Cytoscape 2.x Plugins

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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. As more Plugins become available, they will be listed on this page, and posted to our cytoscape-announce mailing list.

The plugins on this page are categorized into 7 sections:

Current Cytoscape 2.x plugins

Expand All    Collapse All   
  • Core  --  Cytoscape core (0)
  • Analysis  --  Used for analyzing existing networks (28)
    • APID2NET

      • Description: Plugin designed to visualize, explore and analyze the proteins and interactions retrieved from the unified interactome platform APID (which integrates BIND, BioGrid, DIP, HPRD, IncAct and MINT). The retrieved data include the annotations and attributes associated to the network: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs. The tool provides interactive graphical representation of the protein-protein interaction (PPI) networks within Cytoscape, plus new automatic tools to find hubs and concurrent attributes (functional and structural) along the protein pairs of a given network.
        Project website: http://bioinfow.dep.usal.es/apid/apid2net.html
        License: click here

        --

        Version: 1.5
        Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
        Release Date: 2007-11-16
        Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. , Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL) Salama
        Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
        Verified to work in: 2.5
        Note: Compatible with Cytoscape v2.5. Versions for CytoScape v2.4 and v2.3 are available in the Web page (http://bioinfow.dep.usal.es/apid/apid2net.html).
        Download Jar/zip: click here (413.2KB)

        --

        Version: 1.51
        Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
        Release Date: 2007-12-20
        Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
        Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
        Verified to work in: 2.5
        Download Jar/zip: click here (413.5KB)

        --

        Version: 1.52
        Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
        Release Date: 2008-05-14
        Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
        Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
        Verified to work in: 2.6
        Download Jar/zip: click here (414.4KB)


    • BioQualiPlugin

      • Description: BioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data. It diagnoses a regulatory network searching for the regulations that are not consistent with the expression data, and it outputs a set of genes which predicted expression is decided in order to explain the expression data provided.
        The BioQuali Cytoscape Plugin proposes the user to visualize this analysis automatically and in few minutes no matter the size of the network.
        Project website: http://www.irisa.fr/symbiose/projects/bioqualiCytoscapePlugin/
        --

        Version: 1.0
        Release Date: 2008-09-17
        Released by: Annabel Bourdé , Centre INRIA Rennes Bretagne Atlantique, IRISA
        Carito Guziolowski , Centre INRIA Rennes Bretagne Atlantique, IRISA
        Verified to work in: 2.6
        Download Jar/zip: click here (2.19MB)

        --

        Version: 1.1
        Reference: Guziolowski C, Bourde A, Moreews F, Siegel A. "BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks". BMC Genomics (2009), 10(1):244 doi:10.1186/1471-2164-10-244.
        Release Date: 2009-02-01
        Released by: Annabel Bourde and Carito Guziolowski , IRISA
        Verified to work in: 2.6
        Note: This is an updated version of the BioQualiPlugin. We mostly changed the sources in .zip to .jar.
        Download Jar/zip: click here (5.6MB)


    • BLAST2SimilarityGraph

      • Description: This plugin uses an all-vs-all BLAST result file and a sequences file in FASTA format as input to generate a (protein) similarity graph.

        Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.
        Project website: http://transclust.cebitec.uni-bielefeld.de
        --

        Version: 1.0
        Release Date: 2009-04-28
        Released by: Jan Baumbach , International Computer Science Institute, Berkeley
        Tobias Wittkop , Bielefeld University
        Dorothea Emig , Max Planck Institute for Informatics

        Verified to work in: 2.6
        Download Jar/zip: click here (97.1KB)


    • CABIN
    • CentiScaPe

      • Description: CentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.
        Project website: http://profs.sci.univr.it/~scardoni/centiscape/centiscapepage.php
        --

        Version: 1.0
        Release Date: 2008-05-19
        Released by: Giovanni Scardoni, Michele Petterlini , Center for Biomedical Computing (CBMC), University of Verona
        Carlo Laudanna , CBMC, Department of Pathology, University of Verona
        Release notes: http://profs.sci.univr.it/~scardoni/centiscape/centiscapedownload.php
        Verified to work in: 2.6
        Download Jar/zip: click here (3.79MB)
        Download source: http://profs.sci.univr.it/~scardoni/centiscape/centiscapedownload.php

    • clusterExplorerPlugin

      • Description: This plugin can be used to analyse a given similarity graph (edge weight distribution etc.).

        Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.
        Project website: http://transclust.cebitec.uni-bielefeld.de
        --

        Version: 0.9
        Release Date: 2008-09-18
        Released by: Jan Baumbach , University of Bielefeld
        Tobian Wittkp , University of Bielefeld
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (218.3KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/clusterExplorerPlugin
        --

        Version: 1.0
        Release Date: 2009-04-28
        Released by: Jan Baumbach , International Computer Science Institute, Berkeley
        Tobias Wittkop , Bielefeld University
        Dorothea Emig , Max Planck Institute for Informatics

        Verified to work in: 2.6
        Download Jar/zip: click here (1.4MB)


    • clusterMaker

      • Description: Cluster Nodes and/or Edges
        Project website: http://www.rbvi.ucsf.edu/Research/cytoscape/
        --

        Version: 1.1
        Release Date: 2008-11-04
        Released by: Jan Baumbach , Technical University of Bielefeld
        Tobian Wittkop , Technical University of Bielefeld
        Leonard Apeltsin , UCSF
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6.1
        Download Jar/zip: click here (613.9KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/clusterMaker
        --

        Version: 1.0
        Release Date: 2008-09-14
        Released by: Jan Baumbach , Technical University of Bielefeld
        Tobian Wittkop , Technical University of Bielefeld
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (612.6KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/clusterMaker
        --

        Version: 1.5
        Release Date: 2009-01-07
        Released by: Jan Baumbach , Technical University of Bielefeld
        Tobian Wittkop , Technical University of Bielefeld
        Leonard Apeltsin , UCSF
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6.2
        Download Jar/zip: click here (622.7KB)

        --

        Version: 1.6
        Release Date: 2009-02-25
        Released by: John "Scooter" Morris , UCSF
        Jan Baumbach , Technical University of Bielefeld
        Tobian Wittkop , Technical University of Bielefeld
        Release notes: click here
        Verified to work in: 2.6.1,2.6.2
        Note: This plugin will work with 2.6.1 and 2.6.2
        Download Jar/zip: click here (570.8KB)


    • COMA

      • Description: This plugin performs consistency checks for gene expression data given gene regulatory networks (refer to citation for details).

        Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.

        If you use it for your research please cite:

        Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Project website: https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v4/CytoscapePlugins/index.html
        License: click here

        --

        Version: 1.0
        Release Date: 2008-02-13
        Released by: Jan Baumbach , Bielefeld University
        Verified to work in: 2.5
        Download Jar/zip: click here (17.8KB)

        --

        Version: 1.1
        Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (17.7KB)

        --

        Version: 1.101
        Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (17.7KB)


    • CyOog

      • This plugin is not available through the Plugin Manager!

        Description: This plugin provides Power Graph Analysis.
        Project website: http://www.biotec.tu-dresden.de/schroeder/group/powergraphs
        --

        Version: 0.8
        Release Date: 2008-05-15
        Released by: Matthias Reimann , BIOTEC, Technische Universität Dresden
        Verified to work in: 2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • cyto-Hubba

      • Description: Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Bottleneck (BN), Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), and a double screening scheme (DSS) of MNC || DMNC.
        Project website: http://hub.iis.sinica.edu.tw
        --

        Version: 1.0
        Release Date: 2009-06-30
        Released by: Chung-Yen Lin, Chia-Hao, Chin and Min-Tat, Ko , Institute of Information Science, Academia Sinica, TAIWAN
        Verified to work in: 2.6
        Download Jar/zip: click here (87.8KB)


    • dynamicXpr

      • Description: A Plug-In that colors nodes according to their expression across many conditions, as in a movie
        --

        Version: 1.2
        Release Date: 2008-03-18
        Released by: Iliana Avila-Compillo , ISB
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (18.4KB)

        --

        Version: 1.3
        Release Date: 2008-09-18
        Released by: Iliana Avila-Compillo , ISB
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (18.4KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/dynamicXpr

    • EnhancedSearch
    • HiderSlider

      • Description:
        The HiderSlider allows a user to interactively explore a network by hiding/showing nodes or edges with attribute values above an adjustable threshold using a slider bar. The user may choose to slide over any numeric (floating point or integer) attribute for edges or nodes.


        Project website: http://sourceforge.net/projects/hanalyzer/
        License: click here

        --

        Version: 1.0
        Release Date: 2009-03-16
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (15KB)
        Download source: http://sourceforge.net/projects/hanalyzer/

    • jActiveModules

      • Description: ActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.
        --

        Version: 2.2
        Release Date: 2007-03-23
        Released by: Ryan M. Kelley , UCSD
        Verified to work in: 2.5
        Download Jar/zip: click here (110.3KB)

        --

        Version: 2.21
        Release Date: 2008-03-31
        Released by: Ryan Kelley , UCSD
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (113.8KB)

        --

        Version: 2.22
        Release Date: 2008-06-10
        Released by: Ryan Kelley , UCSD
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (115.1KB)

        --

        Version: 2.23
        Release Date: 2008-08-13
        Released by: Ryan Kelley , UCSD
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (115.4KB)


    • MCODE

      • Description: MCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.
        --

        Version: 1.2
        Release Date: 2007-02-15
        Released by: Gary Bader , MSKCC
        Verified to work in: 2.5
        Download Jar/zip: click here (86.5KB)

        --

        Version: 1.3
        Release Date: 2007-12-07
        Released by: Gary Bader, Vuk Pavlovic , University of Toronto
        Verified to work in: 2.5
        Download Jar/zip: click here (95.3KB)

        --

        Version: 1.31
        Release Date: 2009-05-22
        Released by: Gary Bader, Vuk Pavlovic , University of Toronto
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (91.7KB)


    • NetAtlas

      • Description: NetAtlas is a Java plugin application designed to use tissue gene expression data to filter genes in a cellular signaling network. The NetAtlas plugin allows the creation of tissue-defined networks, identification of network components that are more highly expressed in specific tissues, and the identification of network components that show correlated expression across tissues. The default tissue gene expression data available in NetAtlas is from SymAtlas and contains human, mouse, and rat gene expression data for a wide range of tissues and has been previously published by the Genomics Institute of the Novartis Research Foundation. The user is also allowed to import their own tissue gene expression data in text file format.
        Project website: http://sourceforge.net/projects/netatlas/
        License: click here

        --

        Version: 1.1
        Reference: Longlong Yang, John R. Walker, John B. Hogenesch and Russell S. Thomas NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression. In Silico Biol. 8:0005, 2007. http://www.bioinfo.de/isb/2007/08/0005/
        Release Date: 2007-11-20
        Released by: Russell S. Thomas , The Hamner Institutes for Health Sciences
        Longlong Yang , The Hamner Institutes for Health Sciences
        Release notes: http://sourceforge.net/projects/netatlas/
        Verified to work in: 2.4,2.5
        Note: A tutorial can be found at: http://sourceforge.net/projects/netatlas/
        Download Jar/zip: click here (985.3KB)
        Download source: http://sourceforge.net/projects/netatlas/

    • netMatch

      • Description: NetMatch is a Cytoscape plugin that finds user defined network motifs in any Cytoscape network. Node and edge attributes of any type and paths of unknown length can be specified in the search.
        Project website: http://ferrolab.dmi.unict.it/netmatch.html
        --

        Version: 2.1
        Release Date: 2008-11-07
        Released by: A. Ferro , University of Catania
        R. Giugno , University of Catania
        G. Pigola , University of Catania
        A. Pulvirenti , University of Catania
        D. Skripin , University of Catania
        G.D. Bader , University of Toronto
        D. Shasha , New York University
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (1.59MB)


    • NetworkAnalyzer

      • This plugin is not available through the Plugin Manager!

