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2.4 Project Navigator

Once a project has been created or opened, the Project Navigator appears. This interface displays a single project at a time. The Project Navigator has a similar menu and tool bar as the welcome screen, but the window is split into three panes, and the additional Import menu is available. The larger pane on the left side is the Project Navigator Window. The two panes on the right side are the Node Change Log and the User Notes. A project navigator is displayed in Figure 5.

[Picture]

Figure 5: SVS Project Navigator
Project Navigator Window

The Project Navigator window contains a dynamic tree of Navigator Window Nodes, which are created whenever data is imported, spreadsheets or plots are created, or whenever one of the analysis tools is used.

  • Navigator Window Nodes
    Importing a dataset creates two new Navigator Window Nodes under the Project Node: one for the dataset and another for the Spreadsheet Viewer. See Importing Your Data Into A Project on importing data into a SVS project.

    The Navigator Window Nodes are displayed showing the parent/child relationship of the nodes. Subtrees of a Navigator Window Node can be expanded or collapsed by clicking on the + or - next to the node. If there are no signs present, there are no subtrees for that node.

    The ID numbers to the right of the node names indicate the ID number of that particular node. The ID number never changes even if the node is renamed or other nodes are deleted.

    The Linked To column specifies which nodes are linked to each other. When selecting a node linked to other nodes, all nodes linked together are highlighted in blue, and the current node is highlighted in gray.

  • Managing Navigator Window Nodes
    Since the default naming scheme is fairly non-descriptive in some instances, it may be helpful to rename the nodes to more descriptive names to help you find your data faster. A node can be renamed by right-clicking on the node or left-clicking and holding for a few seconds.

    A node can be deleted as long as there are no other nodes dependent on it. If a parent node has children nodes with no other dependent nodes, the parent node can be deleted, but all children nodes will also be deleted. If a dataset has only one spreadsheet attached to it, deleting either the spreadsheet or the dataset will delete both nodes. A dataset cannot exist in the project without a corresponding spreadsheet viewer.

    A node can be opened by either a double left-click or by right-clicking and selecting Open Viewer.

    A dataset can be created for a subset or child spreadsheet by right-clicking and selecting Create Top Level Spreadsheet. This can be used to remove dependencies associated with a navigator window node to allow for the deletion of the parent node. (See Create Top-Level Spreadsheet.)

Node Change Log Window

The Node Change Log logs and displays messages generated by the system for each Navigator Window Node. Each node has an initial log entry with it’s unique ID, date and time the node was created, and how the node was created (if not the result of a simple import). The log shows all messages associated with the currently highlighted Navigator Window Node. If a node is deleted all of the associated log messages are also deleted.

User Notes Window

The User Notes window can be a valuable documentation tool as well as the repository for information needed to create project reports. The User Notes window can be edited by clicking in the text box below the User Notes header. The information displayed in the User Notes window is deleted if the associated Navigator Node is deleted.

Customizing the Project Navigator

You can customize the Project Navigator by resizing and moving the Node Change Log or User Notes panes around, moving either of these two panes moves the Project Navigator Window as well. To move a pane left click and drag the pane’s title bar to the location you want. To resize the panes left click and drag the vertical or horizontal divider between the panes you want to resize.

