Search Plugins

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  • Network generation  --   (27)
    • AdvancedNetworkMerge
    • 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
        Authors: 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
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Note: Please remove versions 2.68 and 2.69.
        Download Jar/zip: click here (5.04MB)

        --

        Version: 2.71
        Release Date: 2009-07-01
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6.3
        Download Jar/zip: click here (5.04MB)

        --

        Version: 2.76
        Release Date: 2011-03-15
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (5.95MB)

        --

        Version: 2.77
        Release Date: 2011-09-12
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (5.95MB)


    • AlternativeTableImport

      • Description: Cytoscape plugin to load nodes, edges and attributes from comma separated value files. http://apps.cytoscape.org/apps/alternativetableimport
        Project website: http://apps.cytoscape.org/apps/alternativetableimport
        --

        Version: 1.0
        Release Date: 2012-07-07
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Verified to work in: 2.8
        Download Jar/zip: click here (1.16MB)
        Download source: https://trac.nbic.nl/brs2011p07/
        --

        Version: 1.1
        Release Date: 2012-10-01
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (1.16MB)
        Download source: https://trac.nbic.nl/brs2011p07/
        --

        Version: 1.2
        Release Date: 2012-12-03
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Release notes: https://trac.nbic.nl/brs2011p07/changeset/526/trunk/alternative-table-import
        Verified to work in: 2.8
        Download Jar/zip: click here (1.16MB)
        Download source: https://trac.nbic.nl/brs2011p07/
        --

        Version: 1.3
        Release Date: 2013-03-22
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (1.16MB)


    • 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: 1.01
        Release Date: 2009-04-28
        Authors: Jan Baumbach ,International Computer Science Institute, Berkeley
        Tobias Wittkop ,Bielefeld University
        Dorothea Emig ,Max Planck Institute for Informatics

        Verified to work in: 2.7
        Download Jar/zip: click here (97.2KB)

        --

        Version: 1.0
        Release Date: 2009-04-28
        Authors: 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
    • CluePedia
    • ConReg

      • Description: Transcription factors (TFs) play a fundamental role in cellular regulation by binding to promoter regions of target genes (TGs) in order to control their gene expression. TF-TG networks are widely used as representations of regulatory mechanisms, e.g. for modeling the cellular response to input signals and perturbations. As the experimental identification of regulatory interactions is time consuming and expensive, one tries to use knowledge from related species when studying an organism of interest. Here, we present ConReg, an interactive web application to store regulatory relations for various species and to investigate their level of conservation in related species. Currently, ConReg contains data for eight model organisms. The regulatory relations stored in publicly available databases cover only a small fraction both of the actual interactions and also of the regulatory relations described in the scientific literature. Therefore, we included regulatory relations extracted from PubMed and PubMedCentral using sophisticated text-mining approaches and from binding site predictions into ConReg. ConReg can be used to analyze and visualize regulatory networks and their conservation among eight model organisms. It also provides direct links to annotations including literature references to potentially conserved regulatory relations.
        Project website: http://services.bio.ifi.lmu.de/ConReg/
        --

        Version: 0.1
        Release Date: 2012-09-15
        Authors: Robert Pesch ,LMU Munich
        Verified to work in: 2.8
        Download Jar/zip: click here (1.81MB)


    • ContigScape

      • Description: Due to the repeats and low quality regions in NGS sequencing, gap closing is often evitable. ContigScape will guide you in designing primers after 454 or mate-paired sequencing by showing the possible relationship between contigs in a network representation.


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

        --

        Version: 1.0
        Reference: Tang B, Wang Q, Yang M, Xie F, Zhu Y, Zhuo Y, Wang S, Gao H, Ding X, Zhang L, Zhao G, Zheng H. ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. BMC Genomics. 2013 Apr 30;14(1):289.
        Release Date: 2013-05-01
        Authors: Qi Wang ,IM, CAS
        Biao Tang ,Fudan University
        Release notes: http://www.sourceforge.net/projects/contigscape/
        Verified to work in: 2.8
        Note: 1.0
        Download Jar/zip: click here (200.9KB)
        Download source: http://downloads.sourceforge.net/project/contigscape/1.0/ContigScape.jar

    • CySBML

      • Description: CySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML annotations within the network context.
        Project website: http://www.charite.de/sysbio/people/koenig/software/cysbml/
        --

        Version: 1.2
        Release Date: 2012-06-14
        Authors: Matthias König ,Charite Berlin
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (9.85MB)


    • CyTargetLinker
    • CytoITMprobe

      • Description:

        Earlier, we developed a network information flow framework and implemented it as a web application, called ITM Probe. Given a context consisting of one or more user-selected nodes, ITM Probe retrieves other network nodes most related to that context. Although ITM Probe has several desirable features such a requiring neither restriction to subnetwork of interest nor additional and possibly noisy information, it still has a few limitations. For example, users can only query pre-compiled protein interaction networks. Also, manipulating the layout of significant subnetworks is non-trivial. Most importantly, it is difficult to integrate the results of ITM Probe within workflows involving other analysis methods. To resolve these difficulties. we thus developed CytoITMprobe, a Cytoscape plugin.


        CytoITMprobe provides access to ITM Probe either through a web server or locally. The input, consisting of desired origins and/or destinations of information and a dissipation coefficient, is specified through a query form. The results are shown as a subnetwork of significant nodes and several summary tables. Users can control the composition and appearance of the subnetwork.


        Saving results as node and network attributes, CytoITMprobe allows Cytoscape users to manipulate and visualize context-specific information in a manner more flexible than its web predecessor. It also enables seamless integration of ITM Probe results with other Cytoscape plugins having complementary functionality for data analysis.


        License: click here

        --

        Version: 1.4
        Release Date: 2011-11-30
        Authors: Aleksandar Stojmirovic ,NCBI/NLM/NIH
        Alexander Bliskovsky ,NCBI/NLM/NIH
        Release notes: http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/itm_probe/doc/
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.31MB)
        Download source: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/CytoITMprobe/src/
        --

        Version: 1.5
        Release Date: 2012-03-12
        Authors: Aleksandar Stojmirovic ,NCBI/NLM/NIH
        Alexander Bliskovsky ,NCBI/NLM/NIH
        Release notes: http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/itm_probe/doc/
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.35MB)
        Download source: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/CytoITMprobe/src/

    • CytoSEED

      • Description: The CytoSEED plugin enables viewing, manipulating and analyzing metabolic models created by the Model SEED (http://www.theseed.org/models)
        Project website: http://www.cs.hope.edu/cytoseed/
        --

        Version: 1.0
        Release Date: 2011-09-09
        Authors: Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad, Travis McGeehan ,Hope College
        Release notes: http://www.cs.hope.edu/cytoseed/
        Verified to work in: 2.8.1,2.8.2
        Download Jar/zip: click here (3.36MB)
        Download source: http://www.cs.hope.edu/cytoseed/
        --

        Version: 1.1
        Release Date: 2011-10-27
        Authors: Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad, Travis McGeehan ,Hope College
        Verified to work in: 2.8.1,2.8.2
        Note: I submitted this plugin on Monday, and just found a small bug, so I am submitting this jar file with the fix and change to version 1.1. No other changes to Release notes, URLs, etc. Please let me know if this is OK. Thanks, Matt DeJongh
        Download Jar/zip: click here (3.36MB)


    • DisGeNET

      • This plugin is not available through the Plugin Manager!

        Description: DisGeNET is a plugin for Cytoscape to query and analyze a network representation of human gene-disease databases. For this purpose, we have developed a new gene-disease database integrating data from several public sources. DisGeNET allows user-friendly access to our database, which includes queries restricted to (i) the original data source, (ii) the association type, (iii) the disorder class of interest and (iv) specific diseases, respectively genes. It represents gene-disease associations in terms of bipartite graphs and additionally provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Moreover, DisGeNET permits multicoloring of nodes (genes/diseases) according to their disease classes for expedient visualization. DisGeNET is distributed under the GNU GPL licence.
        Project website: http://ibi.imim.es/DisGeNET/DisGeNETweb.html
        License: click here

        --

        Version: 1.02
        Reference: Anna Bauer-Mehren; Michael Rautschka; Ferran Sanz; Laura I. Furlong: DisGeNET - a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq538
        Release Date: 2010-09-21
        Authors:
        Verified to work in: 2.7
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

    • DomainGraph

      • Description: The main functionality of the DomainGraph plugin is the
        visual analysis of the effects of alternative splicing
        on genes, protein isoforms, molecular interactions,
        pathways and miRNA binding sites. Statistical results
        of Exon Array data computed with AltAnalyze can be
        imported into DomainGraph and affected genes, pathways and
        miRNA binding sites are automatically annotated. From
        these annotations, genes, gene products, and pathways
        can directly be loaded and visualized via DomainGraph and
        occurrences of alternative splicing are highlighted. Therefore,
        an in-depth analysis of Exon Array data regarding
        alternative splicing events and their biological impact
        is easily possible without the need of prior knowledge.
        Furthermore, the detailed analysis of interaction networks
        and pathways is possible. Given a gene interaction
        network, DomainGraph visualizes the genes together with
        all known encoded protein isoforms and their respective
        domain compositions. Given a protein interaction network,
        DomainGraph decomposes the proteins into their domains and
        visualizes the domain interactions underlying the protein
        interactions. These networks can be integrated with
        exon expression data produced by the Affymetrix Exon
        Array. Genes, protein isoforms and domains are highlighted
        according to potentially occurring alternative splicing
        events or differential expression in different groups of samples.
        Project website: http://domaingraph.bioinf.mpi-inf.mpg.de
        --

        Version: 1.0
        Release Date: 2008-08-15
        Authors: 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
        Authors: 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
        Authors: 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)

        --

        Version: 3.01
        Release Date: 2009-12-01
        Authors: Dorothea Emig,Thomas Lengauer,Mario Albrecht ,Max Planck Institute for Informatics
        Nathan Salomonis ,The Gladstone Institutes

        Verified to work in: 2.6
        Download Jar/zip: click here (3.56MB)


    • 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
        Authors: 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
        Authors: 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

    • FluxViz
    • GeneMANIA

      • Description: GeneMANIA helps you predict the function of your favourite genes and gene sets.
        The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.
        Project website: http://www.genemania.org/
        License: click here

        --

        Version: 1.0
        Release Date: 2010-08-27
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: http://www.genemania.org/plugin/
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (16.79MB)

        --

        Version: 2.0
        Release Date: 2010-12-01
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: http://www.genemania.org/plugin/
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (16.93MB)

        --

        Version: 2.1
        Release Date: 2011-03-16
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (16.86MB)
        Download source: http://www.genemania.org/plugin/
        --

        Version: 2.2
        Release Date: 2011-07-21
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (9.94MB)

        --

        Version: 2.3
        Release Date: 2011-12-20
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (9.49MB)

        --

        Version: 2.4
        Release Date: 2012-01-31
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (9.83MB)

        --

        Version: 2.5
        Release Date: 2012-05-10
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (9.83MB)

        --

        Version: 3.0
        Release Date: 2012-10-09
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (10.3MB)

        --

        Version: 3.1
        Release Date: 2012-10-17
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (10.3MB)

        --

        Version: 3.2
        Release Date: 2012-10-17
        Authors: GeneMANIA Team ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (10.31MB)


    • GESTODifferent

      • This plugin is not available through the Plugin Manager!

        Description: GESTODifferent is a Cytoscape plugin for the identification of Boolean Gene Regulatory Networks describing a cellular stochastic differentiation process.
        Project website: http://bimib.disco.unimib.it/index.php/Retronet#GESTODifferent
        License: click here

        --

        Version: 1.0
        Release Date: 2012-10-31
        Authors: Silvia Crippa ,BIMIB, DISCo, Università degli Studi di Milano Bicocca
        Alex Graudenzi ,BIMIB, DISCo, Università degli Studi di Milano Bicocca
        Verified to work in: 2.8
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • 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
        Authors: 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://monet.kisti.re.kr/
        --

        Version: 2.1
        Reference: Lee et al., Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics (2005) 21, 2739-2747
        Release Date: 2010-09-13
        Authors: Younghoon Kim, Yongseong Cho, Doheon Lee ,KAIST
        Verified to work in: 2.3,2.4,2.5,2.6,2.7
        Download Jar/zip: click here (671.5KB)
        Download source: http://monet.kisti.re.kr/

    • MostHighlyConnectedSubgraphPlugin

      • Description: This plugin finds the most highly edge connected sugraph of the current network and view, and selects this subgraph. This plugin works on multigraphs, but it does NOT work on directed graphs.
        Project website: https://github.com/dhouck/MHCS
        --

        Version: 1.0
        Release Date: 2013-03-20
        Authors: Daniel Houck, Suzanne Gallagher, and Debra Golberg ,University of Colorado at Boulder
        Release notes: click here
        Verified to work in: 2.5,2.6,2.7,2.8
        Download Jar/zip: click here (30.6KB)
        Download source: https://github.com/dhouck/MHCS

    • NDBReaderPlugin

      • Description: Genomica NDB file format reader.
        --

        Version: 0.1
        Release Date: 2012-07-31
        Authors: Mike Smoot ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (7.5KB)


    • OWLPlugin

      • Description: This plugin builds a cyto-network from OWL/RDF ontologies. Using OWL-API library and Pellet Reasoner, OWLPlugin generates the graph of each ontology elements with some extra-information: the type of relationships, individuals, classes,... We are working in including new extra features and user dialogs. In next versions, we make public the source repository and more relevant information. For any thing, please do not hesitate to contact me.
        --

        Version: 1.0
        Release Date: 2012-02-28
        Authors: Isaac Lera ,Universitat de les Illes Balears
        Verified to work in: 2.8.2
        Download Jar/zip: click here (20.32MB)


    • PhyloTree

      • Description: This plugin provides the ability to read phylogenetic tree formats and display them in Cytoscape as trees
        --

        Version: 0.1
        Release Date: 2011-04-19
        Authors: Chinmoy Bhatiya
        Verified to work in: 2.8
        Download Jar/zip: click here (867.9KB)


    • RandomNetworks
    • Reactome FIs

      • This plugin is not available through the Plugin Manager!

