Data-dependent visualization of biological networks in the web-browser with NDExEdit
Florian Auer1, Simone Mayer1, Frank Kramer1
1Department of IT-Infrastructure for Translational Medical Research, Faculty of Applied Computer Science, University of Augsburg, Augsburg, Germany.
Plos Computational Biology
|June 8, 2022
Summary
Biological network visualization is challenging. NDExEdit offers a web-based solution for easy network editing and sharing, improving collaboration and data integrity.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- Biological networks represent complex associations between entities, crucial for bioinformatics.
- Interpreting and visualizing these networks is challenging, with Cytoscape being a prominent tool.
- Network distribution and collaborative editing pose challenges in typical workflows.
Purpose of the Study:
- To introduce NDExEdit, a web-based application for simplifying biological network modification.
- To enhance the usability of biological networks for presentations and publications.
- To facilitate seamless integration with existing platforms like Cytoscape and NDEx.
Main Methods:
- NDExEdit is a web-based application, requiring no installation.
- It allows direct editing of biological networks within a web browser.
- The tool supports the Cytoscape Exchange (CX) format for data interoperability.
Main Results:
- NDExEdit enables easy enhancement of plain networks for various uses.
- Network data is stored locally, ensuring user privacy and preventing unintentional publication.
- Modified networks can be exported to the NDEx platform or saved as CX files.
Conclusions:
- NDExEdit provides an accessible and efficient solution for biological network editing and visualization.
- It streamlines collaborative workflows by enabling easy sharing and modification of network data.
- The tool promotes data integrity and simplifies the dissemination of biological network insights.