File Menu
  • New Project
    Creates a new project file. If you have a project open and have made changes to it since you last manually saved it (see Save Project below), you will be asked whether you want to save or discard your changes.
  • Open Project
    Lets you open an existing project file. If you have a project open and have made changes to it since you last manually saved it (see Save Project below), you will be asked whether you want to save or discard your changes.
  • Save Project
    Every operation you perform in SVS is auto-saved upon completion. By choosing this option you can manually save your project at a specific point, which enables you to discard auto-saved changes if needed and revert your project back to the point at which you last manually saved it.
  • Save Copy of Project
    Leads you through saving a copy of the project in its current auto-saved state to a location you specify. If you have a project open and have made changes to it since you last manually saved it (see Save Project above), you will asked whether you want to save or discard your changes.
  • Close Project
    If you try to close the project without saving the recent changes you will be asked whether you want to save the project (keeping the auto-saved version) or discard the changes (keeping the manually saved version).
  • Clean and Compact Project
    This option removes temporary files and clears the cache. It is recommended that you run this operation before sending large projects to another user.
  • About Project
    This dialog displays all of the properties of the current project including the name, project location, size, origination date and time, and date and time of the last save.
  • Recent Project Files
    Lists up to the last eight projects in the order they were opened, with the most recent at the top of the list. Clicking on a project file in the list will open that project.
  • Quit
    Closes down the application.
Tools Menu
  • Current Project’s Options
    Sets defaults for analysis that will apply to all analysis windows for the project. Also allows a password to be set for the project.
  • View Project Log
    The node change log messages are displayed in a text box either in Navigator Window Node order or in chronological order.
  • Manage Genome Maps
    Genome maps contain information about the number and size of the chromosomes for a particular species and build. Genome maps can be created or viewed through this dialog.

    For more information about genome maps, see Genome Maps.

  • Manage Annotation Tracks
    Annotation tracks contain information about genes, coding regions, etc for a particular species and build. Tracks can be viewed in the Genome Browser.

    For more information about annotation tracks, see Annotation Track Manager.

  • Manage Marker Maps
    Genetic marker maps are files containing distance data for individual genetic markers relative to some origin, as well as other data relative to the markers. They can be applied to spreadsheets with genetic data.

    For more information about genetic marker maps, see Genetic Marker Maps and Affymetrix Library Files.

  • Pre-Study Power Calculation
    Uses the PBAT approach to analytical power calculations for FBATs by [Lange 2002a, Lange 2002b, Lange 2002c]. They allow the user to assess the power of family-based association tests (FBATs) for a large variety of different designs. See Pre-Study Power Calculation for help with this feature.
  • Run Python Script
    You can run Python scripts saved as *.py files.
    For more information about Python scripts, see Running Scripts.
  • Open Python Editor
    The Python Editor is a powerful interface for writing and editing Python scripts.

    For more information about the Python editor, see The Python Editor Window.

  • Open Python Shell
    You can use the features of SVS in a command line scripting mode via a Python shell.

    For more information about the Python shell see The Python Shell Window

  • Open Folder
    • AppData Folder: Launches (or puts into focus, if one already exists) a file browser window from your operating system which is open to the root directory of your AppData. This folder can be used to access genome maps, marker maps, annotations and the UserScripts folder.
    • UserScripts Folder: Launches (or puts into focus, if one already exists) a file browser window from your operating system which is open to the root directory of your user scripts. You may then use this window to conveniently open a Python script using a text editor of your choice.
    • Marker Maps Folder: Launches (or puts into focus, if one already exists) a file browser window from your operating system which is open to the root directory of your marker maps. You may then use this window to view the marker maps in your local directory.
    • Genome Maps Folder: Launches (or puts into focus, if one already exists) a file browser window from your operating system which is open to the root directory of your genome maps. You may then use this window to view the genome maps in your local directory.
    • Annotations Tracks Folder: Launches (or puts into focus, if one already exists) a file browser window from your operating system which is open to the root directory of your annotation tracks. You may then use this window to view the annotation tracks in your local directory.
  • Update Software
    This option is only available from the Program Welcome Screen. To update the software, close the open project and then select this option.
Import Menu

Several types of data formats can be imported into SVS for use in analysis.

See Importing Your Data Into A Project for information on these file formats.

Please see Illumina for instructions on how to import data directly from Illumina text files, and see Affymetrix Files for instructions on how to import data from Affymetrix formats.

