Cytoscape 1.1 PlugIns

About Cytoscape PlugIns:

Cytoscape includes a flexible PlugIn architecture that enables developers to add extra functionality beyond that provided in the core. PlugIns also provide a convenient place for testing out new Cytoscape features.

Note that PlugIns on this page will only work with Cytoscape 1.1. Refer to the current plugin page for a list of plugins registered with the plugin manager Current Cytoscape 2.x Plugins.

PlugIn License Policy:

Although the Cytoscape core application is distributed under a Library GNU Public License (LGPL), plugins are separate works which use Cytoscape as a Java code library. Plugins are therefore governed by independent software licenses distributed with and specific to each plugin. The Cytoscape project has no intent to capture plugins under the license terms of the core Cytoscape LGPL.

Current Cytoscape 1.1 PlugIns:

Biomodules Version: 1.0 Release Date: March 1, 2004	Biological modules are loose associations of preferred molecular interaction partners that perform a collective function. Biomodules is a Cytoscape plugin that identifies modules in molecular networks and analyzes their expression patterns and biological functions. This information is integrated, visualized, and analyzed in an interactive graphical representation. Released by: Galitski Lab at the Institute for Systems Biology	Verified to work in Cytoscape 1.1	[Biomodules Home Page]

Data Services Plug-In Version: 0.04 Release Date: September 5, 2003	This PlugIn enables Cytoscape to import/export to multiple file formats. The current release includes support for: Proteomics Standards Initiative Molecular Interaction (PSI-MI) XML Format. NCBI GEO Simple Omnibus Format in Text (SOFT). This product includes software developed by the Apache Software Foundation (http://www.apache.org). Released by: Sander Group, Computational Biology Center, Memorial Sloan Kettering Cancer Center.	Verified to work in Cytoscape 1.1.1	[Release Notes] [Download .tar.gz] [Download .zip]

Expression Data Viewers Version: 1.0 Release Date: October 13, 2003	This package contains two plugins. The first enables the user to view the expression profiles of selected genes in a Cytoscape network across all the experimental conditions. The second enables the user to find genes with a high degree of correlation with a node or set of nodes of interest. This package includes the Visad library (http://www.ssec.wisc.edu/~billh/visad.html). Released by: Institute for Systems Biology	Verified to work in Cytoscape 1.1	[Release Notes] [License] [Download]

jActiveModules Version: 1.0 Release Date: February 20, 2004	This plugin enables Cytoscape to search for significant networks as described in Bioinformatics. 2002 Jul;18 Suppl 1:S233-40. This product was developed using tools from the Apache Software Foundation (http://www.apache.org). Released by: The Ideker Lab, Department of Bioengineering, UCSD	Verified to work in Cytoscape 1.1	[Release Notes] [Download] [Source]

pathBLAST Version: 1.0 Release Date: March 5, 2004	This plugin to Cytoscape automates the process of aligning two protein-protein interaction networks and mining for evolutionarily conserved pathways, as described in PNAS 2003 100: 11394-11399. Released by: The Ideker Lab, Department of Bioengineering, UCSD	Verified to work in Cytoscape 1.1	[Release Notes] [Download] [Tutorial] [Tutorial Files]

SBML Reader Version: 1.0 Release Date: October 3, 2003	This plugin allows you to load a level 1 SBML file from Cytoscape's File menu, and to display the model as a Cytoscape network. You can also run Cytoscape with this plugin using Java Web Start, or view a snapshot of a sample SBML model of the Repressilotor System (Elowitz & Leibler, 2000). Released by: Institute for Systems Biology	Verified to work in Cytoscape 1.1	[Release Notes] [Download]