        Description: This plugin accesses the Reactome Functional Interaction (FI) network, a highly reliable, manually curated pathway-based protein functional interaction network covering close to 50% of human proteins. This plugin was designed to find network patterns related to cancer and other types of diseases. The plug-in allows you to construct a FI sub-network based on a set of genes, query the FI data source for the underlying evidence for the interaction, build and analyze network modules of highly-interacting groups of genes, perform functional enrichment analysis to annotate the modules, expand the network by finding genes related to the experimental data set, display pathway diagrams, and overlay with a variety of information sources such as cancer gene index annotations.
        Project website: http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin
        --

        Version: 1.0
        Reference: Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010; 11(5). PubMedID: 20482850
        Release Date: 2010-10-05
        Authors: Guanming Wu ,The Ontario Institute for Cancer Research (OICR)
        Lincoln Stein ,The Ontario Institute for Cancer Research (OICR)
        Release notes: click here
        Verified to work in: 2.7
        Note: updated version
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 1.0beta
        Reference: Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010; 11(5). PubMedID: 20482850
        Release Date: 2010-10-01
        Authors: Guanming Wu ,The Ontario Institute for Cancer Research (OICR)
        Lincoln Stein ,The Ontario Institute for Cancer Research (OIC
        Release notes: http://brie8.cshl.edu:8080/caBigR3WebApp/Cytoscape/index.html
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://brie8.cshl.edu:8080/caBigR3WebApp/Cytoscape/index.html
        --

        Version: 1.1
        Release Date: 2011-04-04
        Authors: Guanming Wu ,The Ontario Institute for Cancer Research (OICR)
        Lincoln Stein ,The Ontario Institute for Cancer Research (OICR)
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin

    • RINalyzer

      • This plugin is not available through the Plugin Manager!

        Description: RINalyzer provides a number of important methods for analyzing and visualizing residue interaction networks (RINs). A RIN is constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. Network nodes and edges represent amino acid residues and their molecular interactions, respectively. The network topology of RINs is normally characterized by undirected and weighted interaction edges between residue nodes. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, together with the corresponding molecular 3D structure visualized in UCSF Chimera. Furthermore, RINalyzer offers the computation and illustration of a comprehensive set of weighted centrality measures for relating spatially distant residue nodes and discovering critical residues and their long-range interaction paths in protein structures. In addition, RINalyzer allows handling node sets, i.e., sets of selected nodes, for analyzing structural and functional connections between different nodes. Another feature is the network comparison of aligned protein structures by constructing a combined RIN, which enables the detailed comparative analysis of residue interactions in different proteins.
        Project website: http://www.rinalyzer.de
        --

        Version: 1.3
        Reference: Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. Analyzing and visualizing residue networks of protein structures. Trends in Biochemical Sciences, 36(4):179-182, 2011.
        Release Date: 2011-10-17
        Authors: Nadezhda T. Doncheva, Francisco S. Domingues, Mario Albrecht ,Max Planck Institute for Informatics
        Karsten Klein ,TU Dortmund University
        Release notes: click here
        Verified to work in: 2.8
        Note: Please follow the Project URL to download and install manually.
        Download Jar/zip: Please follow the Project URL to download and install manually.

  • Online data import  --   (20)
    • bioCycPlugin
    • BiomartClient
    • CARLSBAD

      • Description: CARLSBAD (Confederated Annotated Research Libraries of Small molecule BioActivity Data) Cytoscape plugin for visualization and exploration of chemical pattern bioactivity networks. http://carlsbad.health.unm.edu
        Project website: http://carlsbad.health.unm.edu/
        --

        Version: 1.0
        Release Date: 2012-03-09
        Authors: Oleg Ursu ,UNM
        Release notes: http://carlsbad.health.unm.edu/news/
        Verified to work in: 2.8
        Download Jar/zip: click here (39.5MB)

        --

        Version: 1.1
        Release Date: 2012-03-21
        Authors: Oleg Ursu ,UNM
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (39.5MB)


    • CyTableReaderPlugin

      • Description: CyTable attribute file format reader.
        --

        Version: 0.1
        Release Date: 2012-07-31
        Authors: Mike Smoot ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (25.1KB)


    • CyTargetLinker

      • Description: The plugin extends biological networks (nodes need to have an attribute containing a biological identifier, eg. Entrez Gene) with regulatory interactions (e.g. miRNA-target gene). Therefore it is necessary to download the provided regulatory interaction networks (RINs) from the website or create your own.

        Project website: http://code.google.com/p/cytargetlinker/
        License: click here

        --

        Version: 1.0
        Release Date: 2012-01-24
        Authors: Martina Kutmon ,Maastricht University
        Thomas Kelder ,TNO
        Pooja Mandaviya ,Maastricht University
        Naime Douallin ,Maastricht University
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (659.8KB)
        Download source: http://code.google.com/p/cytargetlinker/source/checkout

    • CytoSQL

      • Description: A plugin to execute SQL SELECT statements against relational databases, and convert the results table to Cytoscape network elements. It can be used to create new networks, extend existing networks or load extra attributes for selected network elements from any accessible relational database. Check the website (http://www.ptools.ua.ac.be/CytoSQL)for common use cases.
        Project website: http://www.ptools.ua.ac.be/CytoSQL
        --

        Version: 0.9
        Release Date: 2009-08-18
        Authors: Kris Laukens and Koen Van Leemput , University of Antwerp - Intelligent Systems Lab
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (3.49MB)

        --

        Version: 1.0
        Reference: Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren and Koenraad Van Leemput (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics 2010, 11:360, doi:10.1186/1471-2105-11-360
        Release Date: 2010-06-28
        Authors: Kris Laukens, Thanh Hai Dang and Koen Van Leemput , University of Antwerp - Intelligent Systems Lab
        Verified to work in: 2.5,2.6,2.7
        Download Jar/zip: click here (3.62MB)


    • GenomeSpacePlugin

      • Description: A plugin that enables communication with GenomeSpace. Requires the GenomeSpace Libs plugin to work!
        --

        Version: 0.1
        Release Date: 2012-07-31
        Authors: Mike Smoot ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (396.1KB)


    • GPML-Plugin
    • HOMECAT

      • Description: A tool for interspecific comparative analysis, to add to an existing network orthologs identifiers and data. Through multiple homology assement sources, the desired specificity and sensitivity in orthology search can be obtained.
        Input identifiers are automatically converted to query and combine orthology sources results. User can also specify output format for data mapping. 30 species are currently supported.
        Comparative networks are represented with metanodes containing input and orthologs elements. A specific function allows user-data mapping with graphical metanodes representation.
        Particular emphasis is given to functional genomic data. More than 70 microarrays formats are supported and data can be directly downloaded from arrayexpress ATLAS service.
        Metanodes and graphical representation require MetaNodes and NodeCharts plugins.
        For the user manual, to download components allowing multiple orthology databases support, and to learn how to easily develop new components, see project website.
        Project website: http://www.cbmc.it/~zorzans/homecat/
        License: click here

        --

        Version: 1.0
        Release Date: 2012-12-11
        Authors: Zorzan Simone ,CBMC,University of Verona
        Release notes: http://www.cbmc.it/~zorzans/homecat/index.php
        Verified to work in: 2.8.2,2.8.3
        Note: This plugins supports several orthology projects through .calss files in a folder inside Cytoscape plugins folder. This allows easy extensibility. Is it possible to create such a folder through the Cytoscape "Manage plugins" function? This is not strictly necessary as user is instructed on how to proceed with the downloading of those files from the plugin website. It seems the submission procedure does not like the release date: releaseDate=Dec 9, 2012 I had to comment it out. Could you please check this? Thank you.
        Download Jar/zip: click here (3.09MB)
        Download source: http://www.cbmc.it/~zorzans/homecat/index.php
        --

        Version: 1.1
        Release Date: 2013-03-22
        Authors: Zorzan Simone ,CBMC,University of Verona
        Release notes: http://www.cbmc.it/~zorzans/homecat/
        Verified to work in: 2.8.2,2.8.3
        Download Jar/zip: click here (3.16MB)
        Download source: http://www.cbmc.it/~zorzans/homecat/
        --

        Version: 1.2
        Reference: Zorzan Simone, Lorenzetto Erika, Ettorre Michele, Pontelli Valeria, Laudanna Carlo, and Buffelli Mario HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration. Bioinformatics first published online April 24, 2013 doi:10.1093/bioinformatics/btt189
        Release Date: 2013-04-29
        Authors: Zorzan Simone ,CBMC,University of Verona
        Release notes: http://www.cbmc.it/~zorzans/homecat/files/changelog.txt
        Verified to work in: 2.8.2,2.8.3
        Download Jar/zip: click here (3.16MB)
        Download source: http://www.cbmc.it/~zorzans/homecat/

    • iCTNet

      • Description: integrated Complex Traits Network (iCTNet) is a large-scale network, assembling human disease-gene association, tissue-gene association, disease-tissue associations, protein-DNA interactions, protein-protein interactions and drug-target information. This network provides a new and comprehensive perspective for human genetic diseases
        Project website: http://ictnet.org
        --

        Version: 0.1
        Release Date: 2011-09-26
        Authors: Lili Wang, Parvin Mousavi ,Queen's University, Canada
        Pouya Khankhanian, Sergio E. Baranzini ,University of California, San Francisco, USA
        Verified to work in: 2.6
        Download Jar/zip: click here (558.4KB)


    • KGMLReader
    • KNIMEConnector

      • Description:

        This plug-in allows networks to be sent and received to and from KNIME (Konstanz Information Miner) a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform.
        Click here for a detailed description of KNIME.

        KNIME enables large attributed graphs to be processed via the Network Mining plug-in. For a detailed description on how to send and receive networks see the Network Visualization section.

        You can access the KNIME Connector from the Cytoscape menu (Plugins->KNIME Connector).


        Project website: http://tech.knime.org/node/36081
        --

        Version: 1.0
        Release Date: 2012-01-10
        Authors: Tobias Koetter ,University of Konstanz
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (46.7KB)

        --

        Version: 1.1
        Release Date: 2013-02-01
        Authors: Tobias Koetter ,University of Konstanz
        Release notes: http://tech.knime.org/node/36081
        Verified to work in: 2.8
        Download Jar/zip: click here (46.7KB)


    • NCBIClient
    • NCBIEntrezGeneUserInterface
    • Pathintegrator

      • Description: Pathintegrator obtains a list of pathways from different sources (Pathway Commons, NetPath, Wikipathways and KEGG) in which a protein of interest has a role, merges the information contained in the networks and displays it.
        --

        Version: 1.0
        Release Date: 2010-11-01
        Authors: Juan Ramón Meneu Hernández , Università degli Studi di Bologna
        Paolo Tieri , Università degli Studi di Bologna
        Verified to work in: 2.7
        Download Jar/zip: click here (23.87MB)
        Download source: http://sourceforge.net/projects/pathintegrator/files/

    • PhosphositePlus Web Service Client Module

      • This plugin is not available through the Plugin Manager!

        Description: This plugin downloads enzyme-substrate connections from PhosphositePlus web site and extends a users network with new edges that were downloaded. For the most part, these will be kinase-substrate connections.
        Project website: www.phosphosite.org
        --

        Version: 1.0
        Release Date: 2010-07-07
        Authors: Sasha Tkachev ,Cell Signaling Technology, Inc.
        Verified to work in: 2.7
        Note: Jar file can be downloaded from http://www.phosphosite.org/downloads/phosphositeClient.jar
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • PSICQUICUniversalClient
    • 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
        Authors: 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

    • SFLDLoader
    • Superpathways-Plugin
  • Graph analysis  --   (10)
    • 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.Information about the plugin that will be displayed to users.
        Please use html tags for all formatting and do not add newlines.


        Project website: http://profs.sci.univr.it/%7Escardoni/centiscape/centiscapepage.php
        --

        Version: 1.0
        Release Date: 2008-05-19
        Authors: 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
        --

        Version: 1.1
        Reference: Analyzing biological network parameters with CentiScaPe Giovanni Scardoni; Michele Petterlini; Carlo Laudanna Bioinformatics 2009; doi: 10.1093/bioinformatics/btp517
        Release Date: 2009-11-26
        Authors: Giovanni Scardoni , Center for Biomedical Computing (CBMC), 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 (4.08MB)

        --

        Version: 1.2
        Reference: Analyzing biological network parameters with CentiScaPe Giovanni Scardoni; Michele Petterlini; Carlo Laudanna Bioinformatics 2009; doi: 10.1093/bioinformatics/btp517
        Release Date: 2010-07-14
        Authors: Giovanni Scardoni , Center for Biomedical Computing (CBMC), University of Verona
        Release notes: http://profs.sci.univr.it/~scardoni/centiscape/centiscapedownload.php
        Verified to work in: 2.7
        Note: This is a new version, a compatibility problem with Cytoscape 2.7.0 have been solved.
        Download Jar/zip: click here (4.08MB)

        --

        Version: 1.21
        Reference: Analyzing biological network parameters with CentiScaPe Giovanni Scardoni; Michele Petterlini; Carlo Laudanna Bioinformatics 2009; doi: 10.1093/bioinformatics/btp517
        Release Date: 2011-12-28
        Authors: Giovanni Scardoni , Center for Biomedical Computing (CBMC), University of Verona

        Release notes: http://www.cbmc.it/%7Escardonig/centiscape/centiscape.php
        Verified to work in: 2.8
        Note: This version solves compatibility problems with Cytoscape 2.8.2.
        Download Jar/zip: click here (4.08MB)


    • cytoHubba

      • Description:

        Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.


