About Cytoscape Plugins:
Cytoscape includes a flexible Plugin architecture that enables developers to add extra
functionality beyond that provided in the core. Plugins also provide a convenient place
for testing out new Cytoscape features. As more Plugins become available, they will be
listed on this page, and posted to our
cytoscape-announce
mailing list.
The plugins on this page are categorized into 7 sections:
Current Cytoscape 2.x plugins
Expand All
Collapse All
- Core -- Cytoscape core (0)
- Analysis -- Used for analyzing existing networks (21)
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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
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Version: 1.5
Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
Release Date: 2007-11-16
Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. , Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL) Salama
Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
Verified to work in: 2.5
Note: Compatible with Cytoscape v2.5. Versions for CytoScape v2.4 and v2.3 are available in the Web page (http://bioinfow.dep.usal.es/apid/apid2net.html).
Download Jar/zip: click here (413.2KB)
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Version: 1.51
Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
Release Date: 2007-12-20
Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
Verified to work in: 2.5
Download Jar/zip: click here (413.5KB)
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Version: 1.52
Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
Release Date: 2008-05-14
Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
Verified to work in: 2.6
Download Jar/zip: click here (414.4KB)
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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/
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Version: 1.0
Release Date: 2008-09-17
Released by: Annabel Bourdé , Centre INRIA Rennes Bretagne Atlantique, IRISA
Carito Guziolowski , Centre INRIA Rennes Bretagne Atlantique, IRISA
Verified to work in: 2.6
Download Jar/zip: click here (2.19MB)
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CABIN
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CentiScaPe
Description: CentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.
Project website: http://profs.sci.univr.it/~scardoni/centiscape/centiscapepage.php
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Version: 1.0
Release Date: 2008-05-19
Released by: Giovanni Scardoni, Michele Petterlini , Center for Biomedical Computing (CBMC), University of Verona
Carlo Laudanna , CBMC, Department of Pathology, University of Verona
Release notes: http://profs.sci.univr.it/~scardoni/centiscape/centiscapedownload.php
Verified to work in: 2.6
Download Jar/zip: click here (3.79MB)
Download source: http://profs.sci.univr.it/~scardoni/centiscape/centiscapedownload.php
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clusterExplorerPlugin
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clusterMaker
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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
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Version: 1.0
Release Date: 2008-02-13
Released by: Jan Baumbach , Bielefeld University
Verified to work in: 2.5
Download Jar/zip: click here (17.8KB)
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Version: 1.1
Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
Release Date: 2008-04-21
Released by: Jan Baumbach , Bielefeld University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (17.7KB)
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Version: 1.101
Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
Release Date: 2008-04-21
Released by: Jan Baumbach , Bielefeld University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (17.7KB)
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dynamicXpr
Description: A Plug-In that colors nodes according to their expression across many conditions, as in a movie
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Version: 1.2
Release Date: 2008-03-18
Released by: Iliana Avila-Compillo , ISB
John "Scooter" Morris , UCSF
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (18.4KB)
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Version: 1.3
Release Date: 2008-09-18
Released by: Iliana Avila-Compillo , ISB
John "Scooter" Morris , UCSF
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (18.4KB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/dynamicXpr
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EnhancedSearch
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jActiveModules
Description: ActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.
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Version: 2.2
Release Date: 2007-03-23
Released by: Ryan M. Kelley , UCSD
Verified to work in: 2.5
Download Jar/zip: click here (110.3KB)
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Version: 2.21
Release Date: 2008-03-31
Released by: Ryan Kelley , UCSD
Verified to work in: 2.5,2.6
Download Jar/zip: click here (113.8KB)
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Version: 2.22
Release Date: 2008-06-10
Released by: Ryan Kelley , UCSD
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (115.1KB)
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Version: 2.23
Release Date: 2008-08-13
Released by: Ryan Kelley , UCSD
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (115.4KB)
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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.
