

This summary is machine-generated.

The Network Data Exchange (NDEx) is a web resource for managing biological network models. It integrates with Cytoscape for analysis and visualization, simplifying workflows and data sharing for researchers.

Keywords:

Cytoscape JavaScript NDEx R REST API enrichment analysis neighborhood query network biology network models pathway python subnetwork systems biology

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Area of Science:

Network biology
Bioinformatics
Computational biology

Background:

Network models are crucial for understanding complex biological systems.
Managing and sharing these models can be challenging.
Integration with analysis tools is essential for effective workflows.

Purpose of the Study:

Introduce researchers to the Network Data Exchange (NDEx) platform.
Highlight NDEx's capabilities for network model management and sharing.
Demonstrate NDEx's integration with Cytoscape and programmatic access.

Main Methods:

Utilizing the NDEx web-based resource for network data storage and retrieval.
Integrating NDEx with Cytoscape for network analysis and visualization.
Employing the 'ndex2' Python client library for programmatic network manipulation.

Main Results:

NDEx simplifies common network biology tasks, including finding, storing, sharing, and publishing network models.
The platform streamlines publication and access to network data.
Programmatic access via Python, JavaScript, and R is demonstrated.

Conclusions:

NDEx, in conjunction with Cytoscape, forms a core component of the Cytoscape Ecosystem.
The platform enhances network biology workflows through improved data management and accessibility.
Researchers can leverage NDEx for efficient handling and dissemination of biological network models.