        Description: NetworkAnalyzer performs analysis of biological networks and calculates network topology parameters including the diameter of a network, the average number of neighbors, and the number of connected pairs of nodes. It also computes the distributions of more complex network parameters such as node degrees, average clustering coefficients, topological coefficients, and shortest path lengths. It displays the results in diagrams, which can be saved as images or text files.
        Project website: http://med.bioinf.mpi-inf.mpg.de/networkanalyzer/
        License: click here

        --

        Version: 2.5.1
        Reference: Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284, 2008
        Release Date: 2007-12-11
        Released by: Yassen Assenov , Max Planck Institute for Informatics
        Mario Albrecht , Max Planck Institute for Informatics
        Verified to work in: 2.5
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 2.6.1
        Reference: Reference: Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284, 2008
        Release Date: 2008-07-10
        Released by: Yassen Assenov , Max Planck Institute for Informatics
        Mario Albrecht , Max Planck Institute for Informatics
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • OmicsViz

      • This plugin is not available through the Plugin Manager!

        Description: OmicsViz is a Cytoscape plugin (cytoscape2.4 and 2.5) dedicated to providing useful visualization and an integrated analysis tool for large-scale omics data. OmicsViz imports omics data into Cytoscape and visualizes it on a graph according to the change of gene experimental values (Figure 1). OmicsViz also provides a mapping function between two different species or between probe set and experimental names and node names in a network. For example, when you load an Arabidopsis metabolic pathway in Cytoscape and you have a Grape gene expression file, OmicsViz can associate the file with the Arabidopsis pathway based on gene mapping file which contains orthologous genes between the two species.
        Project website: http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm
        --

        Version: 2.2
        Release Date: 2007-06-01
        Released by: Tian Xia, , Program of Bioinformatics and Computational Biology,Iowa state university
        Julie Dickerson , Program of Bioinformatics and Computational Biology,2Department of Electrical and Computer Engineering,Iowa state university
        Verified to work in: 2.4,2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • PerturbationAnalyzer

      • Description: The PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/
        Project website: http://biotech.bmi.ac.cn/PerturbationAnalyzer
        --

        Version: 0.1
        Release Date: 2009-03-23
        Released by: Fei Li , NUDT/BMI
        Wenjian Xu , BMI
        Peng Li , BMI
        Verified to work in: 2.5,2.6.1,2.6.2
        Download Jar/zip: click here (1.75MB)
        Download source: http://code.google.com/p/perturbation-analyzer/
        --

        Version: 0.2
        Release Date: 2009-05-24
        Released by: Fei Li , NUDT/BMI
        Wenjian Xu , BMI
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (1.73MB)
        Download source: http://code.google.com/p/perturbation-analyzer/
        --

        Version: 1.0
        Release Date: 2009-06-18
        Released by: Fei Li , NUDT/BMI
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (1.73MB)


    • PinnacleZ

      • Description: An implementation of the PinnacleZ algorithm as specified in Chuang, H. Y. and Lee, E., et al., "Network-based classification of breast cancer metastasis," Molecular Systems Biology 3:140 (2007).
        --

        Version: 1.0
        Release Date: 2008-06-16
        Released by: Samad Lotia and Han-Yu Chuang , UCSD
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (164KB)

        --

        Version: 1.1
        Release Date: 2008-10-10
        Released by: Samad Lotia and Han-Yu Chuang , UCSD
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (165KB)


    • RandomNetworks
    • RDFScsape

      • This plugin is not available through the Plugin Manager!

        Description: RDFScape is a project that brings Semantic Web \"features\" to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape. A full list of features is reporte in Features. Unlike other ontology-based features in Cytoscape, RDFScape doesn\'t consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology. Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL,RDQL,Strings, interactive browsing) and a customizable visualization features.
        Project website: http://www.bioinformatics.org/rdfscape/
        License: click here

        --

        Version: 0.4
        Reference: To appear in BMC Bioinformtics
        Release Date: 2008-02-07
        Released by: Andrea Splendiani , University of Rennes 1
        , Leaf Bioscience s.r.l.
        Verified to work in: 2.5
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://www.bioinformatics.org/rdfscape/

    • ReOrientPlugin

      • Description:
        Applies node positions from a network in any stored Cytoscape session file to the currently selected network.

        A network can be created, laid out, and stored with an existing data set. When new data becomes available, a new network can be created and easily compared to the old network by placing nodes in the same positions.

        To use the plugin, select "from Saved Session" from the Layout menu.

        The current version allows the user to select any network from a saved session as the source network.


        Project website: http://sourceforge.net/projects/hanalyzer/
        License: click here

        --

        Version: 0.3
        Reference: Tipney, H., Schuyler, R., Hunter, L., 'Consistant visualizations of changing knowledge', AMIA Summit on Translational Bioinformatics, San Francisco 2009
        Release Date: 2009-01-22
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (7.5KB)
        Download source: http://sourceforge.net/projects/hanalyzer/
        --

        Version: 1.0
        Reference: Tipney, H., Schuyler, R., Hunter, L., 'Consistant visualizations of changing knowledge', AMIA Summit on Translational Bioinformatics, San Francisco 2009
        Release Date: 2009-01-22
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (9.4KB)
        Download source: http://sourceforge.net/projects/hanalyzer/

    • ShortestPath Plugin

      • Description: ShortestPath is a plugin for Cytoscape 2.1 to show the shortest path between 2 selected nodes in the current network. It supports both directed and undirected networks and it gives the user the possibility to choose which node (of the selected ones) should be used as source and target (useful for directed networks). The plugin API makes possible to use its functionality from another plugin.
        License: click here

        --

        Version: 1.1
        Release Date: 2007-07-25
        Released by: Marcio Rosa da Silva
        Verified to work in: 2.4,2.5
        Download Jar/zip: click here (8KB)


    • structureViz

      • Description: This plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.
        Project website: http://www.rbvi.ucsf.edu/Research/cytoscape/structureViz.html
        --

        Version: 1.0
        Release Date: 2007-05-01
        Released by: John "Scooter" Morris UCSF Resource for Biocomputing, Visualization, and Informatics
        Verified to work in: 2.5
        Download Jar/zip: click here (67.8KB)

        --

        Version: 1.2
        Reference: Morris, Huang, Babbitt, Ferrin. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1;23(17):2345-7
        Release Date: 2008-03-18
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (74.1KB)

        --

        Version: 1.3
        Reference: Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10.
        Release Date: 2008-09-18
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (77.8KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/structureViz

    • TransClust

      • Description: This plugin clusters a given similarity graph by using transitivity clustering, i.e. solving the weighted transitive graph projection problem.

        Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.
        Project website: http://transclust.cebitec.uni-bielefeld.de
        --

        Version: 1.0
        Release Date: 2009-04-28
        Released by: Jan Baumbach , International Computer Science Institute, Berkeley
        Tobias Wittkop , Bielefeld University
        Dorothea Emig , Max Planck Institute for Informatics

        Verified to work in: 2.6
        Download Jar/zip: click here (567.2KB)


    • VistaClaraPlugin

      • Description: A visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.
        License: click here

        --

        Version: 1.0
        Reference: The following paper describes the original standalone implementation on which this plugin is based: R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, 167-174. http://doi.acm.org/10.1145/967900.967935
        Release Date: 2008-04-09
        Released by: Robert Kincaid and Allan Kuchinsky , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Note: VistaClara provides a more graphical and interactive alternative to the standard attribute browser. Enhanced coordination between the tabular view and the network view is also supported. VistaClara is designed primarily ratio-based expression data, but has been used successfully for other data types.
        Download Jar/zip: click here (777.3KB)

        --

        Version: 1.01
        Reference: The following paper describes the original standalone implementation on which this plugin is based: R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, 167-174. http://doi.acm.org/10.1145/967900.967935
        Release Date: 2008-07-28
        Released by: Robert Kincaid and Allan Kuchinsky , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (681.9KB)

        --

        Version: 1.02
        Reference: The following paper describes the original standalone implementation on which this plugin is based: R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, 167-174. http://doi.acm.org/10.1145/967900.967935
        Release Date: 2009-04-23
        Released by: Robert Kincaid and Allan Kuchinsky , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6.2
        Download Jar/zip: click here (682.8KB)


  • Network and Attribute I/O  --  Used for importing networks and attributes in different file formats (17)
    • BiNoM

      • Description: BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure.
        • Import of BioPAX, SBML and CellDesigner formats
        • Export to BioPAX, SBML and CellDesigner formats after user manipulations
        • Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
        • Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces
        • Browsing, editing, extracting parts, merging BioPAX files with network graph interface
        • Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
        • Support of generating network modular view
        • BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
        • Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)

        Project website: http://bioinfo.curie.fr/projects/binom
        License: click here

        --

        Version: 1.0
        Reference: Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2007. Accepted in Bioinformatics.
        Release Date: 2007-09-01
        Released by: Andrei Zinovyev , Institut Curie
        Eric Viara , Institut Curie
        Laurence Calzone , Institut Curie
        Emmanuel Barillot , Institut Curie
        Release notes: http://bioinfo.curie.fr/projects/binom
        Verified to work in: 2.5
        Note: The jar provided is dependent on many other jars. For self-containing versions of jar, visit http://bioinfo.curie.fr/projects/binom
        Download Jar/zip: click here (1.26MB)
        Download source: http://bioinfo.curie.fr/projects/binom/docs/BiNoM_src.zip

    • BiomartClient
    • BioNetBuilder

      • Description: Accesses BIND,BioGrid,DIP,HPRD,KEGG,IntAct,MINT,MPPI, and Prolinks as well as interolog networks derived from these sources for all species represented in NCBI HomoloGene.
        --

        Version: 2.0
        Reference: Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss and Richard Bonneau BioNetBuilder: automatic integration of biological networks Bioinformatics 2007 23(3):392-393; doi:10.1093/bioinformatics/btl604
        Release Date: 2008-06-18
        Released by: Jay Konieczka , University of Arizona
        Kevin Drew , Courant Institute, NYU.
        Release notes: http://err.bio.nyu.edu/cytoscape/bionetbuilder/index.php
        Verified to work in: 2.6
        Download Jar/zip: click here (2.21MB)
        Download source: https://err.bio.nyu.edu/svn/bionetbuilder/

    • CoryneRegNetLoader

      • Description: This plugin downloads gene regulatory networks from the corynebacterial reference database CoryneRegNet (compatible with at least release 4.0). Downloaded are the gene/protein IDs, the gene/protein names, the evidence, and the regulation type (-1 for repression and +1 for activation).

        Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.

        If you use it for your research please cite:

        Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Project website: https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v4/CytoscapePlugins/index.html
        License: click here

        --

        Version: 1.0
        Release Date: 2008-02-13
        Released by: Jan Baumbach , Bielefeld University
        Verified to work in: 2.5
        Download Jar/zip: click here (15.4KB)

        --

        Version: 1.1
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Verified to work in: 2.6
        Download Jar/zip: click here (15.5KB)

        --

        Version: 1.101
        Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (15.5KB)


    • DroID
    • Genoscape

      • Description: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.

        Project website: http://www.pasteur.fr/recherche/unites/Gim/genoscape/
        License: click here

        --

        Version: 1.1
        Release Date: 2009-07-01
        Released by: M.Clement-Ziza , TU-Dresden
        C.Malabat , Pasteur institute
        C.Weber , Pasteur institute
        T.Aittokallio
        C.Letondal , Pasteur institute and LRI
        S.Rousseau , Pasteur institute
        Verified to work in: 2.0,2.1,2.2,2.3,2.4,2.5,2.6,2.6.1
        Download Jar/zip: click here (373.6KB)
        Download source: http://www.pasteur.fr/recherche/unites/Gim/genoscape/

    • GPML-Plugin
    • IntActWSClient

      • Description: Web Service Client for IntAct Database.

        Users can import network data from IntAct interaction database. This is a web service client and accessible from other plugins through WebServiceClientManager.