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Version: 1.2
Release Date: 2007-02-15
Released by: Gary Bader , MSKCC
Verified to work in: 2.5
Download Jar/zip: click here (86.5KB)
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Version: 1.3
Release Date: 2007-12-07
Released by: Gary Bader, Vuk Pavlovic , University of Toronto
Verified to work in: 2.5
Download Jar/zip: click here (95.3KB)
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NetAtlas
Description: NetAtlas is a Java plugin application designed to use tissue gene expression data to filter genes in a cellular signaling network. The NetAtlas plugin allows the creation of tissue-defined networks, identification of network components that are more highly expressed in specific tissues, and the identification of network components that show correlated expression across tissues. The default tissue gene expression data available in NetAtlas is from SymAtlas and contains human, mouse, and rat gene expression data for a wide range of tissues and has been previously published by the Genomics Institute of the Novartis Research Foundation. The user is also allowed to import their own tissue gene expression data in text file format.
Project website: http://sourceforge.net/projects/netatlas/
License: click here
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Version: 1.1
Reference: Longlong Yang, John R. Walker, John B. Hogenesch and Russell S. Thomas
NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression. In Silico Biol. 8:0005, 2007.
http://www.bioinfo.de/isb/2007/08/0005/
Release Date: 2007-11-20
Released by: Russell S. Thomas , The Hamner Institutes for Health Sciences
Longlong Yang , The Hamner Institutes for Health Sciences
Release notes: http://sourceforge.net/projects/netatlas/
Verified to work in: 2.4,2.5
Note: A tutorial can be found at: http://sourceforge.net/projects/netatlas/
Download Jar/zip: click here (985.3KB)
Download source: http://sourceforge.net/projects/netatlas/
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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
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Version: 2.1
Release Date: 2008-11-07
Released by: A. Ferro , University of Catania
R. Giugno , University of Catania
G. Pigola , University of Catania
A. Pulvirenti , University of Catania
D. Skripin , University of Catania
G.D. Bader , University of Toronto
D. Shasha , New York University
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (1.59MB)
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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
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Version: 2.5.1
Reference: Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M.
Computing topological parameters of biological networks.
Bioinformatics, 24(2):282-284, 2008
Release Date: 2007-12-11
Released by: Yassen Assenov , Max Planck Institute for Informatics
Mario Albrecht , Max Planck Institute for Informatics
Verified to work in: 2.5
Download Jar/zip: Please follow the Project URL to download and install manually.
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Version: 2.6.1
Reference: Reference: Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284, 2008
Release Date: 2008-07-10
Released by: Yassen Assenov , Max Planck Institute for Informatics
Mario Albrecht , Max Planck Institute for Informatics
Verified to work in: 2.6
Download Jar/zip: Please follow the Project URL to download and install manually.
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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
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Version: 2.2
Release Date: 2007-06-01
Released by: Tian Xia, , Program of Bioinformatics and Computational Biology,Iowa state university
Julie Dickerson , Program of Bioinformatics and Computational Biology,2Department of Electrical and Computer Engineering,Iowa state university
Verified to work in: 2.4,2.5,2.6
Download Jar/zip: Please follow the Project URL to download and install manually.
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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).
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Version: 1.0
Release Date: 2008-06-16
Released by: Samad Lotia and Han-Yu Chuang , UCSD
Verified to work in: 2.5,2.6
Download Jar/zip: click here (164KB)
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Version: 1.1
Release Date: 2008-10-10
Released by: Samad Lotia and Han-Yu Chuang , UCSD
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (165KB)
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RandomNetworks
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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
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Version: 0.4
Reference: To appear in BMC Bioinformtics
Release Date: 2008-02-07
Released by: Andrea Splendiani , University of Rennes 1
, Leaf Bioscience s.r.l.
Verified to work in: 2.5
Download Jar/zip: Please follow the Project URL to download and install manually.
Download source: http://www.bioinformatics.org/rdfscape/
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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
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Version: 1.1
Release Date: 2007-07-25
Released by: Marcio Rosa da Silva
Verified to work in: 2.4,2.5
Download Jar/zip: click here (8KB)
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structureViz
Description: This plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.