        License: click here

        --

        Version: 1.0
        Release Date: 2009-06-30
        Authors: 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)

        --

        Version: 1.1
        Release Date: 2009-10-08
        Authors:
        Verified to work in: 2.6
        Download Jar/zip: click here (906.9KB)

        --

        Version: 1.2
        Release Date: 2011-05-25
        Authors: Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin , Institute of Information Science, Academia Sinica, Taiwan
        Chin-Wen Ho , National Central University, Taiwan
        Chung-Yen Lin , National Taiwan University, Taiwan
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (912.4KB)
        Download source: http://hub.iis.sinica.edu.tw/cytoHubba/
        --

        Version: 1.3
        Release Date: 2011-06-25
        Authors: Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin , Institute of Information Science, Academia Sinica, Taiwan
        Chin-Wen Ho , National Central University, Taiwan
        Chung-Yen Lin , National Taiwan University, Taiwan
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (912.1KB)
        Download source: http://hub.iis.sinica.edu.tw/cytoHubba/
        --

        Version: 1.4
        Release Date: 2011-06-25
        Authors: Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin , Institute of Information Science, Academia Sinica, Taiwan
        Chin-Wen Ho , National Central University, Taiwan
        Hsin-Hung Wu , Research Center of Information Technology Innovation, Academia Sinica, Taiwan
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (1.07MB)

        --

        Version: 1.5
        Release Date: 2011-11-15
        Authors: Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin , Institute of Information Science, Academia Sinica, Taiwan
        Chin-Wen Ho , National Central University, Taiwan
        Hsin-Hung Wu , Research Center of Information Technology Innovation, Academia Sinica, Taiwan
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (1.07MB)

        --

        Version: 1.6
        Release Date: 2012-04-25
        Authors: Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin , Institute of Information Science, Academia Sinica, Taiwan
        Chin-Wen Ho , National Central University, Taiwan
        Hsin-Hung Wu , Research Center of Information Technology Innovation, Academia Sinica, Taiwan
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (1.07MB)
        Download source: http://hub.iis.sinica.edu.tw/cytoHubba/

    • CytoKavosh

      • Description: Attribute browser
        License: click here

        --

        Version: 1.0
        Reference: Ali Masoudi-Nejad, Mitra Ansariola, Zahra Razaghi K.M, Ali Salehzadeh-Yazdi, Sahand Khakabimamaghani (2012) CytoKavosh: a Cytoscape Plug-in for Finding Network Motifs in Large Biological Networks
        Release Date: 2012-05-23
        Authors:
        Release notes: http://lbb.ut.ac.ir/Download/LBBsoft/CytoKavosh/
        Verified to work in: 2.5,2.6,2.7,2.8
        Note: This plug-in is executable only under Linux operating system. This requires new releases of Linux or older ones supported with libstdc++ and other library files associated with C language. It has been tested under Ubuntu 10.0, fedora 14.0 and Redhat 5 distributions.
        Download Jar/zip: click here (187.5KB)
        Download source: http://lbb.ut.ac.ir/Download/LBBsoft/CytoKavosh/
        --

        Version: 1.1
        Reference: Ali Masoudi-Nejad, Mitra Ansariola, Zahra Razaghi K.M, Ali Salehzadeh-Yazdi, Sahand Khakabimamaghani (2012) CytoKavosh: a Cytoscape Plug-in for Finding Network Motifs in Large Biological Networks
        Release Date: 2012-07-10
        Authors:
        Release notes: http://lbb.ut.ac.ir/Download/LBBsoft/CytoKavosh/
        Verified to work in: 2.5,2.6,2.7,2.8
        Note: This plug-in is executable only under Linux operating system. This requires new releases of Linux or older ones supported with libstdc++ and other library files associated with C language. It has been tested under Ubuntu 10.0, fedora 14.0 and Redhat 5 distributions.
        Download Jar/zip: click here (187.4KB)
        Download source: http://lbb.ut.ac.ir/Download/LBBsoft/CytoKavosh/

    • GraphletCounter

      • Description: GraphletCounter is a software tool for computing the graphlet signatures of nodes and motifs in biological networks. GraphletCounter can operate on its own or as a plugin to the network analysis environment Cytoscape. GraphletCounter computes the graphlet signatures of individual nodes or of motifs, which can be specified by files generated by the motif-finding tool mfinder. It displays graphlet signatures visually within Cytoscape, and can output graphlet data for integration with larger workflows. Graphlet signatures were introduced by the Przulj group at the University of California at Irvine; please see the following references:

        Przulj, N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23(2), e177-e183.

        Milenkovic, T. and Przulj, N. (2008) Uncovering Biological Network Function via Graphlet Degree Signatures. Cancer Informatics, 6, 257-273.

        Also refer to the mfinder home page for information on motif finding and a description of its output file format.
        Project website: http://sonmezsysbio.org/software/graphletcounter
        License: click here

        --

        Version: 1.0
        Release Date: 2010-05-01
        Authors: Christopher Whelan and Kemal Sonmez ,Oregon Health & Science University
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (45.6KB)
        Download source: http://www.csee.ogi.edu/~whelanch/graphletcounter/
        --

        Version: 1.2
        Release Date: 2011-11-11
        Authors: Christopher Whelan and Kemal Sonmez ,Oregon Health & Science University
        Release notes: http://sonmezsysbio.org/software/graphletcounter
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (161.9KB)
        Download source: http://code.google.com/p/graphletcounter/

    • Interference

      • Description:

        Interference is a Cytoscape plug-in for virtual experimental network topological analysis allowing virtual knock-out experiments on complex networks

        Centrality indexes allow categorizing nodes in complex networks according to their topological relevance (see CentiScaPe plugin). In a node-oriented perspective, centralities are very useful topological parameters to compute in order to quantify the effect of individual node(s) alteration. We have introduced the notion of interference and developed the Cytoscape plugin Interference to evaluate the topological effects of single or multiple nodes removal from a network. In this perspective, interference allows virtual node knock-out experiments: it is possible to remove one or more nodes from a network and analyze the consequences on network structure, by looking to the variations of the node centralities values. As the centrality value of a node is strictly dependent on the network structure and on the properties of other nodes in the network, the consequences of a node deletion are well captured by the variation on the centrality values of all the other nodes.

        Potential Applications

        The interference approach can model common situations where real nodes are removed or added from/to a physical network:

        -Biological networks, where one or more nodes (genes, proteins, metabolites) are possibly removed from the network because of gene deletion, pharmacological treatment or protein degradation. Interference can be used to:

        -Simulate pharmacological treatment: one can potentially predict side effects of the drug by looking at topological properties of nodes in a drug-treated network, meaning with that a network in which a drug-targeted node (protein) was removed. To inhibit a protein (for instance a kinases) corresponds to removing the node from the network

        -Simulate gene deletion: gene deletion implies losing encoded proteins, thus resulting in the corresponding removal of one or more nodes from a protein network

        -Social and financial networks, where the structure of the network is naturally modified over time

        -Power grid failures

        -Traffic jam or work in progress in a road network

        -Temporary closure of an airport in an airline network


        Project website: http://www.cbmc.it/~scardonig/interference/Interference.php
        License: click here

        --

        Version: 1.0
        Release Date: 0000-00-00
        Authors: Giovanni Scardoni , Center for Biomedical Computing (CBMC), University of Verona

        Release notes: http://www.cbmc.it/~scardonig/interference/Interference.php
        Verified to work in: 2.8.2
        Download Jar/zip: click here (8.1MB)
        Download source: http://www.cbmc.it/~scardonig/interference/Interference.php

    • NetDS

      • Description: NetDS is a novel Cytoscape plugin that conveniently simulates dynamics related to robustness, and examines structural properties with respect to feedforward/feedback loops. It can evaluate how robustly a network sustains a stable state against mutations by employing a Boolean network model. In addition, the plugin can examine all feedforward/feedback loops appearing in a network and determine whether or not a pair of loops is coupled. Random networks can also be generated to evaluate whether or not an interesting finding in real biological networks is significantly random.
        Project website: http://netds.sourceforge.net/
        --

        Version: 3.0
        Reference: Duc-Hau Le and Yung-Keun Kwon (2011) NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks, Bioinformatics, 27, 2767-2768.
        Release Date: 2012-06-13
        Authors:
        Release notes: http://netds.sourceforge.net/
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.52MB)


    • 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
        Authors: 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)

        --

        Version: 2.2
        Release Date: 2011-05-02
        Authors: 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: 2.7,2.8.1
        Download Jar/zip: click here (1.65MB)


    • 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
        Authors: 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
        Authors: 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.

    • RemainingDegreeDistribution
    • 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
        Authors: Marcio Rosa da Silva
        Verified to work in: 2.4,2.5
        Download Jar/zip: click here (8KB)


  • Clustering  --   (15)
    • AllegroMCODE

      • Description:

        AllegroMCODE Plugin is a high-performance MCODE cluster finder supporting both of CPU and GPU clustering. Clusters in a protein interaction network can be considered as protein complexes and functional modules, which can be identified as highly interconnected subgraphs.

        It finds the same clusters as the MCODE plugin does, but to process large complex networks, it is totally redesigned for fast analysis, low memory consumption, and interactive cluster exploring without creating a network view or subnetwork.

        It includes our proprietary highly parallel algorithm based on the original sequential MCODE algorithm and exploits massively parallel GPU computing architecture to make your analysis task faster than ever. Its GPU analysis usually takes less than a second to analyze a large complex network.

        For more information, please visit us at http://allegroviva.com/allegromcode/. If you have any problems or questions, please create a new topic in our support forums: http://allegroviva.com/support/


        Project website: http://allegroviva.com/allegromcode/
        License: click here

        --

        Version: 1.0
        Reference: Jun S. Yoon and Won-Hyong Chung, "A GPU-accelerated bioinformatics application for large-scale protein interaction networks", APBC poster presentation, 2011. http://allegroviva.com/csplugins/allegromcode/APBC2011_Poster_GPU_APP_PPI.pdf
        Release Date: 2011-02-08
        Authors: Jun S. Yoon ,AllegroViva Corporation
        Won-Hyung Jung ,Korea Research Institute of Bioscience and Biotechnology
        Release notes: http://www.allegroviva.com/allegromcode
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (419.7KB)
        Download source: http://allegroviva.com/csplugins/allegromcode/AllegroMCODE-source-1.0.zip
        --

        Version: 2.0
        Release Date: 2013-05-11
        Authors: Jun S. Yoon ,AllegroViva Inc.
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (12.37MB)

        --

        Version: 2.1
        Release Date: 2013-05-20
        Authors: Jun S. Yoon ,AllegroViva Inc.
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (12.37MB)


    • APCluster

      • Description: The plugin provides a user-friendly implementation of affinity propagation - a general purpose graph clustering algorithm (Brendan J. Frey and Delbert Dueck, Science 2007). It can be used to identify coherent modules in biological networks.
        Project website: http://bioputer.mimuw.edu.pl/modevo
        --

        Version: 2.1
        Release Date: 2010-03-05
        Authors: Michal Wozniak ,University of Warsaw
        Janusz Dutkowski ,University of Warsaw
        Release notes: click here
        Verified to work in: 2.6.3
        Download Jar/zip: click here (272KB)


    • 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
        Authors: 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: 1.01
        Release Date: 2009-12-01
        Authors: Jan Baumbach ,International Computer Science Institute, Berkeley
        Tobias Wittkop ,Bielefeld University
        Dorothea Emig ,Max Planck Institute for Informatics

        Verified to work in: 2.7
        Download Jar/zip: click here (1.4MB)

        --

        Version: 1.0
        Release Date: 2009-04-28
        Authors: 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
    • ClusterONE

      • Description: The ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.
        License: click here

        --

        Version: 0.1
        Reference: Nepusz T, Yu H, Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. In preparation.
        Release Date: 2010-07-12
        Authors: Tamas Nepusz and Alberto Paccanaro ,RHUL
        Release notes: click here
        Verified to work in: 2.6
        Note: Project homepage is at http://www.paccanarolab.org/software/cluster-one
        Download Jar/zip: click here (311.8KB)
        Download source: http://launchpad.net/cl1
        --

        Version: 0.9
        Reference: Nepusz T, Yu H, Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. In preparation.
        Release Date: 2010-09-20
        Authors: Tamas Nepusz and Alberto Paccanaro ,RHUL
        Release notes: click here
        Verified to work in: 2.6,2.7
        Note: Project homepage is at http://www.paccanarolab.org/software/cluster-one
        Download Jar/zip: click here (363.1KB)
        Download source: http://launchpad.net/cl1
        --

        Version: 0.91
        Reference: Nepusz T, Yu H, Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. In preparation.
        Release Date: 2010-12-17
        Authors: Tamas Nepusz and Alberto Paccanaro ,RHUL
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Note: Project homepage is at http://www.paccanarolab.org/software/cluster-one
        Download Jar/zip: click here (380.1KB)
        Download source: http://launchpad.net/cl1
        --

        Version: 0.92
        Reference: Nepusz T, Yu H, Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. In preparation.
        Release Date: 2011-07-14
        Authors: Tamas Nepusz and Alberto Paccanaro ,RHUL
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Note: Project homepage is at http://www.paccanarolab.org/software/cluster-one
        Download Jar/zip: click here (401.5KB)
        Download source: http://github.com/ntamas/cl1
        --

        Version: 0.93
        Reference: Nepusz T, Yu H, Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. In preparation.
        Release Date: 2011-10-20
        Authors: Tamas Nepusz and Alberto Paccanaro ,RHUL
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (409KB)
        Download source: http://github.com/ntamas/cl1

    • ClusterViz

      • Description: ClusterViz finds clusters (highly interconnected regions, protein complexes or functional module) in a network using various clustering algorithms.This project is supported by graduate student creative funding of HuNan, China, NO. CX2009B040.
        Project website: http://code.google.com/p/clusterviz-cytoscape/
        License: click here

        --

        Version: 1.0
        Release Date: 0000-00-00
        Authors: Juan Cai, Min Li, Jianxin Wang and Gang Chen ,Central South University, China
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (107.9KB)
        Download source: http://code.google.com/p/clusterviz-cytoscape/
        --

        Version: 1.1
        Reference: Juan Cai, Gang Chen, and Jianxin Wang. ClusterViz: a Cytoscape plugin for graph clustering and visualization. School of Information Science and Engineering, Central South University, Changsha, China, Feb 2010.
        Release Date: 2010-02-22
        Authors: Juan Cai, Gang Chen and Jianxin Wang ,Central South University, China
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (109.4KB)
        Download source: http://code.google.com/p/clusterviz-cytoscape/
        --

        Version: 1.2
        Reference: Juan Cai, Gang Chen, and Jianxin Wang. ClusterViz: a Cytoscape plugin for graph clustering and visualization. School of Information Science and Engineering, Central South University, Changsha, China, Feb 2010.
        Release Date: 2010-04-12
        Authors: Juan Cai, Gang Chen and Jianxin Wang ,Central South University, China
        Release notes: click here
        Verified to work in: 2.7
        Download Jar/zip: click here (12.38MB)
        Download source: http://code.google.com/p/clusterviz-cytoscape/source/checkout

    • CommFinder

      • Description: Information about the plugin that will be displayed to users.
        Community Finding Tool.