        License: click here

        --

        Version: 0.60
        Release Date: 2008-10-09
        Released by: Keiichiro Ono , UCSD Bioengineering Ideker Lab
        Release notes: http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients
        Verified to work in: 2.6
        Download Jar/zip: click here (3.28MB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/kono/IntActClient
        --

        Version: 0.65
        Release Date: 2008-11-16
        Released by: Keiichiro Ono , UCSD Bioengineering Ideker Lab
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (3.28MB)


    • MetScape

      • Description:

        MetScape is a Cytoscape plugin which is used to visualize and analyze metabolomic data. It uses the data from Edinburgh Human Metabolic Network reconstruction (Ma et al., Mol Syst Biol. 2007; 3: 135). It allows user to visualize compound networks and display related information about reactions, enzymes and pathways. This work was supported by grant U54DA021519 from NIH.


        --

        Version: 0.8
        Release Date: 2009-03-13
        Released by: Jing Gao, Alla Karnovsky, Glenn Tarcea, James Cavalcoli and H. V. Jagadish , CCMB/NCIBI University of Michigan
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (248.2KB)
        Download source: http://metabplugin.ncibi.org/

    • MiMIplugin

      • Description:

        MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The Plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching

        Reference: Jing Gao, Alex S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H.V. Jagadish, and David J. States. Integrating and Annotating the Interactome using the MiMI plugin for Cytoscape. Bioinformatics 2009 25(1):137-138; doi:10.1093/bioinformatics/btn501. PMID: 18812364


        --

        Version: 2.0
        Reference: Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. (2007) "Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together." Nucleic Acids Res. 35(Database issue):D566-71. Epub 2006 Nov 27.
        Release Date: 2007-08-31
        Released by: Jing Gao, Alex Ade
        Verified to work in: 2.5
        Download Jar/zip: click here (91.7KB)

        --

        Version: 2.1
        Release Date: 2007-10-08
        Released by: Jing Gao, Alex Ade and David States , University of Michigan CCMB/NCIBI
        Verified to work in: 2.5
        Download Jar/zip: click here (98.9KB)

        --

        Version: 2.2
        Release Date: 2008-04-14
        Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (107.3KB)
        Download source: http://mimiplugin.ncibi.org/
        --

        Version: 3.0
        Release Date: 2008-07-01
        Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Verified to work in: 2.6
        Download Jar/zip: click here (140.8KB)
        Download source: http://mimiplugin.ncibi.org/
        --

        Version: 3.01
        Release Date: 2008-08-12
        Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (226KB)
        Download source: http://mimiplugin.ncibi.org/

    • NCBIClient
    • NCBIEntrezGeneUserInterface
    • PICRClient
    • ReConn

      • This plugin is not available through the Plugin Manager!

        Description: ReConn connects Cytoscape to the Reactome database. ReConn offers the user the following features: 1. Loading pathways by name. 2. Generating a new pathway by taking a given metaboliteas a starting point. Cytoscape can then display all reactions that are related to the reactions that consumes the given metabolite. 3. After a pathway has been loaded into Cytoscape, one can load data (e.g. from micro-array experiments) on top of it. This data is then visualized by changing the node colours. For instance, with micro-array data the colour and its intensity corresponds to the level of expression of the gene associated with the reaction. 4. ReConn can work also in the oposite direction: the user can see how the data is mapped onto the various pathways of Reactome. Therefore one can select the pathway of interest by looking at the data, instead of starting with a pathway. 5. ReConn can generate a subgraph containing all paths from one reaction to another. This is possible because of the graph-like data structure of Reactome. For clarity, one can limit the subgraph to paths shorter than a certain cut-off length. It is also possible to exclude certain reactions from this subgraph.
        Project website: http://bmi.bmt.tue.nl/reconn/
        License: click here

        --

        Version: 1.0
        Release Date: 0000-00-00
        Released by: Willem P.A. Ligtenberg , BioModeling & bioInformatics, Department of BioMedical Engineering, Eindhoven University of Technology
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://bmi.bmt.tue.nl/reconn/ReConn_source.zip

    • SessionForWeb

      • Description: Saves the current Cytoscape session as a web page with images thumbnails, and legends of each network, or as zip file compatible with the CellCircuit website.
        --

        Version: 3.0
        Release Date: 2008-01-30
        Released by: Samad Lotia , UCSD
        Verified to work in: 2.5
        Download Jar/zip: click here (68.3KB)

        --

        Version: 3.1
        Release Date: 2008-10-15
        Released by: Samad Lotia , UCSD
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (108.7KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/SessionForWebPlugin/

    • SFLDLoader
    • StringWSClient

      • Description: Provides connectivity to the STRING database (http://www.string-db.org).This version supports only import of interaction networks; upcoming versions will be ableto extend existing networks, filter them using STRING specific criteria, etc.
        Project website: http://www.string-db.org
        License: click here

        --

        Version: 1.0
        Reference: Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. Epub 2008 Oct 21. http://www.ncbi.nlm.nih.gov/pubmed/18940858
        Release Date: 2009-02-27
        Released by: Milan Simonovic , University of Zurich
        Christian von Mering , University of Zurich
        Verified to work in: 2.6.1
        Download Jar/zip: click here (392KB)


  • Network Inference  --  Used for inferring new networks (6)
    • AgilentLiteratureSearch

      • Description: Creates a CyNetwork based on searching the scientific literature.
        Project website: http://www.agilent.com/labs/research/litsearch.html
        License: click here

        --

        Version: 2.55
        Release Date: 2007-07-17
        Released by: Allan Kuchinsky and Aditya Vailaya, , Agilent Labs
        Michael Creech, , Blue Oak Software
        Verified to work in: 2.5
        Note: See plugin.props file for various field info.
        Download Jar/zip: click here (4.14MB)

        --

        Version: 2.70
        Release Date: 2008-10-03
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6.2
        Note: Please remove versions 2.68 and 2.69.
        Download Jar/zip: click here (5.04MB)


    • Cytoprophet

      • Description: Cytoprophet is a Cytoscape plugin that helps researchers infer new potential protein (PPI) and domain (DDI) interactions. Users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score.
        Project website: http://cytoprophet.cse.nd.edu/
        License: click here