Project website: http://www.rbvi.ucsf.edu/Research/cytoscape/structureViz.html
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Version: 1.0
Release Date: 2007-05-01
Released by: John "Scooter" Morris UCSF Resource for Biocomputing, Visualization, and Informatics
Verified to work in: 2.5
Download Jar/zip: click here (67.8KB)
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Version: 1.2
Reference: Morris, Huang, Babbitt, Ferrin. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1;23(17):2345-7
Release Date: 2008-03-18
Released by: John "Scooter" Morris , UCSF
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (74.1KB)
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Version: 1.3
Reference: Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10.
Release Date: 2008-09-18
Released by: John "Scooter" Morris , UCSF
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (77.8KB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/structureViz
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VistaClaraPlugin
Description: A visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.
License: click here
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Version: 1.0
Reference: The following paper describes the original standalone implementation on which this plugin is based:
R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, 167-174.
http://doi.acm.org/10.1145/967900.967935
Release Date: 2008-04-09
Released by: Robert Kincaid and Allan Kuchinsky , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Note: VistaClara provides a more graphical and interactive alternative to the standard attribute browser. Enhanced coordination between the tabular view and the network view is also supported. VistaClara is designed primarily ratio-based expression data, but has been used successfully for other data types.
Download Jar/zip: click here (777.3KB)
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Version: 1.01
Reference: The following paper describes the original standalone implementation on which this plugin is based: R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, 167-174. http://doi.acm.org/10.1145/967900.967935
Release Date: 2008-07-28
Released by: Robert Kincaid and Allan Kuchinsky , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (681.9KB)
- Network and Attribute I/O -- Used for importing networks and attributes in different file formats (14)
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BiNoM
Description: BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. - Import of BioPAX, SBML and CellDesigner formats
- Export to BioPAX, SBML and CellDesigner formats after user manipulations
- Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
- Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces
- Browsing, editing, extracting parts, merging BioPAX files with network graph interface
- Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
- Support of generating network modular view
- BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
- Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)
Project website: http://bioinfo.curie.fr/projects/binom
License: click here
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Version: 1.0
Reference: Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2007. Accepted in Bioinformatics.
Release Date: 2007-09-01
Released by: Andrei Zinovyev , Institut Curie
Eric Viara , Institut Curie
Laurence Calzone , Institut Curie
Emmanuel Barillot , Institut Curie
Release notes: http://bioinfo.curie.fr/projects/binom
Verified to work in: 2.5
Note: The jar provided is dependent on many other jars. For self-containing versions of jar, visit http://bioinfo.curie.fr/projects/binom
Download Jar/zip: click here (1.26MB)
Download source: http://bioinfo.curie.fr/projects/binom/docs/BiNoM_src.zip
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BiomartClient
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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.
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Version: 2.0
Reference: Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss and Richard Bonneau BioNetBuilder: automatic integration of biological networks
Bioinformatics 2007 23(3):392-393; doi:10.1093/bioinformatics/btl604
Release Date: 2008-06-18
Released by: Jay Konieczka , University of Arizona
Kevin Drew , Courant Institute, NYU.
Release notes: http://err.bio.nyu.edu/cytoscape/bionetbuilder/index.php
Verified to work in: 2.6
Download Jar/zip: click here (2.21MB)
Download source: https://err.bio.nyu.edu/svn/bionetbuilder/
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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
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Version: 1.0
Release Date: 2008-02-13
Released by: Jan Baumbach , Bielefeld University
Verified to work in: 2.5
Download Jar/zip: click here (15.4KB)
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Version: 1.1
Release Date: 2008-04-21
Released by: Jan Baumbach , Bielefeld University
Verified to work in: 2.6
Download Jar/zip: click here (15.5KB)
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Version: 1.101
Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
Release Date: 2008-04-21
Released by: Jan Baumbach , Bielefeld University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (15.5KB)
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DroID
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GPML-Plugin
Description: The GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways
See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.