        Project website: http://www.cs.utsa.edu/~jruan/commFinder/commFinder.htm
        --

        Version: 1.1
        Release Date: 2010-09-29
        Authors: Tamim and Ruan ,UTSA
        Verified to work in: 2.6.3
        Download Jar/zip: click here (950.4KB)


    • CyClus3D
    • CytoSeVis

      • Description: Visualizing networks by semantic similarities
        Project website: https://sites.google.com/site/cytosevis/home
        License: click here

        --

        Version: 1.0
        Reference: Pietro Hiram Guzzi Mario Cannataro - Data Management of Protein Interaction Networks (Wiley Series in Bioinformatics) [Hardcover] ISBN-13: 978-0470770405
        Release Date: 2012-02-06
        Authors: Pietro Hiram Guzzi ,Unicz
        Francesco Tafuri ,Unicz
        Release notes: click here
        Verified to work in: 2.7
        Download Jar/zip: click here (20.8KB)


    • mcl-new

      • Description: This plugin used for clustering of Networks
        --

        Version: 1.1
        Release Date: 2010-06-24
        Authors:
        Download Jar/zip: click here (1.22MB)


    • 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
        Authors: Gary Bader ,MSKCC
        Verified to work in: 2.5
        Download Jar/zip: click here (86.5KB)

        --

        Version: 1.3
        Release Date: 2007-12-07
        Authors: 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
        Authors: Gary Bader, Vuk Pavlovic ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (91.7KB)

        --

        Version: 1.32
        Release Date: 2011-06-28
        Authors: Gary Bader, Vuk Pavlovic ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (104.1KB)


    • MINE

      • Description: MINE is an agglomerative clustering method that is able to identify highly modular sets of gene products within dense molecular interaction networks. It was created in response to the challenge of discovering high quality modules of gene products from dense biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters.


        --

        Version: 1.0
        Reference: Kahn Rhrissorrakrai and Kristin C. Gunsalus. "MINE: Module Identification in NEtworks." BMC Bioinformatics, submitted.
        Release Date: 2010-10-18
        Authors: Kahn Rhrissorrakrai ,NYU
        Kristin C. Gunsalus ,NYU
        Verified to work in: 2.6
        Download Jar/zip: click here (61.1KB)

        --

        Version: 1.5
        Reference: Kahn Rhrissorrakrai and Kristin C. Gunsalus. MINE: Module Identification in NEtworks. BMC Bioinformatics, in submission.
        Release Date: 2010-10-18
        Authors: Kahn Rhrissorrakrai ,NYU
        Kristin C. Gunsalus ,NYU
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (123.1KB)


    • ModuLand

      • This plugin is not available through the Plugin Manager!

        Description: The Cytoscape ModuLand plug-in is a clustering tool can be used on any kind of undirected network. It determines and visualizes the overlapping modules (aka. clusters/communities) by calculating the assignment strength of each node to each discovered module. It builds the hierarchy of these communities providing multiple level of module structures with different resolutions. Finally it calculates many useful measures helping to characterize the nodes according to their roles in the module structure (like \'module central\', \'overlapping\' or \'bridge\' nodes). The plug-in is further described here: The plug-in is further described here: Szalay-Beko, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2012) ModuLand plug-in for Cytoscape: extensively overlapping network modules, community centrality and their use in biological networks. Bioinformatics, 28, 2202-2204, http://arxiv.org/abs/1111.3033 The plug-in can be downloaded here: http://www.linkgroup.hu/modules.php
        Project website: http://linkgroup.hu/moduland.php
        --

        Version: 1.4
        Reference: Mate Szalay-Beko, Robin Palotai, Balazs Szappanos, Istvan A. Kovacs, Balazs Papp, Peter Csermely (2012) ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality. Bioinformatics 2012; doi: 10.1093/bioinformatics/bts352
        Release Date: 2012-05-01
        Authors: Mate Szalay-Beko, Robin Palotai, Istvan A. Kovacs, Peter Csermely ,Linkgroup, Semmelweis University, Budapest
        Balazs Szappanos, Balazs Papp ,Biological Research Centre, Hungarian Academy of Sciences, Szeged
        Verified to work in: 2.8
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 1.5
        Release Date: 2012-07-14
        Authors: Mate Szalay-Beko ,LinkGroup, Semmelweis University, Budapest
        Peter Csermely ,LinkGroup, Semmelweis University, Budapest
        Verified to work in: 2.8
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • NeMo

      • Description: NeMo is a network community-finding plugin for cytoscape. This plugin has the unique ability to find both densely connected networks and densely connected bipartite structures in a unified approach. The quick performance of the plugin allows it to be used interactively for network analysis. The plugin is easy to use because it is free of tunable parameters.
        --

        Version: 1.3
        Reference: Corban G. Rivera, Rachit Vakil, Joel S Bader: "NeMo: Network Module identification in Cytoscape", BMC Bioinformatics 2009, In Press. To appear in the Asian Pacific Bioinformatics Conference (APBC) 2010.
        Release Date: 2009-10-12
        Authors: Corban G. Rivera, Rachit Vakil, Joel S. Bader ,Department of Biomedical Engineering, Johns Hopkins University
        Release notes: http://baderlab.bme.jhu.edu/baderlab/index.php/NeMo
        Verified to work in: 2.6
        Download Jar/zip: click here (117.5KB)
        Download source: http://macbeth.clark.jhu.edu/~cgrivera/NeMo_v1.3_noCyto.zip
        --

        Version: 1.4
        Release Date: 2010-02-26
        Authors: Corban G. Rivera, Rachit Vakil, Joel S. Bader ,Department of Biomedical Engineering, Johns Hopkins University
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (117.5KB)


    • 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
        Authors: 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)

        --

        Version: 1.01
        Release Date: 2009-04-28
        Authors: Jan Baumbach ,International Computer Science Institute, Berkeley
        Tobias Wittkop ,Bielefeld University
        Dorothea Emig ,Max Planck Institute for Informatics

        Verified to work in: 2.7
        Download Jar/zip: click here (567.1KB)


  • Data visualization  --   (11)
    • ChartPlugin

      • Description: Cytoscape Plugin to plot numerical attributes for selected nodes or edges. http://apps.cytoscape.org/apps/chartplugin
        Project website: http://apps.cytoscape.org/apps/chartplugin
        --

        Version: 1.0
        Release Date: 2012-07-07
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Verified to work in: 2.8
        Download Jar/zip: click here (2.05MB)
        Download source: https://trac.nbic.nl/brs2011p07/
        --

        Version: 1.1
        Release Date: 2012-10-01
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (2.04MB)
        Download source: https://trac.nbic.nl/brs2011p07/

    • 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
        Authors: 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)

        --

        Version: 1.2
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093
        Release Date: 2009-07-23
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/www.ici.upmc.fr/cluego/cluegoDownload.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 (55.32MB)

        --

        Version: 1.3
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2010-05-18
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/www.ici.upmc.fr/cluego/cluegoDownload.shtml
        Verified to work in: 2.7
        Download Jar/zip: click here (33.85MB)

        --

        Version: 1.31
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2010-05-18
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoDescription.shtml
        Verified to work in: 2.7
        Note: Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml
        Download Jar/zip: click here (33.85MB)

        --

        Version: 1.4
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2011-03-01
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/www.ici.upmc.fr/cluego/cluegoDownload.shtml
        Verified to work in: 2.8
        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 (36.2MB)


    • CyAnimator
    • CytoHiCPlugin

      • Description: allow users to view and visually compare spatial maps of genomic landmarks, based on normalized Hi-C data.
        --

        Version: 1.0
        Reference: See http://www.cl.cam.ac.uk/~ys388/CytoHiC/
        Release Date: 2012-02-01
        Authors: Yoli Shavit , Computer Laboratory University of Cambridge
        Pietro Lio , Computer Laboratory University of Cambridge
        Release notes: http://www.cl.cam.ac.uk/~ys388/CytoHiC/
        Verified to work in: 2.8.3
        Note: We have submitted a paper describing CytoHiC and the paper is currently under review.
        Download Jar/zip: click here (40KB)
        Download source: http://www.cl.cam.ac.uk/~ys388/CytoHiC/CytoHiCPluginSrcCode.jar

    • GoogleChartFunctions

      • Description: Functions that create image URLs from attribute values using the Google Chart API.
        License: click here

        --

        Version: 1.1
        Release Date: 2011-08-05
        Authors: Mike Smoot ,UC San Diego
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (192.7KB)


    • KeyPathwayMiner

      • Description: A plugin for the combined analysis of differential expression data and biological networks.
        Project website: > http://keypathwayminer.mpi-inf.mpg.de/cytoscape.html
        --

        Version: 1.0
        Reference: Alcaraz NM, Kucuk H, Weile J, Wipat A, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int Math. (in press).
        Release Date: 2011-07-10
        Authors: Nicolas Alcaraz and Hande Kucuk ,MPII
        Release notes: http://keypathwayminer.mpi-inf.mpg.de/
        Verified to work in: 2.8
        Download Jar/zip: click here (847.1KB)

        --

        Version: 2.0
        Release Date: 2011-09-16
        Authors: Nicolas Alcaraz ,MPII
        Verified to work in: 2.8
        Download Jar/zip: click here (965KB)

        --

        Version: 2.1
        Release Date: 2011-10-13
        Authors: Nicolas Alcaraz ,MPII
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (965.1KB)

        --

        Version: 3.0
        Release Date: 2012-01-26
        Authors: Nicolas Alcaraz ,MPII
        Joachim Mueller ,MPII
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (975.3KB)


    • MultiColoredNodes

      • Description: This plugin allows to visualize several node attribute values simultaneously.

        If you use the plugin in published work, you may cite:
        G. Warsow, B. Greber, S. Falk, C. Harder, M. Siatkowski, S. Schordan, A. Som, N. Endlich, H. Scholer, D. Repsilber, K. Endlich, and G. Fuellen: ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation network. BMC Systems Biology Vol. 4(1) 2010, 164.
        Project website: https://sourceforge.net/projects/multicolor/
        --

        Version: 2.432
        Release Date: 2012-07-11
        Authors: Gregor Warsow ,Gregor Warsow
        Verified to work in: 2.8
        Download Jar/zip: click here (1.37MB)

        --

        Version: 2.500
        Release Date: 2012-07-24
        Authors: Gregor Warsow ,Gregor Warsow
        Verified to work in: 2.8
        Download Jar/zip: click here (1.44MB)

        --

        Version: 2.533
        Reference: G. Warsow, B. Greber, S. Falk, C. Harder, M. Siatkowski, S. Schordan, A. Som, N. Endlich, H. Scholer, D. Repsilber, K. Endlich, and G. Fuellen: ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation network. BMC Systems Biology Vol. 4(1) 2010, 164.
        Release Date: 2013-02-22
        Authors: Gregor Warsow ,Gregor Warsow
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (1.44MB)

        --

        Version: 2.540
        Release Date: 2013-03-20
        Authors: Gregor Warsow ,Gregor Warsow
        Verified to work in: 2.8
        Download Jar/zip: click here (1.44MB)
        Download source: http://sourceforge.net/projects/multicolor/

    • NetCirChro

      • Description: NetCirChro is a Cytoscape plug-in for network visualization on circular chromosomes. It enables mapping of interaction networks and node/edge attributes on circular genomes. This plug-in allows users to dynamically analyze the association between gene interactions and gene organization on chromosomes.

        Web: http://exon.niaid.nih.gov/netcirchro
        Email: NetCirChroSupport@niaid.nih.gov
        Project website: http://exon.niaid.nih.gov/netcirchro
        License: click here

        --

        Version: 1.0
        Reference: Jie Li, Qina Tan, Vijayaraj Nagarajan, Mariam Quinones, Yasmin Mohamoud, Yentram Huyen, Bioinformatics and Computational Biosciences Branch (BCBB) / The Office of Cyber Infrastructure and Computational Biology (OCICB) / National Institute of Allergy and Infectious Diseases (NIAID).http://exon.niaid.nih.gov/netcirchro/
        Release Date: 2009-11-25
        Authors: Jie Li, Qina Tan, Vijayaraj Nagarajan, Mariam Quinones, Yasmin Mohamoud, Yentram Huyen ,Bioinformatics and Computational Biosciences Branch (BCBB) / The Office of Cyber Infrastructure and Computational Biology (OCICB) / National Institute
        Release notes: click here
        Verified to work in: 2.6.1,2.6.3
        Download Jar/zip: click here (12.28MB)


    • nodeCharts
    • Viacomplex for Cytoscape

      • This plugin is not available through the Plugin Manager!

