Thursday, October 30, 2008

Cytoscape and its plug-in

Cytoscape is so famous and popular recently in the biological network research field that Wikipedia has a term for it: Cytoscape in Wiki

Now, Cytoscape has 64 plugins in total; they are divided into 6 categories. With the list of plug-ins which are probably useful to use, the categories are:
  • Analysis -- Used for analyzing existing networks (20)
    • 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: 1.52
        Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
        Release Date: 2008-05-14
        Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
        Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
        Verified to work in: 2.6
        Download Jar/zip: click here (414.4KB)


    • BioQualiPlugin

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

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


    • CABIN
    • CentiScaPe
    • clusterExplorerPlugin
    • clusterMaker
    • 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: 1.101
        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)


    • dynamicXpr

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

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

        --

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

    • EnhancedSearch
    • jActiveModules

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

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


    • MCODE

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

        --

        Version: 1.3
        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)


    • NetAtlas

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

        --

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

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

    • OmicsViz

      • This plugin is not available through the Plugin Manager!

        Description: OmicsViz is a Cytoscape plugin (cytoscape2.4 and 2.5) dedicated to providing useful visualization and an integrated analysis tool for large-scale omics data. OmicsViz imports omics data into Cytoscape and visualizes it on a graph according to the change of gene experimental values (Figure 1). OmicsViz also provides a mapping function between two different species or between probe set and experimental names and node names in a network. For example, when you load an Arabidopsis metabolic pathway in Cytoscape and you have a Grape gene expression file, OmicsViz can associate the file with the Arabidopsis pathway based on gene mapping file which contains orthologous genes between the two species.
        Project website: http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm
        --
        Verified to work in: 2.4,2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • RandomNetworks
    • RDFScsape

      • This plugin is not available through the Plugin Manager!

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

        --

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

    • ShortestPath Plugin

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

        --

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

  • Network and Attribute I/O -- Used for importing networks and attributes in different file formats (14)
    • BiNoM

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

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

        --

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

    • BioNetBuilder

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

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

    • CoryneRegNetLoader

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

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

        If you use it for your research please cite:

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

        --

        --

        Version: 1.101
        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)

    • NCBIClient
    • NCBIEntrezGeneUserInterface
    • PICRClient
    • ReConn

      • This plugin is not available through the Plugin Manager!

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

        --

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

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

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

        --

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

        --

        Version: 2.68
        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)

        --

        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)


    • Cytoprophet

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

        --

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

    • DomainGraph

      • This plugin is not available through the Plugin Manager!

        Description: DomainGraph decomposes protein networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using the Affymetrix Human Exon 1.0 ST Array, which supports the analysis of alternative splicing events and the characterization of their effects on protein and domain interaction networks.
        Project website: http://domaingraph.bioinf.mpi-inf.mpg.de/
        --

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

    • ExpressionCorrelation

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

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

        --

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

    • MetaNetter

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

        --

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


    • MONET

      • Description: 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
        --

        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)
    • 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

        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/

    • 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

        --

        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

    • HyperEdgeEditor

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

        --

        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)
    • 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.

        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)


    • JavaScriptEngine

      • Description:

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


        License: click here

        --

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


    • MiSink

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

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


    • PythonScriptingEngine
    • RubyScriptingEngine
    • ScriptEngineManager
  • Other -- None of the above (13)
There are also several useful plugins in this categories, for example, AdvancedNetworkMerg which is for merging networks by set operations (union, intersection and difference), BiLayout which is for computing a bipartite network layout for two user-selected disjoint groups of nodes, edgeLengthPlugin which is for calculating edge lengths and stores them in an edge attribut, edgeLister which is for tracking edge selection( it will be very useful in the random trail), NamedSelection which is for "remembering" a group of selected nodes, and so on.


Here are some tutorials:
  1. Network analysis with Cytoscape, 15-16.12.2005
  2. Cytoscape Wiki -- Getting started guide
  3. Cytoscape Wiki -- Plugin tutorial. It will help us a lot in case we are to develop our approach into a software, say, a plugin of Cytoscape.
  4. Cytoscape Wiki -- User manual
Posted by at
Labels:

No comments:

Post a Comment

Subscribe to: Post Comments (Atom)