Project website: http://www.pathvisio.org/Cytoscape_plugin
License: click here
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Version: 0.1
Release Date: 2008-01-08
Released by: Thomas Kelder , Maastricht University
Verified to work in: 2.5
Download Jar/zip: click here (382.4KB)
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Version: 0.4
Release Date: 2008-08-21
Released by: Thomas Kelder , Maastricht University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (4.8MB)
Download source: http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/cytoscape-gpml/
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Version: 0.2
Release Date: 2008-02-20
Released by: Thomas Kelder , Maastricht University
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (417.5KB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/thomas/gpml/
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Version: 0.3
Release Date: 2008-05-27
Released by: Thomas Kelder , Maastricht University
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (609.8KB)
Download source: http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/cytoscape-gpml/
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Version: 0.5
Release Date: 2008-10-09
Released by: Thomas Kelder , Maastricht University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (4.6MB)
Download source: http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/cytoscape-gpml/
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Version: 0.6
Release Date: 2008-11-14
Released by: Thomas Kelder , Maastricht University
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (4.62MB)
Download source: http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/cytoscape-gpml/
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IntActWSClient
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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
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Version: 2.0
Reference: Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. (2007) "Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together." Nucleic Acids Res. 35(Database issue):D566-71. Epub 2006 Nov 27.
Release Date: 2007-08-31
Released by: Jing Gao, Alex Ade
Verified to work in: 2.5
Download Jar/zip: click here (91.7KB)
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Version: 2.1
Release Date: 2007-10-08
Released by: Jing Gao, Alex Ade and David States , University of Michigan CCMB/NCIBI
Verified to work in: 2.5
Download Jar/zip: click here (98.9KB)
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Version: 2.2
Release Date: 2008-04-14
Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
Verified to work in: 2.5,2.6
Download Jar/zip: click here (107.3KB)
Download source: http://mimiplugin.ncibi.org/
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Version: 3.0
Release Date: 2008-07-01
Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
Verified to work in: 2.6
Download Jar/zip: click here (140.8KB)
Download source: http://mimiplugin.ncibi.org/
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Version: 3.01
Release Date: 2008-08-12
Released by: Jing Gao, Alex Ade, David States , CCMB/NCIBI University of Michigan
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (226KB)
Download source: http://mimiplugin.ncibi.org/
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NCBIClient
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NCBIEntrezGeneUserInterface
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PICRClient
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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
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Version: 1.0
Release Date: 0000-00-00
Released by: Willem P.A. Ligtenberg , BioModeling & bioInformatics, Department of BioMedical Engineering, Eindhoven University of Technology
Verified to work in: 2.6
Download Jar/zip: Please follow the Project URL to download and install manually.
Download source: http://bmi.bmt.tue.nl/reconn/ReConn_source.zip
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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.
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Version: 3.0
Release Date: 2008-01-30
Released by: Samad Lotia , UCSD
Verified to work in: 2.5
Download Jar/zip: click here (68.3KB)
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Version: 3.1
Release Date: 2008-10-15
Released by: Samad Lotia , UCSD
Verified to work in: 2.5,2.6
Download Jar/zip: click here (108.7KB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/SessionForWebPlugin/
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SFLDLoader
- Network Inference -- Used for inferring new networks (6)
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AgilentLiteratureSearch
Description: Creates a CyNetwork based on searching the scientific literature.
Project website: http://www.agilent.com/labs/research/litsearch.html
License: click here
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Version: 2.55
Release Date: 2007-07-17
Released by: Allan Kuchinsky and Aditya Vailaya, , Agilent Labs
Michael Creech, , Blue Oak Software
Verified to work in: 2.5
Note: See plugin.props file for various field info.
Download Jar/zip: click here (4.14MB)
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Version: 2.68
Release Date: 2008-03-28
Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (4.28MB)
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Version: 2.69
Release Date: 2008-09-08
Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (4.28MB)
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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
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Version: 1.0
Reference: Morcos, F., Lamanna, C., Sikora, M. and Izaguirre, J. Cytoprophet: A Cytoscape plug-in for protein and domain interaction network inference. Bioinformatics. (Submitted)
Release Date: 2008-04-18
Released by: Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre , University of Notre Dame
Release notes: http://cytoprophet.cse.nd.edu/
Verified to work in: 2.6
Note: More information, documentation and the API are available at the website (http://cytoprophet.cse.nd.edu/).