        Description: The ViaComplex for Cytoscape generates functional landscapes onto networks by using Jzy3d, a java library that allows a rapid display with high resolution of 3D surfaces.
        Project website: www.lbbc.ibb.unesp.br/viacomplex
        License: click here

        --

        Version: 1.0
        Release Date: 2012-10-03
        Authors: Esther Camilo ,Universidade Estadual Paulista
        Verified to work in: 2.8
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://code.google.com/p/cyviacomplex/source/

    • 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
        Authors: 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
        Authors: 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
        Authors: Robert Kincaid and Allan Kuchinsky ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Download Jar/zip: click here (682.8KB)

        --

        Version: 1.05
        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: 2011-03-01
        Authors: Robert Kincaid and Allan Kuchinsky ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Verified to work in: 2.8
        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 (774.8KB)


  • Scripting  --   (12)
  • Integrated analysis  --   (15)
    • 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
        Authors: 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
        Authors: 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
        Authors: 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
        Authors: Annabel Bourd ,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
        Authors: 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)

        --

        Version: 2.0
        Release Date: 2011-04-15
        Authors: Carito Guziolowski ,University of Heidelberg
        Anne Siegel , INRIA Rennes
        Release notes: click here
        Verified to work in: 2.8
        Note: This is a newer version of the BioqualiPlugin compatible with Cytoscape 2.8
        Download Jar/zip: click here (3.68MB)
        Download source: http://www.irisa.fr/symbiose/projects/bioqualiCytoscapePlugin/

    • ChemViz
    • CytoCopteR

      • Description: Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R.
        --

        Version: 1.0
        Release Date: 2012-05-03
        Authors: Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Martijn van Iersel ,EMBL-European Bioinformatics Institute
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Release notes: http://sourceforge.net/projects/cytocopter/files/Release_notes_v1.0.txt/download
        Verified to work in: 2.8
        Download Jar/zip: click here (5.07MB)
        Download source: https://sourceforge.net/p/cytocopter/code/6/tree/
        --

        Version: 1.1
        Release Date: 2012-10-09
        Authors: Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Martijn van Iersel ,EMBL-European Bioinformatics Institute
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (5.24MB)


    • 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
        Authors: 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
        Authors: 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

    • ExprEssence
    • GPEC

      • Description: Finding genes associated with a disease is an important issue in the biomedical area and many gene prioritization methods have been proposed for this goal. Among these, network-based approaches are recently proposed and outperformed functional annotation-based ones. Here, we introduce a novel Cytoscape plug-in, GPEC, to help identify putative genes likely to be associated with specific diseases or pathways. In the plug-in, gene prioritization is performed through a random walk with restart algorithm, a state-of-the art network-based method, along with a gene/protein relationship network. The plug-in also allows users efficiently collect biomedical evidence for highly ranked candidate genes. A set of known genes, candidate genes and a gene/protein relationship network can be provided in a flexible way.
        Project website: http://gpec.sourceforge.net/
        --

        Version: 1.1
        Reference: Duc-Hau, Le and Yung-Keun, Kwon (2012) GPEC: a Cytoscape plugin for random walk-based gene prioritization and biomedical evidence collection, Computational Biology and Chemistry, 37(0):17-23
        Release Date: 2012-06-14
        Authors:
        Release notes: http://gpec.sourceforge.net/
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (11.17MB)


    • 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
        Authors: 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
        Authors: 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
        Authors: 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
        Authors: Ryan Kelley ,UCSD
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (115.4KB)


    • MetScape

      • Description:

        MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.

        For more information contact the MetScape development team: metscape-help@umich.edu

        This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..


        Project website: http://metscape.ncibi.org/metscape2/
        --

        Version: 0.8
        Release Date: 2009-03-13
        Authors: 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/
        --

        Version: 1.0
        Release Date: 2009-09-01
        Authors: Jing Gao, Alla Karnovsky, Glenn Tarcea, Barbara Mirel, Terry Weymouth, James Cavalcoli, H.V. Jagadish , CCMB/NCIBI University of Michigan
        Release notes: http://metscape.ncibi.org/releaseNotes_1.0.html
        Verified to work in: 2.6
        Download Jar/zip: click here (290.7KB)
        Download source: http://metscape.ncibi.org/tutorial.html
        --

        Version: 1.01
        Reference: Jing Gao, V. Glenn Tarcea, Alla Karnovsky, Barbara R. Mirel, Terry E. Weymouth, Christopher W. Beecher, James D. Cavalcoli, Brian D. Athey, Gilbert S. Omenn, Charles F. Burant, and H. V. Jagadish Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks Bioinformatics 2010 26: 971-973; doi:10.1093/bioinformatics/btq048
        Release Date: 2010-04-29
        Authors: Jing Gao, Alla Karnovsky, Glenn Tarcea, Barbara Mirel, Terry Weymouth, James Cavalcoli, H.V. Jagadish , CCMB/NCIBI University of Michigan
        Verified to work in: 2.7
        Download Jar/zip: click here (312.8KB)
        Download source: http://metscape.ncibi.org/
        --

        Version: 2.3
        Release Date: 2011-10-03
        Authors: Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth , University of Michigan
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (6.56MB)

        --

        Version: 2.31
        Release Date: 2011-10-05
        Authors: Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth , University of Michigan
        Verified to work in: 2.8
        Download Jar/zip: click here (6.56MB)

        --

        Version: 2.32
        Release Date: 2012-07-16
        Authors: Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth , University of Michigan
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (6.77MB)

        --

        Version: 2.33
        Release Date: 2012-07-16
        Authors: Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth , University of Michigan
        Release notes: http://metscape.ncibi.org
        Verified to work in: 2.8
        Download Jar/zip: click here (6.77MB)


    • NetAtlas

      • Description: Information about the plugin that will be displayed to users.
        Please use html tags for all formatting and do not add newlines.


        Project website: http://sourceforge.net/projects/netatlas/
        --

        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
        Authors: 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/
        --

        Version: 1.2
        Release Date: 2010-05-01
        Authors: Longlong Yang and Russell S. Thomas ,The Hamner Institutes for Health Sciences
        Release notes: click here
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1008.5KB)


    • OmicsAnalyzer

      • This plugin is not available through the Plugin Manager!

        Description: OmicsAnalyzer is a Cytoscape plugin dedicated to providing useful visualization and an integrated analysis tool for large-scale omics data.
        Project website: http://vrac.iastate.edu/~jlv/omicsanalyzer/
        --

        Version: 1.0
        Release Date: 2009-10-27
        Authors: Tian Xia ,Iowa State University
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • PanGIA

      • Description: PanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies "modules" as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules.
        Project website: http://prosecco.ucsd.edu/PanGIA
        --

        Version: 1.0
        Release Date: 2010-12-09
        Authors: Gregory Hannum, Rohith Srivas, Johannes Ruscheinski, Kei Ono, Peng-Liang Wang, Michael Smoot, Trey Ideker ,UCSD
        Release notes: http://prosecco.ucsd.edu/PanGIA/
        Verified to work in: 2.8
        Download Jar/zip: click here (479.9KB)
        Download source: http://prosecco.ucsd.edu/PanGIA/
        --

        Version: 1.1
        Reference: Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. PMID: 21886098
        Release Date: 2011-02-24
        Authors: Gregory Hannum, Rohith Srivas, Johannes Ruscheinski, Kei Ono, Peng-Liang Wang, Michael Smoot, Trey Ideker ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (483.3KB)


    • 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
        Authors: Fei Li ,NUDT/BMI
        Wenjian Xu ,BMI
        Peng Li ,BMI
        Verified to work in: 2.5,2.6.1
        Download Jar/zip: click here (1.75MB)
        Download source: http://code.google.com/p/perturbation-analyzer/
        --

        Version: 0.2
        Release Date: 2009-05-24
        Authors: 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
        Authors: Fei Li ,NUDT/BMI
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (1.73MB)

        --

        Version: 1.1
        Release Date: 2009-08-14
        Authors: Fei Li ,BMI NUDT
        Verified to work in: 2.5
        Download Jar/zip: click here (1.74MB)

        --

        Version: 1.2
        Release Date: 2009-10-04
        Authors: Fei Li ,BMI NUDT
        Verified to work in: 2.5,2.6.3
        Download Jar/zip: click here (1.74MB)


    • 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
        Authors: 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
        Authors: 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)


    • SLiMScape

      • Description: This plugin add Short Linear Motif discovery functionality to Cytoscape
        Project website: http://bioware.ucd.ie/slimscape/
        License: click here

        --

        Version: 1.0
        Release Date: 2013-01-09
        Authors: Kevin O'Brien ,University College Dublin

        Verified to work in: 2.8.3
        Download Jar/zip: click here (2.8MB)

        --

        Version: 1.2
        Release Date: 2013-01-09
        Authors: Kevin O'Brien ,University College Dublin

        Verified to work in: 2.8.3
        Download Jar/zip: click here (2.8MB)

        --

        Version: 1.5
        Release Date: 2013-01-09
        Authors: Kevin O\'Brien ,University College Dublin

        Verified to work in: 2.8.3
        Note: Please delete older versions of this plugin. They are no longer fully functional. Thanks
        Download Jar/zip: click here (2.8MB)

        --

        Version: 1.6
        Release Date: 2013-01-09
        Authors: Kevin O\'Brien ,University College Dublin

        Verified to work in: 2.8.3
        Download Jar/zip: click here (3.26MB)


  • Interaction database  --   (10)
    • BiogridPlugin

      • Description:

        The BiogridPlugin allows direct import of data from BioGRID .tab files (which are available from www.thebiogrid.org/downloads.php) into a Cytoscape network, with a custom visual style.


        Project website: http://www.thebiogrid.org
        --

        Version: 0.1
        Release Date: 2009-10-30
        Authors: Andrew Winter, BioGRID, Tyers Group, Wellcome Trust Centre for Cell Biology, University of Edinburgh and The Samuel Lunenfeld Research Institute, Moun
        Verified to work in: 2.6
        Download Jar/zip: click here (28.9KB)

        --

        Version: 0.2
        Release Date: 2010-02-09
        Authors: Andrew Winter, BioGRID, Tyers Group, Wellcome Trust Centre for Cell Biology, University of Edinburgh.
        Release notes: click here
        Download Jar/zip: click here (21.7KB)


    • 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
        Authors: 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/

    • BisoGenet

      • Description: This plugin allows searching molecular interactions from SysBiomics, our in-house database, and displaying the result as an interaction network within Cytoscape. SysBiomics integrates data from well-known interaction databases including DIP, BIOGRID, HPRD, BIND, MINT and INTACT.
        BisoGenet provides an easy to use interface allowing users to customize the searches by specifying a target set of genes/proteins to retrieve interactions data for, specifying a subcontext around the targets to narrow the interactions data searching space, defining a selection filter to discard/include interactions (within the specified subcontext) given its nature, primary databases and supporting experimental methods.
        Interaction network's gene/protein associated info includes annotations from NCBI, UniProt, KEGG, and GO databases while interaction info includes the supporting experimental methods and hyperlinks to their primary databases entries and related publications.
        BisoGenet also includes network topology analysis tools such as Shortest Paths between a set of nodes, determination of Equivalent Nodes, and Network Statistics reports in combination to interactive Transparency filter to help discernig such analytical results in the context of dense networks.
        Project website: http://bio.cigb.edu.cu/bisogenet-cytoscape/
        License: click here

        --

        Version: 1.40
        Reference: Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R. A new tool for gene network building, visualization and analysis. BMC Bioinformatics , 10:91 , 2010
        Release Date: 2009-12-07
        Authors: Maria E. Ochagavia, Ricardo Bringas, Alexander Martin, Jamilet Miranda, Jorge Fdez. de Cossio, Laya del Carmen Rabasa ,Centre for Genetic Engineering and Biotechnology (CIGB)
        Verified to work in: 2.6
        Download Jar/zip: click here (6.37MB)
        Download source: http://bio.cigb.edu.cu/
        --

        Version: 1.41
        Reference: http://www.biomedcentral.com/1471-2105/11/91/abstract
        Release Date: 2010-06-10
        Authors: Maria E. Ochagavia, Ricardo Bringas, Alexander Martin, Jamilet Miranda, Jorge Fdez. de Cossio, Laya del Carmen Rabasa ,Centre for Genetic Engineering and Biotechnology (CIGB)
        Release notes: click here
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (6.4MB)
        Download source: http://bio.cigb.edu.cu/bisogenet-cytoscape/plugins/BisoGenet.jar

    • ConsensusPathDBplugin

      • Description: This plugin mines evidences for user-specified protein-protein interactions in the form of publications, containing databases, interaction detection methods and pathways. The annotation basis is ConsensusPathDB - a meta-database that integrates tens of resources for functional interactions in human, yeast and mouse.
        Project website: http://cpdb.molgen.mpg.de
        --

        Version: 1.0
        Release Date: 2010-07-01
        Authors: Konstantin Pentchev, Atanas Kamburov and Ralf Herwig ,MPIMG
        Keiichiro Ono and Trey Ideker ,UCSD
        Release notes: click here
        Verified to work in: 2.7
        Download Jar/zip: click here (145.9KB)
        Download source: http://cpdb.molgen.mpg.de/download/ConsensusPathDBplugin.jar

    • DroID
    • 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. This is minor update (bug fix only).


