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    BiologicalNetworks

    Category  Cross-Omics>Pathway Analysis/Tools

    Abstract  BiologicalNetworks is a Systems Biology software platform
    for biological pathways analysis, querying and visualization of gene
    regulation and protein interaction networks, metabolic and signaling
    pathways. It is equipped with filtering and visualization tools, to provide
    high quality, easily understood scientific presentations of your pathway
    analysis results.

    BiologicalNetworks includes PathSys (see G6G Product Number
    20068), a general-purpose scalable warehouse of biological
    information, which integrates over 20 curated and publicly contributed
    data sources, experimental biological data and PubMed data for the 8
    representative genomes ( S. cerevisiae, D.melanogaster, etc.).

    BiologicalNetworks is also supported with curated pathways from a
    number of public databases like KEGG and various scientific studies.

    BiologicalNetworks identifies relationships among genes, proteins,
    small molecules and other cellular objects, and draws pathways,
    linked to the original sources of information.

    BiologicalNetworks is equipped with an enhanced graphic
    manipulation and query language, data mining and filtering tools, a
    storage mechanism and a generic data-importing mechanism through
    schema-mapping.

    BiologicalNetworks Features/Capabilities:

    Build Pathways features - Assemble your pathway using multiple
    search algorithms:

    1) expend pathways; 2) find the shortest path between two genes or all
    the shortest paths covering a group of genes; 3) find only direct
    interactions; 4) find common targets or find common regulators; 5) find
    intersections with known curated pathways (for example with KEGG
    pathways).

    Use filtering to include in your pathway only specific types of biological
    objects, such as genes, proteins, complexes, small molecules,
    cellular processes and others.

    Use filtering to include in your pathway only specific types of biological
    interactions such as binding interactions, post-translational regulation,
    genetic interaction, expression regulation, enzymatic activity, molecular
    synthesis, transport, and others.

    File Formats features - 1) You can export your pathway in several text
    (SIF, GML, XML, tab delimited) based formats; 2) SBML compatible:
    Level 1 & 2; 3) You can export your pathway in several graphical based
    formats.

    Explore Pathways - 1) You can move, drag and drop biological
    components on the workspace, apply different intelligent layout
    algorithms, change and customize the shape and color of visual
    components; 2) Its automatic graphical optimization allows large
    pathways to be resized for optimal viewing; 3) You can add, modify or
    redefine interactions to further validate associations; 4) You can add
    Notes and Annotation to the model workspace; 5) You can Cut, Copy,
    Paste and Delete biological components; 6) Offers Undo and Redo
    operations. Up to 10 operations can be undone and redone using the
    icons in the toolbar; 7) You can zoom in /out/fit and Zoom in a selected
    region to investigate different types of associations and reference
    source descriptions. This feature becomes useful when the model
    size becomes big; 8) Offers direct links to the PubMed abstract and
    exact source sentence where findings are referenced; 9) You can view
    a variety of preloaded curated common pathways such as MAPK, p53,
    apoptosis, Wnt, Cell Cycle and all KEGG pathways; or specific
    networks and pathways from different scientific studies; 10) You can
    also export publication quality graphics in a variety of file formats.

    Visual Data Abstraction features - 1) Offers Meta-Network, in which a
    node (Meta-Node) has its own internal network structure, supports
    multi-scale visualization of bio-networks, and is ideal for the 'network'
    of functional modules; 2) Meta-Nodes and Meta-Edges make the
    effective analysis of cellular processes and dealing with their
    complexity a lot easier;  3) You can double click the Meta-Nodes to
    collapse them to simplify your network, and then, double click the Meta-
    Nodes again to recover the original network; 4) Meta-Edges are
    automatically recalculated based on the connections of the 'nodes'
    inside the Meta-Nodes.

    Network Analysis and Statistics features - Offers 1) Network statistics;
    2) Finding cycles; 3) Pathway Homology; 4) Node and Connector
    Tables.

    Import Gene/Protein Lists features - 1) Product can import Lists of
    Genes, Proteins and other biological entities from Yeast, Fly, etc; 2)
    Supports multiple ID types including: Unigene IDs, Accession
    Numbers, LocusLink, Swiss-Prot, Affymetrix GeneChip IDs, Gene
    Names and Gene Symbols; 3) Has the ability to create gene lists that
    are exportable for manipulation in other software packages.

    Use your Microarray Gene Expression Data for Pathway Analysis - 1)
    Import your microarray gene expression data sets; 2) Filter, Normalize,
    make Data Transformations with your expression data; 3) Sort and
    search your expression data; 4) Apply different clustering methods to
    your experimental data; 5) Do clustering analysis in the context of
    biological pathways; 6) Overlay Expression Experiment results onto an
    existing pathway diagram; 7) Derive microarray expression correlation
    networks; 8) Extract pathways from expression data; 9) Find up or
    down regulated genes through various biological states and identify
    key regulators or targets of interest; 10) Build Pathways for selected
    expression values; 11) Work with groups/clusters and pathways in
    conjunction with expression experiments.

    System Requirements  BiologicalNetworks pathways analysis
    software supports Windows 2000 and XP, Linux and Macintosh
    operating systems. BiologicalNetworks is a freely distributed Java-
    based web application.

    Manufacturer   



    Price  Freely distributed.

    G6G Product Number  20067

    G6G Manufacturer Number  101833
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