Download Jar/zip: click here (61.1KB)
Download source: http://cytoprophet.cse.nd.edu/
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DomainGraph
This plugin is not available through the Plugin Manager!
Description: DomainGraph decomposes a user-given protein interaction network into their underlying domain-domain interactions.
Gene interaction networks can be also be loaded to visualize all their transcripts and domains compositions.
For the networks, DomainGraph accepts UniProt, Ensembl and Entrez identifiers.
Several structure-based and predicted domain interaction datasets are provided with the plugin.
Additionally, DomainGraph allows integrating Affymetrix Exon Array data (raw data or preprocessed via AltAnalyze).
The gene, protein and domain nodes are then colored according to the expression data and differential expression is highlighted.
Project website: http://domaingraph.bioinf.mpi-inf.mpg.de
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Version: 1.0
Release Date: 2008-08-15
Released by: Dorothea Emig, Thomas Lengauer, Mario Albrecht , Max Planck Institute for Informatics
Melissa S. Cline , Department of Molecular Cell and Developmental Biology, UCSC
Verified to work in: 2.5,2.6
Download Jar/zip: Please follow the Project URL to download and install manually.
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Version: 2.0
Reference: Emig, D, Cline, MS, Lengauer, T, Albrecht, M, Integrating expression data with domain interaction networks. Bioinformatics, 2008, 24(21):2546-2548.
Release Date: 2008-11-17
Released by: Dorothea Emig,Thomas Lengauer,Mario Albrecht , Max Planck Institute for Informatics
Melissa S. Cline , UCSC
Anne Kunert,Karsten Klein,Petra Mutzel , University of Dortmund
Nathan Salomonis , The Gladstone Institutes
Verified to work in: 2.5,2.6
Download Jar/zip: click here (3.26MB)
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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
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Version: 1.01
Release Date: 2008-10-07
Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , Memorial Sloan-Kettering Cancer Center
Chris Sander , Memorial Sloan-Kettering Cancer Center
Shirley Hui and Laetitia Morrison , University of Toronto
Release notes: click here
Verified to work in: 2.5,2.6
Note: This is an update to the previously submitted version 1.0 that contains a bug fix and some updated author information.
Download Jar/zip: click here (94.9KB)
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Version: 1.0
Release Date: 2008-09-24
Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , MSKCC
Shirley Hui and Laetitia Morrison , University of Toronto
Release notes: click here
Verified to work in: 2.5,2.6
Download Jar/zip: click here (94.9KB)
Download source: http://www.baderlab.org/Software/ExpressionCorrelation
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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
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Version: 2.1
Reference: Jourdan F, Breitling R, Barrett M and Gilbert D. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2007) In press Bioinformatics.
Release Date: 2007-07-24
Released by: Fabien Jourdan , INRA
Release notes: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
Verified to work in: 2.5
Note: MetaNetter is a plugin for the inference of metabolomic networks based on high resolution mass spectrometry data.
Download Jar/zip: click here (67.2KB)
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MONET
Description: MONET is a genetic interaction network inference algorithm based on Bayesian networks, which enables reliable network inference with large-scale data(ex. microarray) and genome-scale network inference from expression data. Network inference can be finished in reasonable time with parallel processing technique with supercomputing center resources.
Project website: http://delsol.kaist.ac.kr/~monet/home/index.html
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Version: 1.1
Reference: Phil Hyoun Lee, Doheon Lee (2005) Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics. 21, 2739-2747.
Release Date: 2007-12-20
Released by: Younghoon Kim , BISL Lab, Dept. of Bio and Brain Engineering, KAIST
Doheon Lee , BISL Lab, Dept. of Bio and Brain Engineering, KAIST
Release notes: http://delsol.kaist.ac.kr/~monet/home/news.html
Verified to work in: 2.3,2.4,2.5
Download Jar/zip: click here (1.97MB)
Download source: http://delsol.kaist.ac.kr/~monet/home/downloads.html
- Functional Enrichment -- Used for functional enrichment of networks (4)
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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/
License: click here
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Version: 2.1
Reference: Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449.