        License: click here

        --

        Version: 0.66
        Release Date: 2009-08-05
        Authors: Keiichiro Ono ,UCSD Bioengineering Ideker Lab
        Release notes: click here
        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/

    • iRefScape

      • Description: iRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.
        http://irefindex.uio.no/wiki/iRefScape


        Project website: http://irefindex.uio.no
        License: click here

        --

        Version: 0.82
        Release Date: 2010-04-27
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.6
        Download Jar/zip: click here (1.18MB)

        --

        Version: 0.87
        Reference: PMID=18823568 iRefIndex: A consolidated protein interaction database with provenance Sabry Razick, George Magklaras and Ian M Donaldson, BMC Bioinformatics. 2008 Sep 30;9:405
        Release Date: 2010-06-21
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.6
        Download Jar/zip: click here (1.32MB)
        Download source: ftp://ftp.no.embnet.org/irefindex/Cytoscape/
        --

        Version: 0.86
        Release Date: 2010-06-18
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.6
        Download Jar/zip: click here (1.31MB)

        --

        Version: 0.88
        Reference: PMID=18823568 iRefIndex: A consolidated protein interaction database with provenance Sabry Razick, George Magklaras and Ian M Donaldson, BMC Bioinformatics. 2008 Sep 30;9:405
        Release Date: 2010-06-22
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.6
        Download Jar/zip: click here (1.32MB)
        Download source: ftp://ftp.no.embnet.org/irefindex/Cytoscape/
        --

        Version: 0.89
        Reference: PMID=18823568 iRefIndex: A consolidated protein interaction database with provenance Sabry Razick, George Magklaras and Ian M Donaldson, BMC Bioinformatics. 2008 Sep 30;9:405
        Release Date: 2010-06-23
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.6
        Download Jar/zip: click here (1.32MB)
        Download source: ftp://ftp.no.embnet.org/irefindex/Cytoscape/
        --

        Version: 0.90
        Reference: PMID=18823568 iRefIndex: A consolidated protein interaction database with provenance Sabry Razick, George Magklaras and Ian M Donaldson, BMC Bioinformatics. 2008 Sep 30;9:405
        Release Date: 2010-06-23
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x
        Verified to work in: 2.7
        Download Jar/zip: click here (1.32MB)
        Download source: ftp://ftp.no.embnet.org/irefindex/Cytoscape/
        --

        Version: 1.16
        Release Date: 2011-06-28
        Authors: Ian Donaldson and Sabry Razick ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_1.0x
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.72MB)

        --

        Version: 1.17
        Reference: iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M Donaldson. BMC Bioinformatics 2011, 12:388doi:10.1186/1471-2105-12-388. http://www.biomedcentral.com/1471-2105/12/388
        Release Date: 2011-10-10
        Authors: Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M Donaldson ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://www.biomedcentral.com/1471-2105/12/388
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.73MB)
        Download source: http://irefindex.uio.no/wiki/README_Cytoscape_plugin_1.0x
        --

        Version: 1.18
        Reference: iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M Donaldson. BMC Bioinformatics 2011, 12:388doi:10.1186/1471-2105-12-388. http://www.biomedcentral.com/1471-2105/12/388
        Release Date: 2011-11-18
        Authors: Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M Donaldson ,Biotechnology Centre of Oslo, University of Oslo
        Release notes: http://irefindex.uio.no/wiki/iRefScape_1.0
        Verified to work in: 2.7,2.8
        Note: This is an incremental update with minor adjustments to the previous 1.17 release.
        Download Jar/zip: click here (811.9KB)
        Download source: http://irefindex.uio.no/hg/iRefScape/file/e12f853c5951

    • 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.


        --

        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
        Authors: 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
        Authors: 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
        Authors: 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
        Authors: 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: 2010-04-29
        Authors: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Release notes: click here
        Verified to work in: 2.7
        Download Jar/zip: click here (225KB)
        Download source: http://mimiplugin.ncibi.org/
        --

        Version: 3.1
        Release Date: 2011-02-24
        Authors: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (206.4KB)

        --

        Version: 3.11
        Release Date: 2011-04-05
        Authors: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (202.8KB)


    • PSICQUICUniversalClient
    • 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
        Authors: Milan Simonovic ,University of Zurich
        Christian von Mering ,University of Zurich
        Verified to work in: 2.6.1
        Download Jar/zip: click here (392KB)

        --

        Version: 1.1
        Release Date: 2009-07-17
        Authors: Milan Simonovic ,University of Zurich
        Christian von Mering ,University of Zurich
        Verified to work in: 2.6
        Note: 2.6.x compatible version
        Download Jar/zip: click here (384.7KB)

        --

        Version: 1.2
        Release Date: 2010-08-29
        Authors: Milan Simonovic ,University of Zurich
        Christian von Mering ,University of Zurich
        Release notes: click here
        Verified to work in: 2.7
        Download Jar/zip: click here (384.5KB)


  • Ontology analysis  --   (12)
    • 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
        Authors: 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
        Authors: 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
        Authors: Steven Maere ,VIB
        Verified to work in: 2.6
        Download Jar/zip: click here (12.31MB)

        --

        Version: 2.42
        Reference: Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449
        Release Date: 2010-08-01
        Authors: Steven Maere ,VIB
        Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO/
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (14.53MB)
        Download source: http://www.psb.ugent.be/cbd/papers/BiNGO/
        --

        Version: 2.44
        Release Date: 2010-08-01
        Authors: Steven Maere ,VIB
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (14.53MB)


    • 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. To extend it's functionality get as well CluePedia.
        Project website: http://www.ici.upmc.fr/cluego
        License: click here

        --

        Version: 1.5
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2012-10-11
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoNews.shtml
        Verified to work in: 2.8
        Note: The license for academic users will be only used to estimate the number of ClueGO users.
        Download Jar/zip: click here (72.98MB)
        Download source: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml
        --

        Version: 1.6
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2012-11-29
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoNews.shtml
        Verified to work in: 2.8
        Download Jar/zip: click here (74.89MB)
        Download source: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml
        --

        Version: 1.7
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2012-12-10
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoNews.shtml
        Verified to work in: 2.8
        Download Jar/zip: click here (74.9MB)
        Download source: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml
        --

        Version: 1.71
        Release Date: 2013-01-07
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoNews.shtml
        Verified to work in: 2.8
        Download Jar/zip: click here (74.9MB)
        Download source: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml
        --

        Version: 1.8
        Reference: Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093 PM:19237447
        Release Date: 2013-01-07
        Authors: Gabriela Luana Bindea,Bernhard Mlecnik,Jerome Galon ,INSERM U872 Integrative Cancer Immunology (ICI) Team 15
        Release notes: http://www.ici.upmc.fr/cluego/cluegoNews.shtml
        Verified to work in: 2.8
        Download Jar/zip: click here (75.27MB)


    • CytoSaddleSum

      • Description:

        CytoSaddleSum is a Cytoscape functional enrichment plugin that provides interface to SaddleSum functionality. It works by querying SaddleSum either locally (using the standalone version) or remotely, through an HTTP request to a web server. The results of a functional enrichment query are shown as a term relationship network, where nodes represent terms linked by edges showing term relationships. The statistics and other query details for each term are written as node attributes, allowing easy integration into network-based data analysis workflows.


        License: click here

        --

        Version: 1.4
        Release Date: 2011-09-19
        Authors: Aleksandar Stojmirovic ,NCBI/NLM/NIH
        Alexander Bliskovsky ,NCBI/NLM/NIH
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (888.5KB)
        Download source: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/CytoSaddleSum/src/CytoSaddleSum-1.4-src.zip
        --

        Version: 1.5
        Release Date: 2011-12-14
        Authors: Aleksandar Stojmirovic ,NCBI/NLM/NIH
        Alexander Bliskovsky ,NCBI/NLM/NIH
        Release notes: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/CytoSaddleSum/CHANGES
        Verified to work in: 2.7,2.8
        Note: Version 1.5 - added import / export functionality.
        Download Jar/zip: click here (996.4KB)
        Download source: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/CytoSaddleSum/src/CytoSaddleSum-1.5-src.zip

    • EnrichmentMap

      • Description: Enrichment Map is a network-based method to visualize and interpret gene-set enrichment results.
        Project website: http://www.baderlab.org/Software/EnrichmentMap
        --

        Version: 1.0
        Reference: Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One. 2010 Nov 15;5(11):e13984. http://www.ncbi.nlm.nih.gov/pubmed/21085593
        Release Date: 2010-11-16
        Authors: Gary Bader, Daniele Merico, Ruth Isserlin, Oliver Stueker ,University of Toronto
        Release notes: http://www.baderlab.org/EnrichmentMap
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (346KB)
        Download source: http://www.baderlab.org/Software/EnrichmentMap
        --

        Version: 1.1
        Reference: Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation Merico D, Isserlin R, Stueker O, Emili A, Bader GD PLoS One. 2010 Nov 15;5(11):e13984
        Release Date: 2011-02-07
        Authors: Gary Bader, Daniele Merico, Ruth Isserlin, Oliver Stueker ,University of Toronto
        Release notes: click here
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (348.9KB)
        Download source: http://www.baderlab.org/Software/EnrichmentMap
        --

        Version: 1.2
        Reference: Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation Merico D, Isserlin R, Stueker O, Emili A, Bader GD PLoS One. 2010 Nov 15;5(11):e13984
        Release Date: 2011-04-14
        Authors: Gary Bader, Daniele Merico, Ruth Isserlin, Oliver Stueker ,University of Toronto
        Release notes: http://baderlab.org/EnrichmentMap/ReleaseNotesv1.2
        Verified to work in: 2.6,2.7,2.8
        Note: Release of v1.2 of Enrichment Map Plugin
        Download Jar/zip: click here (388KB)
        Download source: http://baderlab.org/Software/EnrichmentMap

    • GFD-Net

      • Description:

        What is GFD-Net

        GFD-Net is a Cytoscape plugin designed to visualize and analyze the functional dissimilarity of gene networks. GFD-Net can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes in it.

        What else

        After the analysis, users can visualize the information retrieved from GO.

        • For each gene the user can see its associated GO terms and its function (specified by a GO term) chosen as the most cohesive function in the set.
        • For each edge the user can see the genes at its ends, the function chosen as the most cohesive function in the set for each one and the dissimilarity between them.

        Project website: http://my-lab-site.org/myCytoscapePlugin
        --

        Version: 1.0
        Release Date: 2013-05-20
        Authors: Juan Jose Diaz Montana ,
        Norberto Diaz Diaz ,School of Engineering. Pablo de Olavide University, Seville, Spain
        Isabel A. Nepomuceno-Chamorro ,Departamento Lenguajes y Sistemas Informaticos, Universidad de Sevilla, Seville, Spain
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (824.4KB)


    • Mosaic

      • Description: Network partition, layout and color based on Gene Ontology or other annotations
        Project website: http://nrnb.org/tools/mosaic/
        --

        Version: 1.0
        Reference: http://nrnb.org/tools/mosaic/
        Release Date: 2011-11-15
        Authors: Chao Zhang ,University of Missouri & GSoC
        Alexander Pico ,Gladstone Institutes, UCSF
        Release notes: http://nrnb.org/tools/mosaic/
        Verified to work in: 2.8
        Note: Note that Mosaic requires the CyThesaurus plugin, version 1.3.1 or higher.
        Download Jar/zip: click here (3.45MB)
        Download source: http://www.rbvi.ucsf.edu/trac/GenMAPP/browser/trunk/avalon/mosaic
        --

        Version: 1.1
        Reference: Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R. Pico. (2012) Mosaic: Making biological sense of complex networks. Bioinformatics 28(14):1943–1944
        Release Date: 2013-04-01
        Authors: Chao Zhang ,Weill Medical College, Cornell University
        Alexander Pico ,Gladstone Institutes, UCSF
        Kristina Hanspers ,Gladstone Institutes, UCSF
        Allan Kuchinsky ,Aglient Technologies
        Nathan Salomonis ,Gladstone Institutes, UCSF
        Release notes: http://nrnb.org/tools/mosaic/
        Verified to work in: 2.8
        Download Jar/zip: click here (3.46MB)
        Download source: http://www.rbvi.ucsf.edu/trac/GenMAPP/browser/trunk/avalon/mosaic

    • NOA
    • PiNGO

      • Description: PiNGO is a plugin to find candidate genes in a network that are associated with user-defined target Gene Ontology (GO) categories.
        Project website: http://www.psb.ugent.be/esb/PiNGO/
        --

        Version: 1.00
        Reference: Maere S (2010) PiNGO: a Cytoscape plugin to find lead genes in biological networks (submitted)
        Release Date: 2010-08-01
        Authors: Steven Maere ,VIB
        Release notes: http://www.psb.ugent.be/esb/PiNGO/
        Verified to work in: 2.6,2.7
        Download Jar/zip: click here (402.9KB)
        Download source: http://www.psb.ugent.be/esb/PiNGO/
        --

        Version: 1.10
        Release Date: 2010-12-06
        Authors: Steven Maere ,VIB
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (1.18MB)

        --

        Version: 1.11
        Release Date: 2011-01-18
        Authors: Steven Maere ,VIB
        Verified to work in: 2.8
        Download Jar/zip: click here (304.4KB)


    • 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
        Authors: 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/

    • SimTrek

      • Description: The plugin provides a user-friendly implementation of ontology- and graph-based similarity assessment in biological networks. It can be used to analyze networks on a “semantic similarity” space to detect potentially novel associations, which may not be explicitly represented in the input network under analysis.
        Project website: http://rosalind.infj.ulst.ac.uk/SimTrek.html
        License: click here

        --

        Version: 1.0
        Reference: Haiying Wang, Huiru Zheng, Francisco Azuaje, "Ontology- and graph-based similarity assessment in biological networks", Bioinformatics, in press (2010)
        Release Date: 2010-08-17
        Authors: Haiying Wang, Huiru Zheng ,Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, UK.
        Francisco Azuaje ,Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sante), L-1150, Luxembourg.
        Release notes: http://rosalind.infj.ulst.ac.uk/SimTrek.html
        Download Jar/zip: click here (860.6KB)
        Download source: http://rosalind.infj.ulst.ac.uk/SimTrek.html

    • STOP

      • Description:

        STOP (Statistical tracking of ontological phrases) is a multi-ontology enrichment analysis tool. It is intended to be used to help from hypothesis about large sets of genes or proteins. The annotations used for enrichment analysis are obtained automatically applying text descriptions of genes and proteins to the NCBO annotator. Text for genes is found using NCBI Entrez Gene, and text for proteins is found using UniProt. The text is then run though NCBO annotator with all the available ontologies.

        Given a list of genes a user may select up to 267 ontologies to be used for a term enrichment analysis (incl. OMIM, Human Phenotype Ontology, Gene Ontology, CHEBI,…). Two networks and a table will be created: a gene network with edges based on common enriched terms, a term network with edges based on common genes and the table of all enriched terms. These three entities are interrting with each other, i.e. selecting a term in the term network will highlight the respective genes and the term in the table etc.

