Getting Started on the Genboree Workbench


  • The Data Selector tree on the left shows the data entities to which you have access.
    • See Help » Legend for a description of various data entities appearing in this panel.
  • Drag items to be used as tool inputs over to the Input Data area.
  • Drag items to be used as output destinations for tool results over to the Output Targets area.
  • Tools which can be run on your selections will be highlighted in green.
  • Unsure about what kinds of items a particular tool needs in the Input Data and Output Targets?
    • Just click the tool button when it is not highlighted to see help information.
  • The Details panel on the right contains information on any data entity, represented as an Attribute-Value Pair.

Detailed description of various panels in Genboree Workbench

  • Data Selector
    • The Data Selector panel contains data entities on which Workbench tools operate (input) and where analysis results (output) are stored.
      • Data entities include input Files (text files, sequence data, etc.), sequence annotation data (tracks), Samples, Sample Sets, entity lists of files or tracks, Groups, Databases and Project pages.
        • See Help » Legend for a description of various data entities appearing in this panel.
      • Groups contain Projects and Databases and provide for controlled access to Group members.
      • Databases can be associated with a reference genome and provide a storage location for input and output.
      • Projects are HTML-based editable pages that link output results that are easily accessible and sharable to Group members.
  • Input Data
    • Workbench tools operate on data entities that you drag over to Input Data from the Data Selector.
    • Input Data accepts items such as tracks, files, folders, Samples, and entity lists of files or tracks.
  • Output Targets
    • Workbench tools deposit analysis results in the output targets that you designate by dragging over from the Data Selector.
    • Output Targets accepts data entities such as Databases, Folders and Projects (where output is showcased in a HTML-based format that is easily accessible and sharable to Group members).
  • Details
    • The Details panel provides information on any data entity.
    • The information represented as an Attribute-Value Pair is displayed automatically for a data entity if it is dragged into Input Data or Output Targets, or highlighted while in the Data Selector.
    • Attribute-Value Pair (AVP) – The term that describes the way a single data entity category is associated with the entry for that category. For example, a Sample 'X' has an attribute called 'Health_Status' and the associated value for Sample 'X' is listed as 'healthy'.
  • Attribute
    • The Attribute is a categorical description of data entity being defined (think column header) that is associated with a Value.
      • For example, if given a group of five Samples that have the following values: 'male', 'male', 'female', 'female', 'female', a reasonable Attribute name to label these Values could be 'Sex'. Click arrow on right corner to sort this column.
  • Value
    • Value is the entry associated with an attribute.
      • For example, if the Attribute for a given Sample is 'Disease_State', a reasonable Value for this Attribute could be 'healthy'.
        Click arrow on right corner to sort this column.

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