Release Date: 2007-08-29
Released by: Steven Maere , VIB
Martin Kuiper , VIB
Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO
Verified to work in: 2.3,2.4,2.5
Download Jar/zip: click here (11.19MB)
Download source: http://www.psb.ugent.be/cbd/papers/BiNGO
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Version: 2.3
Reference: Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449.
Release Date: 2008-08-05
Released by: Steven Maere , VIB
Martin Kuiper , VIB
Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO/
Verified to work in: 2.6
Download Jar/zip: click here (12.05MB)
Download source: http://www.psb.ugent.be/cbd/papers/BiNGO/
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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
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Version: 1.0
Release Date: 2007-08-28
Released by: Alexander Pico, Kristina Hanspers, Nathan Salomonis , The Gladstone Institutes
Allan Kuchinsky , Agilent Technologies
Verified to work in: 2.5
Download Jar/zip: click here (881.2KB)
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Version: 1.1
Release Date: 2008-03-12
Released by: Alexander Pico, Kristina Hanspers, Nathan Salomonis , The Gladstone Institutes
Allan Kuchinsky , Agilent Technologies
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (887.8KB)
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CommonAttributes
Description: Find attributes shared between selected nodes.
Requires background knowledge network files available at the CommonAttributes download site hanalyzer.sourceforge.net.
License: click here
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Version: 1.3
Reference: Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner Jr. Priyanka Kasliwa, Ron Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter, "3R Systems for Biomedical Discovery Acceleration, with Applications to Craniofacial Development" PLoS Computational Biology, submitted.
Release Date: 2008-08-12
Released by: Ronald Schuyler , University of Colorado Health Sciences Center
Release notes: hanalyzer.sourceforge.net
Verified to work in: 2.5,2.6
Download Jar/zip: click here (14.2KB)
Download source: hanalyzer.sourceforge.net
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HyperEdgeEditor
Description: Add, remove, and modify HyperEdges in a Cytoscape Network.
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Version: 2.61
Release Date: 2008-03-28
Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (161.5KB)
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Version: 2.62
Release Date: 2008-04-03
Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
Michael Creech , Blue Oak Software
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (161.5KB)
- Communication/Scripting -- Used for communicating with or scripting Cytoscape (7)
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CyGoose
Description: The CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle.
As of version 2.6 of the plugin, it works with the current (2007-04) revision of the Gaggle API.
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Version: 2.5
Release Date: 2007-07-25
Released by: Sarah Killcoyne Institute for Systems Biology
John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
Verified to work in: 2.4,2.5
Download Jar/zip: click here (1.11MB)
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Version: 2.6
Release Date: 2007-10-29
Released by: Sarah Killcoyne and Dan Tenenbaum , Institute for Systems Biology
John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
Release notes: click here
Verified to work in: 2.5
Download Jar/zip: click here (1.06MB)
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GroovyScriptingEngine
Description: Scripting Engine based on Grooby 1.5.6 implementation.
This plugin is for technology evaluation purpose ONLY! Totally experimental.
License: click here
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Version: 0.01
Release Date: 2008-09-25
Released by: Keiichiro Ono , UCSD Bioengineering
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (6.2MB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/kono/GroovyEnginePlugin
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JavaScriptEngine
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MiSink
Description: Network interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).
Project website: http://dip.doe-mbi.ucla.edu/dip/Software.cgi
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Version: 2.00
Release Date: 2007-07-24
Released by: Lukasz Salwinski UCLA-DOE Institute for Genomics and Proteomics
Verified to work in: 2.5
Download Jar/zip: click here (90.1KB)
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Version: 2.03
Release Date: 2007-11-21
Released by: Lukasz Salwinski , UCLA
Verified to work in: 2.5
Download Jar/zip: click here (76KB)
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Version: 2.04
Reference: Salwinski L, Eisenberg D. The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. Bioinformatics 23:2193-5 (2007)
Release Date: 2008-05-28
Released by: Lukasz Salwinski , UCLA
Verified to work in: 2.6
Note: This is a minor fix to make plugin compatible with Cytoscape 2.6. The downloaded file has been tested from a local download site. It seems to install/work fine with Cytoscape 2.6 and java 1.6 running on linux and windows xp
Download Jar/zip: click here (74.8KB)
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PythonScriptingEngine
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RubyScriptingEngine
Description: Scripting Engine based on jruby 1.1.4 implementation. This version includes bioruby 1.2.1. The console is now integrated with BioRuby Shell.