        For more details please visit http://www.mooneygroup.org/stop


        Project website: http://mooneygroup.org/stop/input
        --

        Version: 1.0
        Release Date: 2013-04-16
        Authors: Chaoyi Du and Tobias Wittkop and Sean D. Mooney ,Buck Institute for Research on Aging
        Verified to work in: 2.8
        Download Jar/zip: click here (55.6KB)


    • WordCloud

      • Description: When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the \\\"biological meaning\\\" of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a ‘tag cloud’, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network. These visualizations provide a concise visual summary of annotations which is helpful for network analysis and interpretation.
        Project website: http://baderlab.org/Software/WordCloudPlugin
        --

        Version: 1.0
        Release Date: 2010-10-14
        Authors: Layla Oesper ,Brown University
        Daniele Merico, Ruth Isserlin, Gary Bader ,University of Toronto
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/soc/layla/WordCloudPlugin/
        --

        Version: 1.0
        Reference: Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code for Biology and Medicine (2011) 6:7.
        Release Date: 2011-04-07
        Authors: Layla Oesper ,Brown University
        Daniele Merico, Ruth Isserlin, Gary D. Bader ,University of Toronoto
        Verified to work in: 2.6
        Download Jar/zip: click here (352.2KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/soc/layla/WordCloudPlugin/

  • Utility  --   (16)
    • batchTool
    • 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
        Authors: 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
        Authors: 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/

    • coreCommands
    • CySBGN

      • Description: SBGN aims to be the standard graphical notation for systems biology. This plugin adds the support to Cytoscape to load SBGN-ML networks.
        License: click here

        --

        Version: 1.0
        Release Date: 2012-05-31
        Authors: Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Martijn van Iersel ,EMBL-European Bioinformatics Institute
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Release notes: http://sourceforge.net/projects/cysbgn/files/Release_notes_v1.0.txt/download
        Verified to work in: 2.8
        Download Jar/zip: click here (1.53MB)
        Download source: https://sourceforge.net/p/cysbgn/code/4/tree/
        --

        Version: 1.1
        Release Date: 2012-09-07
        Authors: Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Martijn van Iersel ,EMBL-European Bioinformatics Institute
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Verified to work in: 2.8
        Download Jar/zip: click here (4.58MB)

        --

        Version: 1.2
        Release Date: 2012-11-26
        Authors: Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Martijn van Iersel ,EMBL-European Bioinformatics Institute
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Verified to work in: 2.8
        Download Jar/zip: click here (4.57MB)


    • cySBML

      • This plugin is not available through the Plugin Manager!

        Description: cySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML network annotations within the network context. SBML models can be imported from BioModels.net or via file or urls. One click access to the annotation resources is provided. SBML validation information about the imported files is available.
        Project website: http://www.charite.de/sysbio/people/koenig/software/cysbml/index.html
        License: click here

        --

        Version: 0.5
        Release Date: 2012-04-01
        Authors: Matthias König ,Charité Berlin, Computational Systems Biochemistry
        Release notes: click here
        Verified to work in: 2.8.2
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • EnhancedSearch

      • Description: Perform search on multiple attributes using logical operators and wildcards. Locate nodes and edges of interest based on their attributes and highlight them on the network. Reference to the simple query syntax is provided through right-click menu.
        Project website: http://bioinformatics.oxfordjournals.org/content/24/12/1465
        License: click here

        --

        Version: 1.1
        Release Date: 2008-02-01
        Authors: Maital Ashkenazi ,HUJI
        Release notes: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/12/1465
        Verified to work in: 2.5,2.6
        Note: This version provides better performance.
        Download Jar/zip: click here (676.2KB)

        --

        Version: 1.2
        Reference: Maital Ashkenazi,Gary D. Bader, Allan Kuchinsky, Menachem Moshelion and David J. States. Cytoscape ESP: simple search of complex biological networks. Bioinformatics (2008) 24: 1465–1466.
        Release Date: 2010-10-30
        Authors: Maital Ashkenazi ,Evogene
        Release notes: click here
        Verified to work in: 2.5,2.6,2.7,2.8
        Download Jar/zip: click here (1.06MB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/soc/maital/EnhancedSearch2/

    • EpiTrace

      • This plugin is not available through the Plugin Manager!

        Description: EpiTrace performs epidemic simulations on networks representing transports of livestock between holdings. The aim of the simulations is to trace contacts based on animal movements and to identify the most likely origins or destinations of an outbreak. EpiTrace is intended to work in combination with another plugin (Trace; distributed only to authorised users) which gives the possibility of importing and exploring interactively livestock movement data from livestock databases trough web services. Although EpiTrace was developed with veterinary epidemiology and traceability in mind, it can also be used autonomously with data imported from other sources and as a generic meta-population and network based simulation tool.
        Project website: http://epitrace.jrc.ec.europa.eu/
        --

        Version: 1.0
        Release Date: 2009-07-22
        Authors: Fabrizio Natale ,European Commission Joint Research Centre Institute for the Protection and Security of the Citizen
        Fabrizio Grassi
        Release notes: http://epitrace.jrc.ec.europa.eu/download/EpiTrace.jar
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://epitrace.jrc.ec.europa.eu/docs/src.zip

    • GenomeSpaceLibsPlugin

      • Description: A plugin of libraries required for the GenomeSpace Plugin. This plugin provides no functionality on its own.
        --

        Version: 0.1
        Release Date: 2012-07-31
        Authors: Mike Smoot ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (12.48MB)


    • 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
        Authors: 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/

    • IDSwitcher

      • Description: ID Switcher allows to redefine the node/edge identifiers based on a node/edge attribute chosen by the user.
        Project website: https://sourceforge.net/projects/expressence/
        License: click here

        --

        Version: 1.0
        Release Date: 2012-07-06
        Authors: Gregor Warsow ,Institute for Biostatistics and Informatics in Medicine and Ageing - University of Rostock, Germany
        Stephan Struckmann ,Institute for Biostatistics and Informatics in Medicine and Ageing - University of Rostock, Germany
        Verified to work in: 2.8
        Download Jar/zip: click here (311.7KB)


    • LayoutSaverPlugin

      • Description: A simple plugin that saves the X/Y positions of nodes in one network so that the positions can be applied to other networks that share the same nodes. Click on the Layout→Save Node Positions to save the node positions in the current network and the Click on the Layout→Cytoscape Layouts→Apply Saved Layout to apply the saved node positions to the current network.
        License: click here

        --

        Version: 1.0
        Release Date: 2012-04-24
        Authors: Mike Smoot ,UCSD
        Release notes: click here
        Verified to work in: 2.8
        Download Jar/zip: click here (4.5KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/LayoutSaver/

    • 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
        Authors: 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
        Authors: 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
    • 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
        Authors: 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
        Authors: Mike Smoot ,UC San Diego
        Verified to work in: 2.6
        Download Jar/zip: click here (5.5KB)


    • SubnetworkCreator

      • Description: Cytoscape Plugin to create subnetworks for disconnected graphs.
        Project website: http://trac.nbic.nl/brs2011p07/
        License: click here

        --

        Version: 1.0
        Release Date: 2012-02-02
        Authors: Tim te Beek ,Netherlands Bioinformatics Centre, Bioinformatics Research Support
        Verified to work in: 2.8
        Download Jar/zip: click here (43.2KB)
        Download source: http://trac.nbic.nl/brs2011p07/

  • Other  --   (43)
    • 3DScape

      • This plugin is not available through the Plugin Manager!

        Description: 3DScape provides 3D network visualization in Cytoscape, it has the following features: 1. Convert Cytoscape network views to 3D. This process can retain the color, size, and shape of nodes. 2. Three-dimensional layout using Fruchterman-Reingold (Fruchterman et al., 1991), Fast Multipole Multilevel Method (FM3) (Hachul et al., 2004), and Span Tree algorithms. 3. Network edges can be rendered in gradient heat map colors, with glowing effect. 4. Animation loops from time points of a series of expression data.
        Project website: http://scape3d.sourceforge.net/download_scape3d.html
        --

        Version: 0.2
        Release Date: 2011-06-01
        Authors: Qi Wang ,Institute of Microbiology, Chinese Academy of Sciences
        Verified to work in: 2.7,2.8
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 0.4
        Reference: Wang, Qi. 3DScape: three dimensional visualization plug-in for Cytoscape. Available from Nature Precedings (2011)
        Release Date: 2012-03-26
        Authors: Qi Wang ,Institute of Microbiology, Chinese Academy of Sciences
        Release notes: click here
        Verified to work in: 2.7,2.8
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • addParentNeighbors
    • AllegroLayout

      • Description:

        AllegroLayout is a high-performance graph layout plugin designed for large-scale networks and provides two kinds of force-based layout algorithms supporting edge-weighted layout. It supports realtime layout animation and both of CPU and GPU layout.

        Its massively parallel GPU layout algorithm makes it possible to perform the layout algorithms for a large complex graph in several seconds. Its GPU implementation is hundreds of times faster than the CPU implementation which exploits single core of the latest CPU.

        It also provides the layout animation which shows the layout progress of a large complex network in realtime. You can even zoom and pan it while the layout is being processed.

        For more information, please visit us at http://allegroviva.com/allegrolayout/. If you have any problems or questions, please create a new topic in our support forums: http://allegroviva.com/support/


        Project website: http://allegroviva.com/allegrolayout/
        License: click here

        --

        Version: 1.0
        Release Date: 2013-05-11
        Authors: Jun S. Yoon ,AllegroViva Inc.
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (8.33MB)

        --

        Version: 1.1
        Release Date: 2013-05-20
        Authors: Jun S. Yoon ,AllegroViva Inc.
        Verified to work in: 2.6,2.7,2.8
        Download Jar/zip: click here (8.34MB)


    • 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
        Authors: 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.

    • 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 3, SBML and CellDesigner formats
        • Export to BioPAX 3, SBML and CellDesigner formats after user manipulations
        • Conversion between standards (CellDesigner->BioPAX 3, BioPAX 3 ->SBML)
        • Full support of BioPAX 3 information (reaction network, interaction network, pathway structure, references), concept of BioPAX 3 index and network interfaces
        • Browsing, editing, extracting parts, merging BioPAX 3 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 3 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://binom.curie.fr/
        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
        Authors: 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
        --

        Version: 2.1
        Release Date: 2012-04-26
        Authors: Eric Bonnet ,Institut Curie
        Laurence Calzone ,Institut Curie
        Daniel Rovera ,Institut Curie
        Emmanuel Barillot ,Institut Curie
        Eric Viara ,Institut Curie
        Andrei Zinovyev ,Institut Curie
        Release notes: http://binom.curie.fr
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (25.31MB)
        Download source: http://binom.curie.fr
        --

        Version: 2.2
        Release Date: 2012-09-04
        Authors: Eric Bonnet ,Institut Curie
        Laurence Calzone ,Institut Curie
        Daniel Rovera ,Institut Curie
        Emmanuel Barillot ,Institut Curie
        Eric Viara ,Institut Curie
        Andrei Zinovyev ,Institut Curie
        Release notes: http://binom.curie.fr
        Verified to work in: 2.7,2.8
        Note: update version 2.2
        Download Jar/zip: click here (25.36MB)
        Download source: http://binom.curie.fr

    • 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 3, SBML and CellDesigner formats
        • Export to BioPAX 3, SBML and CellDesigner formats after user manipulations
        • Conversion between standards (CellDesigner->BioPAX 3, BioPAX 3 ->SBML)
        • Full support of BioPAX 3 information (reaction network, interaction network, pathway structure, references), concept of BioPAX 3 index and network interfaces
        • Browsing, editing, extracting parts, merging BioPAX 3 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 3 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://binom.curie.fr/
        --

        Version: 2.0
        Release Date: 2012-04-26
        Authors: Eric Bonnet ,Institut Curie
        Laurence Calzone ,Institut Curie
        Daniel Rovera ,Institut Curie
        Emmanuel Barillot ,Institut Curie
        Eric Viara ,Institut Curie
        Andrei Zinovyev ,Institut Curie
        Release notes: http://binom.curie.fr
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (24.05MB)
        Download source: http://binom.curie.fr

    • BNMatch

      • Description: The BNMatch plugin is designed to search a target network in an original network according to the given homologous tables and then vividly displays the two network graphs in canvas.
        Project website: http://code.google.com/p/bnmatch/
        Project website: http://code.google.com/p/bnmatch/
        --

        Version: 1.0
        Reference: Yu L, Xie J, Cheng X, Zhang W. "BNMatch: A cytoscape plugin for querying and visualizing matched similar networks", 2010 International Conference on Computer and Computational Intelligence (ICCCI 2010), Nanning, China. 2010.
        Release Date: 2010-01-01
        Authors: Lei Yu ,Shanghai University
        Jiang Xie ,Shanghai University
        Release notes: click here
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (234.5KB)
        Download source: http://code.google.com/p/bnmatch/
        --

        Version: 1.1
        Reference: Yu L, Xie J, Cheng X, Zhang W. "BNMatch: A cytoscape plugin for querying and visualizing matched similar networks", 2010 International Conference on Computer and Computational Intelligence (ICCCI 2010), Nanning, China. 2010.
        Release Date: 2012-01-01
        Authors: Lei Yu ,Shanghai University
        Jiang Xie ,Shanghai University
        Release notes: click here
        Verified to work in: 2.7,2.8
        Download Jar/zip: click here (238.4KB)
        Download source: http://code.google.com/p/bnmatch/

    • 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
        Authors: 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
        Authors: 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)


    • CalculateNodeDegree

      • Description: This plugin calculates and displays the degree of the presently selected node. Note: This plugin will only calculate the degree of one node at a time.
        Project website: N/A
        License: click here

        --

        Version: 1.0
        Reference: N/A
        Release Date: 2009-07-09
        Authors: D. Charles D. Plubell ,Tsinghua University/University of Southern California

        Release notes: N/A
        Note: This plugin calculates and displays the degree of the presently selected node. Note: This plugin will only calculate the degree of one node at a time. A very simple plugin.
        Download Jar/zip: click here (4.8KB)
        Download source: N/A

    • ChemViz
    • 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
        Authors: 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
        Authors: 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
        Authors: Jan Baumbach ,Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (17.7KB)


    • 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
        Authors: 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
        Authors: 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
        Authors: Jan Baumbach ,Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (15.5KB)


    • 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
        Authors: Matthias Reimann ,BIOTEC, Technische Universitt Dresden
        Verified to work in: 2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • CyThesaurus-ID-Mapping
    • Cytomcl

      • Description: A wrapper for the MCL clustering algorithm.
        CytoMCL allows users to cluster networks by using the markov clustering by Van Dongen. (http://micans.org/mcl)

        Clusters, i.e. strongly connected subnetworks, may represent protein complexes.