  • Text
    Text files in either a CSV or TXT format can be imported using this option. Any text file saved with an appropriate text delimiter can be imported.
  • Third Party
    Third party software can be imported into SVS for use in plotting or analysis. Numerous data types can be imported using this feature.
    • NOTE: The new Microsoft Excel XLSX format is now supported for import and export in the Windows versions of SVS, but is not currently available for Linux or Mac.
  • PED/TPED/BED
    The two file PED/MAP format often containing both family-based and regular genotype data popularized by PLINK can be imported into SVS. Both the plain text PED/MAP files as well as the optimized binary PED or BED files (which should have correlating BIM/FAM files) can be imported using this option. Transposed pedigree files in the TPED/TFAM formats can also be imported into SVS.
  • Golden Helix, Inc. DSF
    DSF files saved from a SVS project retain marker maps and on import save the marker map to the project as well as to the Genetic Marker Map’s folder if desired.
  • Golden Helix, Inc. Legacy GHD
    GHD files saved from a SVS project do not retain maker map information, but GHD files can be opened in earlier versions of SVS prior to version 7.0.0.
  • Affymetrix
    Five Affymetrix file types can be imported into SVS for analysis, these are the CHP, CEL, CNT, CNCHP, and CYCHP file formats.
  • Illumina DSF
    A DSF file created using the Illumina Bead/GenomeStudio plug-in can be imported into the project for analysis using this option.
  • Agilent Files
    Agilent copy number data text files can be imported into the project using this option.
  • NimbleGen Data Summary Files
    NimbleGen data summary *segMNT.txt text files can be imported into the project using this option.
  • PBAT
    SVS provides tools for the design and analysis of family-based association studies through the capabilities of the PBAT software package developed by Dr. Christoph Lange of Harvard University.
    http://www.hsph.harvard.edu/faculty/ChristophLange.html

    Please see Importing PBAT Family-Based Data for instructions on how to import pedigree and phenotype data.

  • Import Scripts
    Additional scripts are available for importing specific data types into SVS, nine scripts are shipped with SVS, to be used for importing several different file types.
Download Menu
  • Marker Maps
    Marker Maps for several Affymetrix and Illumina arrays are available for download using this link. The annotation files are hosted on our data repository and Affymetrix files are also available through NetAffx. All downloaded maps will be available in the AppData folder.
  • Example Projects
    Completed tutorial projects can be dowloaded using this link and used for testing or exploring the software.
  • Affymetrix Annotations
    Affymetrix annotation files can be downloaded directly from NetAffx by using this option. They can also be downloaded by going to Tools > Genetic Marker Maps and clicking on the Download Affymetrix Annotations button.
  • Affymetrix Library File
    Affymetrix library files are needed to complete certain Affymetrix-specific operations, such as importing CHP and CEL files. These files can be downloaded to a specified directory using this option.

    For more information about Affymetrix library files, see Genetic Marker Maps and Affymetrix Library Files.

  • Add-on Scripts
    Leads you to a repository of Python scripts written by Golden Helix, Inc. and its customers that you can download and use to enhance the usability of the software. Enhancements range from simple data transformations to completely automated workflows and integration with other packages.
  • Public Data
    Data needed for testing can be downloaded and saved in a specified directory using this link.
Help Menu
  • SVS Manual
    Opens the internal manual.
  • Online Knowledge Base
    Leads you to an online knowledge base providing answers to a range of frequently asked questions about the software and its methods.
  • Online Tutorials
    Leads you to in depth tutorials covering anything from basic getting started operations to more complex analysis workflows.
  • Email Feedback
    Provides a list of email operations to send context sensitive feedback to the Golden Helix, Inc. support staff, including bug reports, feature requests, and the ability to share your experience.
  • About SVS
    Provides information regarding the version of the software you have installed and important license information, which is helpful for troubleshooting, updating your license, adding modules, etc.
Tool Bar

The Tool bar has a row of icons that provide quick access to some of the menu options. A description of the Tool bar icon appears when you place the cursor over the icon. You can perform the following tasks using the Tool bar icons:

  • Create a new project
  • Open a project
  • Close current project
  • Save project
  • Access program or project options
  • Manage genome maps
  • Manage Annotation Tracks
  • Manage genetic marker maps
  • Open a Python shell
  • Give feedback
  • Open the SVS Manual

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