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    Cytoscape

    Category  Cross-Omics>Pathway Analysis/Tools

    Abstract  Cytoscape is an open-source bioinformatics software
    platform that enables researchers to form a visual map of complex
    biological networks increasing their understanding of molecular
    pathways and the biological causes of disease. Cytoscape allows you
    to visualize molecular interaction networks and integrates these
    interactions with gene expression profiles and other state data.
    Additional features are available as plugins. Plugins are available for
    network and molecular profiling analyses, new layouts, additional file
    format support and connection with databases. Plugins may be
    developed using the Cytoscape open Java software architecture by
    anyone and plugin community development is encouraged.

    Cytoscape supports the following features/capabilities:

    Input --

    1) Input and construct molecular interaction networks from raw
    interaction files [Simple Interaction Format (SIF) format] containing lists
    of protein-protein and/or protein-DNA interaction pairs. For yeast and
    other model organisms, large sources of pairwise interactions are
    available through the Biomolecular Interaction Network Database
    (BIND) and Gene Transcription Factor Database (TRANSFAC)
    databases. User-defined interaction types are also supported.

    2) Load and save previously-constructed interaction networks in the
    Graph Markup Language (GML) format.

    3) Load and save networks and node/edge attributes in an eXtensible
    Markup Language (XML) document format called XGMML (eXtensible
    Graph Markup and Modeling Language).

    4) Input mRNA expression profiles from tab- or space-delimited text
    files.

    5) Load and save arbitrary attributes on nodes and edges. For
    example, input a set of custom annotation terms for your proteins;
    create a set of confidence values for your protein-protein interactions;
    etc.

    6) Import gene functional annotations from the Gene Ontology (GO)
    and KEGG databases.

    7) Directly import GO Terms and annotations from Open Biomedical
    Ontologies (OBO) and Gene Association files.

    8) Load and save the 'state' of the Cytoscape session in a Cytoscape
    Session (.cys) file. The Cytoscape Session file includes networks,
    attributes (for node/edge/network), Desktop states (selected/hidden
    nodes and edges, window sizes), Properties, and Visual Styles.

    Visualization --

    1) Customize network data displays using advanced visual styles.

    2) View a superposition of gene expression ratios and p-values on the
    network. Expression data can be mapped to node color, label, border
    thickness, or border color, etc. according to user-configurable colors
    and visualization schemes.

    3) Layout networks in two (2) dimensions. A variety of layout algorithms
    are available, including cyclic and spring-embedded layouts.

    4) Zoom in/out and pan while browsing the network.

    5) Use the network manager to organize multiple networks. The
    structure created by the network manager can also be saved in a
    session file.

    6) Use the 'bird's eye' view to navigate large networks.

    7) Navigate large networks (100,000+ nodes and edges) created by
    our efficient rendering engine.

    Analysis --

    Plugins that are available for network and molecular profile analysis.
    For example:

    1) Filter the network to select subsets of nodes and/or interactions
    based on the current data. For instance, users may select nodes
    involved in a threshold number of interactions, nodes that share a
    particular GO annotation, or nodes whose gene expression levels
    change significantly in one or more conditions according to p-values
    loaded with the gene expression data.

    2) Find active subnetworks/pathway modules. The network is
    screened against gene expression data to identify connected sets of
    interactions, i.e. interaction subnetworks, whose genes show
    particularly high levels of differential expression. The interactions
    contained in each subnetwork provide hypotheses for the regulatory
    and signaling interactions in control of the observed expression
    changes.

    3) Find clusters (highly interconnected regions) in any network loaded
    into Cytoscape. Depending on the type of network, clusters may mean
    different things. For instance, clusters in a protein-protein interaction
    network have been shown to be protein complexes and parts of
    pathways. Clusters in a protein similarity network represent protein
    families.

    More info about 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.

    Current plugins are categorized into five (5) sections:

    1) Analysis Plugins - Used for analyzing existing networks.

    2) Network and Attribute I/O Plugins - Used for importing networks and
    attributes in different file formats.

    3) Network Inference Plugins - Used for inferring new networks.

    4) Functional Enrichment Plugins - Used for functional enrichment of
    networks.

    5) Communication/Scripting Plugins - Used for communicating with or
    scripting Cytoscape.

    System Requirements  

    Cytoscape is a Java application (Java SE 5 or 6 only) verified to run on
    Linux, Windows, and Mac OS X. Although not officially supported, other
    UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java
    version 5 or later is available for the platform.

    The system requirements for Cytoscape depend on the size of the
    networks the user wants to load, view and manipulate.

    Small NetworkVisualization
    1 GHz processor
    512 MB memory
    On board video graphics card
    XGA (1024x768) monitor

    Large Network Analysis/Visualization
    1 GHz processor as fast as possible
    2 GB+ memory
    High end graphics card
    Wide or dual monitor

    Manufacturer   

    The Cytoscape project is an ongoing collaboration between:

    The Institute for Systems Biology
    University of California at San Diego,
    Memorial Sloan Kettering Cancer Center
    Institut Pasteur
    Agilent Technologies
    University of California at San Francisco
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