        Project website: http://bioingegneria.unicz.it/cytomcl/
        License: click here

        --

        Version: 1.0
        Release Date: 0000-00-00
        Authors: Pietro Hiram Guzzi ,Bioinformatics Laboratory, Magna Graecia University of Catanzaro
        Ernesto Puleo ,Bioinformatics Laboratory, Magna Graecia University of Catanzaro
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.
        --

        Version: 1.0
        Release Date: 2010-06-01
        Authors: Pietro Hiram Guzzi Mario Cannataro ,UMG
        Ernesto Puleo ,UMG Student
        Release notes: http://bioingegneria.unicz.it/cytomcl/
        Verified to work in: 2.6
        Note: Linux version
        Download Jar/zip: click here (105.4KB)
        Download source: http://bioingegneria.unicz.it/cytomcl/
        --

        Version: 1.1
        Release Date: 2010-06-05
        Authors: Pietro Hiram Guzzi Mario Cannataro ,MAGNA GRAECIA UNIVERSITY OF CATANZARO
        Ernesto Puleo ,UMG STUDENT
        Release notes: http://bioingegneria.unicz.it/cytomcl/
        Verified to work in: 2.5,2.6,2.7
        Download Jar/zip: click here (1.22MB)
        Download source: http://bioingegneria.unicz.it/cytomcl/
        --

        Version: 1.1
        Release Date: 2010-08-13
        Authors: Pietro Hiram Guzzi Mario Cannataro ,MAGNA GRAECIA UNIVERSITY OF CATANZARO
        Ernesto Puleo ,UMG STUDENT
        Release notes: http://bioingegneria.unicz.it/cytomcl/
        Verified to work in: 2.5,2.6,2.7
        Note: 1.1 (this version fix some bugs of the 1.1 version)
        Download Jar/zip: click here (1.49MB)
        Download source: http://bioingegneria.unicz.it/cytomcl/

    • 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
        Authors: 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/

    • DisplayNetworkFromFlatFile

      • Description: It displays a Network From a Flat File
        --

        Version: 1.0
        Release Date: 2010-11-03
        Authors:
        Verified to work in: 2.7
        Download Jar/zip: click here (3.9KB)


    • DualLayout

      • Description: Layout Network Comparison Toolkit output file. Still an experimental version.
        Project website: http://cytoscape.org
        License: click here

        --

        Version: 0.01
        Release Date: 2009-08-06
        Authors: Ryan Kelley ,UCSD
        Keiichiro Ono ,UCSD
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (25.2KB)


    • DvD

      • Description: Drug versus Disease (DvD) provides a pipeline, availablethrough R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated (enriched) profiles can be used to generate hypotheses of drug-repurposing whilst positively correlated (enriched) profiles may be used to infer side-effects of drugs. DvD provides a pipeline for comparing drug and disease signatures with dynamic access to databases Array Express, GEO and data from the Connectivity Map.
        License: click here

        --

        Version: 1.0
        Release Date: 2012-11-07
        Authors: Clare Pacini ,EMBL-European Bioinformatics Institute
        Francesco Iorio ,EMBL-EBI and Wellcome Trust Sanger Institute
        Emanuel Goncalves ,EMBL-European Bioinformatics Institute
        Murat Iskar ,European Molecular Biology Laboratory
        Thomas Klabunde ,Sanofi Aventis
        Peer Bork ,European Molecular Biology Laboratory
        Julio Saez-Rodriguez ,EMBL-European Bioinformatics Institute
        Verified to work in: 2.8
        Download Jar/zip: click here (110.23MB)


    • edgeLengthPlugin
    • 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
        Authors: 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.

    • FM3

      • Description: one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul(2005).
        --

        Version: 1.1
        Reference: stefan hachul, michael juenger: a provably fast multipole method, 2005
        Release Date: 2010-10-13
        Authors: Di Chang ,University of Dortmund, Germany
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (115.3KB)


    • FunNetViz

      • Description: FunNetViz is a Cytoscape plug-in associated to FunNet tool for transcriptional interaction analysis. It provides important additional functionalities, including the selection of annotation systems as well as various parameters required for the analysis of networks and modules. Furthermore, it allows for interactional centrality assessment to facilitate exploration and visualization of important transcripts in co-expression networks. It is built upon the powerful Cytoscape open-source platform that includes other tools for biological network analysis and visualization, readily available to the scientific community.
        Project website: http://funnet.info/index.php?menu=9
        License: click here

        --

        Version: 1.0
        Release Date: 2010-07-01
        Authors: Edi Prifti, Karine Clement, Shakti Rielland, Corneliu Henegar and Jean-Daniel Zucker ,INSERM, UMR-S 872, Les Cordeliers, Eq. 7 Nutriomique, Paris - France;
        Verified to work in: 2.6.3
        Download Jar/zip: click here (14.39MB)


    • 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
        Authors: 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/
        --

        Version: 1.11
        Reference: Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. M.Clement-Ziza; C.Malabat; C.Weber; I.Moszer; T.Aittokallio; C.Letondal; S.Rousseau Bioinformatics 2009; doi: 10.1093/bioinformatics/btp464
        Release Date: 2009-08-05
        Authors: 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
        Release notes: click here
        Verified to work in: 2.4,2.5,2.6
        Download Jar/zip: click here (371KB)
        Download source: http://www.pasteur.fr/recherche/unites/Gim/genoscape/
        --

        Version: 1.2
        Reference: Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Clment-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S. Bioinformatics. 2009 Oct 1;25(19):2617-8
        Release Date: 2009-10-10
        Authors: 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
        Release notes: click here
        Verified to work in: 2.4,2.5,2.6
        Note: Update to be compliant with KEGG ftp modifications. The previous versions will not work anymore.
        Download Jar/zip: click here (373.7KB)


    • GraMoFoNe

      • Description: Plugin to resolve the GRAPH MOTIF problem : find connected occurrences of a motif (i.e. set or multiset of proteins) in a Protein Protein Interaction networks.
        Project website: http://igm.univ-mlv.fr/AlgoB/gramofone/
        License: click here

        --

        Version: 0.12
        Reference: Guillaume Blin, Florian Sikora, and Stphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. 2nd International Conference on Bioinformatics and Computational Biology (BICoB 2010). International Society for Computers and their Applications (ISCA). 24-26 March 2010. Note: To appear
        Release Date: 2010-03-10
        Authors: Blin,Sikora,Vialette ,University Paris-Est LIGM
        Verified to work in: 2.6
        Download Jar/zip: click here (4.93MB)
        Download source: http://igm.univ-mlv.fr/AlgoB/gramofone/program/gramofone.jar

    • GraphMLReader

      • Description: GraphML reader plugin. You can load basic information (network and attributes) from GraphML files. Experimental GraphML export function is also available for testing.
        License: click here

        --

        Version: 0.11
        Release Date: 2010-12-11
        Authors: Kozo Nishida ,NAIST
        Keiichiro Ono ,UCSD
        Release notes: http://code.google.com/p/graphmlreader/
        Verified to work in: 2.8
        Note: GraphMLReader currently doesn't support hypergraph
        Download Jar/zip: click here (24.6KB)
        Download source: http://code.google.com/p/graphmlreader/source/checkout

    • GroupTool
    • HyperEdgeEditor

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

        Version: 2.61
        Release Date: 2008-03-28
        Authors: 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
        Authors: 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
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Download Jar/zip: click here (162KB)

        --

        Version: 2.66
        Release Date: 2009-07-01
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6.3
        Download Jar/zip: click here (162.5KB)

        --

        Version: 2.68
        Release Date: 2011-05-25
        Authors: Allan Kuchinsky and Aditya Vailaya ,Agilent Labs
        Michael Creech ,Blue Oak Software
        Release notes: http://chianti.ucsd.edu/svn/csplugins/trunk/agilent/creech/HyperEdgeEditor/release-notes.html
        Verified to work in: 2.8
        Download Jar/zip: click here (187.9KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/agilent/creech/HyperEdgeEditor/

    • IgraphPlugin

      • Description: This plugin brings some of igraph's features into Cytoscape.
        Project website: http://plato.cgl.ucsf.edu/trac/GenMAPP/wiki/GerardoHuck
        License: click here

        --

        Version: 0.1
        Release Date: 2011-09-13
        Authors: Gerardo Huck ,Google Summer of Code 2011
        Release notes: click here
        Verified to work in: 2.8.1,2.8.2
        Download Jar/zip: click here (1.37MB)


    • KGMLReader

      • Description: Reader plugin for KEGG pathway datasets in KGML format. Visit Google Code Site for more information. If you have questions or feature request, please send them to cytoscape-discuss mailing list.
        --

        Version: 0.06
        Release Date: 2010-08-18
        Authors: Kozo Nishida ,Nara Institute of Science and Technology
        Keiichiro Ono ,UC, San Diego Department of Medicine
        Release notes: http://code.google.com/p/kgmlreader
        Verified to work in: 2.7
        Note: TogoWS client now has a custom User Agent property (Cytoscape KEGG/togoWS REST Client). Confirmed to work on Cytoscape 2.7. 2.8 compatible version will be released shortly.
        Download Jar/zip: click here (651KB)
        Download source: http://code.google.com/p/kgmlreader
        --

        Version: 0.10
        Release Date: 2011-04-27
        Authors: Kozo Nishida ,Nara Institute of Science and Technology
        Keiichiro Ono ,UC, San Diego Department of Medicine
        Release notes: http://code.google.com/p/kgmlreader
        Verified to work in: 2.8
        Note: Minor update version for Cytoscape 2.8.x series.
        Download Jar/zip: click here (613.3KB)
        Download source: http://code.google.com/p/kgmlreader
        --

        Version: 0.11
        Release Date: 2011-04-27
        Authors: Kozo Nishida ,Nara Institute of Science and Technology
        Keiichiro Ono ,UC, San Diego Department of Medicine
        Release notes: http://code.google.com/p/kgmlreader
        Verified to work in: 2.8
        Note: Minor bug fix version.
        Download Jar/zip: click here (694.5KB)
        Download source: https://github.com/kozo2/kgmlreader
        --

        Version: 0.15
        Release Date: 2012-04-10
        Authors: Kozo Nishida ,Nara Institute of Science and Technology
        Keiichiro Ono ,UC, San Diego Department of Medicine
        Release notes: http://cytoscape.github.com/kgmlreader/
        Verified to work in: 2.8
        Note: Everyone should update to this version because KEGG public FTP server is no longer available.
        Download Jar/zip: click here (876KB)
        Download source: https://github.com/cytoscape/kgmlreader

    • MetaNodePlugin2
    • NatureProtocolsWorkflow

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

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


    • NetTwo

      • Description: NetTwo implements algorithms measuring network-based functional relationship between two gene sub-networks. NetTwo provides three different measures of functional similarity between genes sub-networks, along with method for evaluating statistical significance from random sample genes in the network.
        License: click here

        --

        Version: 0.1
        Release Date: 2012-07-24
        Authors: Subhankar Mukherjee ,Samsung India Software Operations
        TaeJin Ahn ,Samsung Advanced Institute of Technology
        Release notes: click here
        Note: Supplementary materials may be provided upon requests.
        Download Jar/zip: click here (364.3KB)


    • NetworkEvolution

      • Description: The plugin allows the user to map selected network regions to interactomes of evolutionary predecessors and descendants, making it possible to interactively inspect evolutionary changes and observe both conservation and diversification of specific network components.
        Project website: http://bioputer.mimuw.edu.pl/modevo
        --

        Version: 2.1
        Release Date: 2010-03-05
        Authors: Michal Wozniak ,University of Warsaw
        Janusz Dutkowski ,University of Warsaw

        Release notes: click here
        Verified to work in: 2.6.3
        Download Jar/zip: click here (499.1KB)


    • 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
        Authors: 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.

    • OrthoNets

      • Description: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. OrthoNets is a Cytoscape plugin that displays PPI networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism.
        Project website: http://wodaklab.org/orthonets/
        --

        Version: 1.0
        Release Date: 2010-12-06
        Authors: Wodak Lab
        Verified to work in: 2.7,2.8
        Note: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays PPI networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism.
        Download Jar/zip: click here (2.18MB)
        Download source: http://wodaklab.org/orthonets

    • PICRClient
    • 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
        Authors: 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
        Authors: 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/

    • 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. For zip file for CellCircuits website, publication information can also be included in the Zip file. Please look at this page (http://www.cellcircuits.org/search/zipFormatDefinition.html) for the directory structure of ZIP file.
        --

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

        --

        Version: 3.1
        Release Date: 2008-10-15
        Authors: 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/
        --

        Version: 3.2
        Release Date: 2009-09-30
        Authors: Peng-Liang Wang ,UCSD
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (124.4KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/SessionForWebPlugin/

    • structureViz
    • SubnetworkCreator
    • VennDiagramGenerator

      • Description: This plugin generates a Venn/Euler diagram of shared nodes for a selection of networks. The diagram generation algorithm is described in Exact and Approximate Area-proportional Circular Venn and Euler Diagrams by Leland Wilkinson.
        --

        Version: 1.0
        Release Date: 2010-09-15
        Authors: Leland Wilkinson ,University of Illinois, Chicago
        Mike Smoot ,UC San Diego
        Release notes: click here
        Verified to work in: 2.5,2.6,2.7
        Download Jar/zip: click here (29.1KB)

        --

        Version: 1.02
        Release Date: 2011-01-03
        Authors: Leland Wilkinson ,University of Illinois, Chicago
        Mike Smoot ,UC San Diego
        Release notes: click here
        Verified to work in: 2.5,2.6,2.7,2.8
        Download Jar/zip: click here (29.1KB)

        --

        Version: 1.4
        Release Date: 2012-02-09
        Authors: Leland Wilkinson ,University of Illinois, Chicago
        Mike Smoot ,UC San Diego
        Verified to work in: 2.5,2.6,2.7,2.8
        Download Jar/zip: click here (31.9KB)


    • VennDiagrams

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Old Plugins

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

Writing Your Own Plugins

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

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.

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.