This plugin is for technology evaluation purpose ONLY! Totally experimental.
License: click here
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Version: 0.10
Release Date: 2008-10-02
Released by: Keiichiro Ono , UCSD Bioengineering
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (15.08MB)
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ScriptEngineManager
Description: Manages scripting engines following Cytoscape scripting engine guideline. Supporting Ruby, JavaScript, Groovy and Python.
This plugin is for technology evaluation purpose ONLY! Still experimental and design will be changed in the future versions.
License: click here
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Version: 0.04
Release Date: 2008-09-24
Released by: Keiichiro Ono , UCSD Bioengineering
Release notes: click here
Verified to work in: 2.6
Download Jar/zip: click here (172.3KB)
Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/kono/ScriptEngineManager/
- Other -- None of the above (13)
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addParentNeighbors
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AdvancedNetworkMerge
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batchTool
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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
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Version: 1.0
Release Date: 2007-11-02
Released by: Dorothea Emig, Thomas Lengauer, Mario Albrecht , Max Planck Institute for Informatics
Anne Kunert, Karsten Klein, Petra Mutzel , University of Dortmund
Verified to work in: 2.5
Download Jar/zip: Please follow the Project URL to download and install manually.
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edgeLengthPlugin
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edgeLister
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GroupTool
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MetaNodePlugin2
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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
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Version: 0.41
Release Date: 2008-01-16
Released by: Pekka Salmela , University of Turku, Finland
Olli S. Nevalainen , University of Turku, Finland
Tero aittokallio , University of Turku, Finland
Release notes: click here
Verified to work in: 2.5
Note: Updated description and developer information.
Download Jar/zip: click here (27.6KB)
Download source: http://kapsi.fi/~speque/mll-plugin/
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Version: 0.6
Release Date: 2008-07-06
Released by: Pekka Salmela , University of Turku, Finland
Olli S. Nevalainen , University of Turku, Finland
Tero aittokallio , University of Turku, Finland
Release notes: click here
Verified to work in: 2.5
Download Jar/zip: click here (72.2KB)
Download source: http://kapsi.fi/~speque/mll-plugin/
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NamedSelection
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NatureProtocolsWorkflow
Description: Groups all of the plugins required for the Nature Protocols workflow.
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Version: 1.0
Release Date: 2007-11-12
Released by: Allan Kuchinsky , Agilent Technologies
Verified to work in: 2.5,2.6
Download Jar/zip: click here (35.1KB)
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NeighborHighlight
Description: The plugin highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
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Version: 1.0
Release Date: 2008-08-26
Released by: Dorothea Emig, Mario Albrecht , Max Planck Institute for Informatics
Verified to work in: 2.6
Download Jar/zip: click here (15.8KB)
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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
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Version: 0.1
Release Date: 2008-04-30
Released by: Mike Smoot , UC San Diego
Verified to work in: 2.6
Download Jar/zip: click here (5.5KB)
Writing Your Own Plugins
If you are interested in building your own Cytoscape Plugin, check out the
Cytoscape Plugin Tutorial
Old Plugins
We also maintain a list of older Cytoscape 2.x plugins and
Cytoscape 1.x Plugins.
PlugIn License Policy:
Although the Cytoscape core application is distributed under a Library GNU Public License (LGPL),
plugins are separate works which use Cytoscape as a Java code library.
Plugins are therefore governed by independent software licenses
distributed with and specific to each plugin. The Cytoscape project
has no intent to capture plugins under the license terms of the core Cytoscape LGPL.