        --

        Version: 1.0
        Reference: Morcos, F., Lamanna, C., Sikora, M. and Izaguirre, J. Cytoprophet: A Cytoscape plug-in for protein and domain interaction network inference. Bioinformatics. (Submitted)
        Release Date: 2008-04-18
        Released by: Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre , University of Notre Dame
        Release notes: http://cytoprophet.cse.nd.edu/
        Verified to work in: 2.6
        Note: More information, documentation and the API are available at the website (http://cytoprophet.cse.nd.edu/).
        Download Jar/zip: click here (61.1KB)
        Download source: http://cytoprophet.cse.nd.edu/

    • DomainGraph

      • Description: DomainGraph decomposes a user-given protein interaction network into their underlying domain-domain interactions.
        Gene interaction networks can be also be loaded to visualize all their transcripts and domains compositions.
        For the networks, DomainGraph accepts UniProt, Ensembl and Entrez identifiers.
        Several structure-based and predicted domain interaction datasets are provided with the plugin.

        Additionally, DomainGraph allows integrating Affymetrix Exon Array data (raw data or preprocessed via AltAnalyze).
        The gene, protein and domain nodes are then colored according to the expression data and differential expression is highlighted.
        Project website: http://domaingraph.bioinf.mpi-inf.mpg.de
        --

        Version: 1.0
        Release Date: 2008-08-15
        Released by: Dorothea Emig, Thomas Lengauer, Mario Albrecht , Max Planck Institute for Informatics
        Melissa S. Cline , Department of Molecular Cell and Developmental Biology, UCSC
        Verified to work in: 2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 2.01
        Reference: Emig, D, Cline, MS, Lengauer, T, Albrecht, M, Integrating expression data with domain interaction networks. Bioinformatics, 2008, 24(21):2546-2548.
        Release Date: 2008-12-12
        Released by: Dorothea Emig,Thomas Lengauer,Mario Albrecht , Max Planck Institute for Informatics
        Melissa S. Cline , UCSC
        Anne Kunert,Karsten Klein,Petra Mutzel , University of Dortmund
        Nathan Salomonis , The Gladstone Institutes

        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (3.26MB)

        --

        Version: 2.0
        Reference: Emig, D, Cline, MS, Lengauer, T, Albrecht, M, Integrating expression data with domain interaction networks. Bioinformatics, 2008, 24(21):2546-2548.
        Release Date: 2008-11-17
        Released by: Dorothea Emig,Thomas Lengauer,Mario Albrecht , Max Planck Institute for Informatics
        Melissa S. Cline , UCSC
        Anne Kunert,Karsten Klein,Petra Mutzel , University of Dortmund
        Nathan Salomonis , The Gladstone Institutes

        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (3.26MB)


    • ExpressionCorrelation

      • Description: ExpressionCorrelation plugin computes a similarity network from
        either the genes or conditions in an expression matrix.
        Project website: http://www.baderlab.org/Software/ExpressionCorrelation
        --

        Version: 1.01
        Release Date: 2008-10-07
        Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , Memorial Sloan-Kettering Cancer Center
        Chris Sander , Memorial Sloan-Kettering Cancer Center
        Shirley Hui and Laetitia Morrison , University of Toronto
        Release notes: click here
        Verified to work in: 2.5,2.6
        Note: This is an update to the previously submitted version 1.0 that contains a bug fix and some updated author information.
        Download Jar/zip: click here (94.9KB)

        --

        Version: 1.0
        Release Date: 2008-09-24
        Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , MSKCC
        Shirley Hui and Laetitia Morrison , University of Toronto
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (94.9KB)
        Download source: http://www.baderlab.org/Software/ExpressionCorrelation

    • MetaNetter

      • Description: Plugin for the inference of metabolic networks based on high resolution metabolomic data.
        Project website: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
        License: click here

        --

        Version: 2.1
        Reference: Jourdan F, Breitling R, Barrett M and Gilbert D. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2007) In press Bioinformatics.
        Release Date: 2007-07-24
        Released by: Fabien Jourdan , INRA
        Release notes: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
        Verified to work in: 2.5
        Note: MetaNetter is a plugin for the inference of metabolomic networks based on high resolution mass spectrometry data.
        Download Jar/zip: click here (67.2KB)


    • MONET

      • Description: Motivation: Although gene expression data has been continuously accumulated and meta-analysis approaches have been developed to integrate independent expression profiles into larger datasets, the amount of information is still insufficient to infer large scale genetic networks. In addition, global optimization such as Bayesian network inference, one of the most representative techniques for genetic network inference, requires tremendous computational load far beyond the capacity of moderate workstations.

        Results: MONET is a Cytoscape plugin to infer genome-scale networks from gene expression profiles. It alleviates the shortage of information by incorporating pre-existing annotations. The current version of MONET utilizes thousands of parallel computational cores in the supercomputing center in KISTI, Korea, to cope with the computational requirement for large scale genetic network inference.

        Reference: Lee et al., Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics (2005) 21, 2739-2747
        Project website: http://delsol.kaist.ac.kr/~monet/home
        --

        Version: 2.01
        Release Date: 2009-06-25
        Released by: Younghoon Kim, Doheon Lee , KAIST
        Verified to work in: 2.3,2.4,2.5,2.6
        Download Jar/zip: click here (667.8KB)


  • Functional Enrichment  --  Used for functional enrichment of networks (5)
    • BiNGO

      • Description: BiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.
        Project website: http://www.psb.ugent.be/cbd/papers/BiNGO/
        --

        Version: 2.1
        Reference: Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449.
        Release Date: 2007-08-29
        Released by: Steven Maere , VIB
        Martin Kuiper , VIB
        Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO
        Verified to work in: 2.3,2.4,2.5
        Download Jar/zip: click here (11.19MB)
        Download source: http://www.psb.ugent.be/cbd/papers/BiNGO
        --

