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A travel guide to Cytoscape plugins.

Rintaro Saito¹, Michael E Smoot, Keiichiro Ono

¹Department of Medicine, University of California, San Diego, La Jolla, California, USA.

|November 8, 2012

Summary

This guide explores 152 Cytoscape plugins for biological network analysis. It aims to organize and improve the quality of these diverse, community-contributed tools.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Cytoscape is a widely used open-source platform for biological network analysis.
Its functionality is extended by a large and diverse collection of community-developed plugins.
The organic growth of plugins has resulted in a powerful but heterogeneous ecosystem.

Purpose of the Study:

To provide a comprehensive overview of publicly available Cytoscape plugins.
To catalog and describe plugins for Cytoscape versions 2.5-2.8.
To outline strategies for organizing and maintaining plugin quality.

Main Methods:

Systematic review and cataloging of 152 Cytoscape plugins.
Analysis of plugin features and contributions.
Description of ongoing efforts in collection management.

Main Results:

A curated list of 152 plugins for Cytoscape 2.5-2.8 is presented.
The heterogeneity and diversity of the plugin collection are highlighted.
Initiatives for improved distribution and quality control are detailed.

Conclusions:

A structured approach is needed to manage the growing Cytoscape plugin ecosystem.
Community efforts are crucial for maintaining the utility and quality of biological network analysis tools.
This work serves as a foundational guide for navigating and contributing to Cytoscape plugins.