A travel guide to Cytoscape plugins

A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.

Abstract

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5-2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.