        Version: 2.3
        Reference: Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449.
        Release Date: 2008-08-05
        Released by: Steven Maere , VIB
        Martin Kuiper , VIB
        Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO/
        Verified to work in: 2.6
        Download Jar/zip: click here (12.05MB)
        Download source: http://www.psb.ugent.be/cbd/papers/BiNGO/
        --

        Version: 2.31
        Release Date: 2009-04-09
        Released by: Steven Maere , VIB
        Verified to work in: 2.6
        Download Jar/zip: click here (12.31MB)


    • BubbleRouter

      • Description: The Bubble Router Plugin allows users to layout a network incrementally and in a semi-automated way. Bubble Router arranges specific nodes in user-drawn regions based on a selected attribute value. Bubble Router works with any node attribute file.
        Project website: http://www.genmapp.org/BubbleRouter/manual.htm
        --

        Version: 1.0
        Release Date: 2007-08-28
        Released by: Alexander Pico, Kristina Hanspers, Nathan Salomonis , The Gladstone Institutes
        Allan Kuchinsky , Agilent Technologies
        Verified to work in: 2.5
        Download Jar/zip: click here (881.2KB)

        --

        Version: 1.1
        Release Date: 2008-03-12
        Released by: Alexander Pico, Kristina Hanspers, Nathan Salomonis , The Gladstone Institutes
        Allan Kuchinsky , Agilent Technologies
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (887.8KB)


    • ClueGO

      • Description: ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.
        Project website: http://www.ici.upmc.fr/cluego
        License: click here

        --

        Version: 1.1
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pages F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009. (in press)
        Release Date: 2009-02-16
        Released by: Gabriela Luana Bindea , Institut for Genomics and Bioinformatics (IGB)
        Bernhard Mlecnik,Jerome Galon , INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoDocumentation.shtml
        Verified to work in: 2.6
        Note: ClueGO is free for all academic and non-profit institutions. A license is freely available at http://www.ici.upmc.fr/cluego/cluegoLicense.shtml and will be used to track the downloads.
        Download Jar/zip: click here (32.36MB)


    • CommonAttributes

      • Description: Find attributes shared between selected nodes.

        Requires background knowledge network files available at the CommonAttributes download site http://sourceforge.net/projects/hanalyzer/.
        Project website: http://sourceforge.net/projects/hanalyzer/
        License: click here

        --

        Version: 1.3
        Reference: Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner Jr. Priyanka Kasliwa, Ron Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter, "3R Systems for Biomedical Discovery Acceleration, with Applications to Craniofacial Development" PLoS Computational Biology, submitted.
        Release Date: 2008-08-12
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Release notes: hanalyzer.sourceforge.net
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (14.2KB)
        Download source: hanalyzer.sourceforge.net
        --

        Version: 2.0
        Reference: "Biomedical Discovery Acceleration, with Applications to Craniofacial Development", Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L. PLoS Comp Bio, 2009, in press.
        Release Date: 2009-02-05
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Bill Baumgartner , University of Colorado Health Sciences Center
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (21KB)
        Download source: http://sourceforge.net/projects/hanalyzer/

    • HyperEdgeEditor

      • Description: Add, remove, and modify HyperEdges in a Cytoscape Network.
        --

        Version: 2.61
        Release Date: 2008-03-28
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (161.5KB)

        --

        Version: 2.62
        Release Date: 2008-04-03
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (161.5KB)

        --

        Version: 2.65
        Release Date: 2009-04-08
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6.2
        Download Jar/zip: click here (162KB)


  • Communication/Scripting  --  Used for communicating with or scripting Cytoscape (7)
    • CyGoose

      • Description: The CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at http://gaggle.systemsbiology.org/docs/geese/.

        New Features:

        • Select a default layout (excluding yFiles layouts) to apply to subsequent incoming network broadcasts
        • A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. Note the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.

        --

        Version: 2.5
        Release Date: 2007-07-25
        Released by: Sarah Killcoyne Institute for Systems Biology
        John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
        Verified to work in: 2.4,2.5
        Download Jar/zip: click here (1.11MB)

        --

        Version: 2.6
        Release Date: 2007-10-29
        Released by: Sarah Killcoyne and Dan Tenenbaum , Institute for Systems Biology
        John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
        Release notes: click here
        Verified to work in: 2.5
        Download Jar/zip: click here (1.06MB)

        --

        Version: 2.7
        Release Date: 2009-03-19
        Released by: Sarah Killcoyne and Dan Tenenbaum , Institute for Systems Biology
        John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
        Release notes: click here
        Verified to work in: 2.6.1,2.6.2
        Download Jar/zip: click here (135.9KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/isb/skillcoyne/CyGoose/tags/CyGoose_2.7/

    • GroovyScriptingEngine

      • Description:

        Scripting Engine based on Grooby 1.5.6 implementation.

        This plugin is for technology evaluation purpose ONLY! Totally experimental.
        License: click here

        --

        Version: 0.01
        Release Date: 2008-09-25
        Released by: Keiichiro Ono , UCSD Bioengineering
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (6.2MB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/kono/GroovyEnginePlugin

    • JavaScriptEngine

      • Description:

        Rhino JavaScript engine version 1.7.1. You can run JavaScript on Cytoscape. To use this, you need ScriptEngineManager Plugin.


        License: click here

        --

        Version: 0.01
        Release Date: 2008-04-15
        Released by: Keiichiro Ono , UCSD Bioengineering
        Release notes: http://www.cytoscape.org/cgi-bin/moin.cgi/ScriptingPlugins
        Verified to work in: 2.6
        Download Jar/zip: click here (964.6KB)


    • MiSink

      • Description: Network interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).
        Project website: http://dip.doe-mbi.ucla.edu/dip/Software.cgi
        --

        Version: 2.00
        Release Date: 2007-07-24
        Released by: Lukasz Salwinski UCLA-DOE Institute for Genomics and Proteomics
        Verified to work in: 2.5
        Download Jar/zip: click here (90.1KB)

        --

        Version: 2.03
        Release Date: 2007-11-21
        Released by: Lukasz Salwinski , UCLA
        Verified to work in: 2.5
        Download Jar/zip: click here (76KB)

        --

        Version: 2.04
        Reference: Salwinski L, Eisenberg D. The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. Bioinformatics 23:2193-5 (2007)
        Release Date: 2008-05-28
        Released by: Lukasz Salwinski , UCLA
        Verified to work in: 2.6
        Note: This is a minor fix to make plugin compatible with Cytoscape 2.6. The downloaded file has been tested from a local download site. It seems to install/work fine with Cytoscape 2.6 and java 1.6 running on linux and windows xp
        Download Jar/zip: click here (74.8KB)


    • PythonScriptingEngine
    • RubyScriptingEngine

      • Description:

        Scripting Engine based on jruby 1.1.4 implementation. This version includes bioruby 1.2.1. The console is now integrated with BioRuby Shell.

        This plugin is for technology evaluation purpose ONLY! Totally experimental.
        License: click here

        --

        Version: 0.10
        Release Date: 2008-10-02
        Released by: Keiichiro Ono , UCSD Bioengineering
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (15.08MB)


    • ScriptEngineManager

      • Description:

        Manages scripting engines following Cytoscape scripting engine guideline. Supporting Ruby, JavaScript, Groovy and Python.

        This plugin is for technology evaluation purpose ONLY! Still experimental and design will be changed in the future versions.
        License: click here

        --

        Version: 0.04
        Release Date: 2008-09-24
        Released by: Keiichiro Ono , UCSD Bioengineering
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (172.3KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/kono/ScriptEngineManager/

  • Other  --  None of the above (15)
    • addParentNeighbors
    • AdvancedNetworkMerge
    • batchTool
    • BiLayout

      • This plugin is not available through the Plugin Manager!

        Description: BiLayout computes a bipartite network layout for two user-selected disjoint groups of nodes.
        Project website: http://bilayout.bioinf.mpi-inf.mpg.de/index.php
        --

        Version: 1.0
        Release Date: 2007-11-02
        Released by: Dorothea Emig, Thomas Lengauer, Mario Albrecht , Max Planck Institute for Informatics
        Anne Kunert, Karsten Klein, Petra Mutzel , University of Dortmund
        Verified to work in: 2.5
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • edgeLengthPlugin
    • edgeLister
    • FERN

      • This plugin is not available through the Plugin Manager!

        Description: FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java. It includes state of the art algorithms for stochastic simulation and a powerful visualization system based on gnuplot and Cytoscape.
        Project website: http://www.bio.ifi.lmu.de/FERN/
        License: click here

        --

        Version: 1.3
        Reference: Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics, 2008, 9, 356
        Release Date: 0000-00-00
        Released by: Florian Erhard, Caroline C. Friedel, Ralf Zimmer , Institut for Informatics, LMU Munich
        Verified to work in: 2.4,2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • GroupTool
    • MetaNodePlugin2

      • Description: This plugin provides a viewer for groups that implements a collapse/expand abstraction
        Project website: http://www.rbvi.ucsf.edu/Research/cytoscape/
        --

        Version: 1.0
        Release Date: 2007-07-07
        Released by: John "Scooter" Morris UCSF Resource for Biocomputing, Visualization, and Informatics
        Verified to work in: 2.5
        Download Jar/zip: click here (17.2KB)

        --

        Version: 1.01
        Release Date: 2007-07-07
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.5
        Download Jar/zip: click here (17.1KB)

        --

        Version: 1.1
        Release Date: 2008-03-18
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (19.4KB)

        --

        Version: 1.2
        Release Date: 2008-09-18
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (21.9KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/metaNodePlugin2/
        --

        Version: 1.5
        Release Date: 2009-02-25
        Released by: John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6.2
        Download Jar/zip: click here (39.5KB)


    • MultilevelLayoutPlugin

      • Description: The plug-in generates network layouts using the multilevel node placement framework introduced by C. Walshaw (2003).The multilevel approach is relative fast and it provides visually pleasant layouts also for larger networks.
        License: click here

        --

        Version: 0.41
        Release Date: 2008-01-16
        Released by: Pekka Salmela , University of Turku, Finland
        Olli S. Nevalainen , University of Turku, Finland
        Tero aittokallio , University of Turku, Finland
        Release notes: click here
        Verified to work in: 2.5
        Note: Updated description and developer information.
        Download Jar/zip: click here (27.6KB)
        Download source: http://kapsi.fi/~speque/mll-plugin/
        --

        Version: 0.6
        Release Date: 2008-07-06
        Released by: Pekka Salmela , University of Turku, Finland
        Olli S. Nevalainen , University of Turku, Finland
        Tero aittokallio , University of Turku, Finland
        Release notes: click here
        Verified to work in: 2.5
        Download Jar/zip: click here (72.2KB)
        Download source: http://kapsi.fi/~speque/mll-plugin/

    • NamedSelection
    • NatureProtocolsWorkflow

      • Description: Groups all of the plugins required for the Nature Protocols workflow.
        --

        Version: 1.0
        Release Date: 2007-11-12
        Released by: Allan Kuchinsky , Agilent Technologies
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (35.1KB)


    • NeighborHighlight

      • Description: The plugin highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
        --

        Version: 1.0
        Release Date: 2008-08-26
        Released by: Dorothea Emig, Mario Albrecht , Max Planck Institute for Informatics

        Verified to work in: 2.6
        Download Jar/zip: click here (15.8KB)


    • NetLink

      • Description: Links network nodes or edges to other networks via the right-click menu based on an attribute (called netlink.connection) that maps the node/edge id to a network name.
        Project website: http://chianti.ucsd.edu/netlink-plugin
        License: click here

        --

        Version: 0.1
        Release Date: 2008-04-30
        Released by: Mike Smoot , UC San Diego
        Verified to work in: 2.6
        Download Jar/zip: click here (5.5KB)


    • Tutorial01
      • Pending Cytoscape staff review

Writing Your Own Plugins

If you are interested in building your own Cytoscape Plugin, check out the Cytoscape Plugin Tutorial

Old Plugins

We also maintain a list of older Cytoscape 2.x plugins and Cytoscape 1.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.