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Navigating the Welcome Screen

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2.3 Navigating the Welcome Screen

The welcome screen (see Figure 3) appears when you do not have a project open. From here, you can open an existing project, create a new project, download example projects, set options for all new projects, and more. The welcome screen also displays relevant license information, the modules you have activated and valuable community resources to help you learn how to use the software more effectively.

[Picture]

Figure 3: SVS Welcome Screen
Getting Started
  • Create New Project: Before you can import or analyze data, you need to create a project. To create a new project, either click on Create New Project under Getting Started or choose File > New Project.

    The New Project window appears prompting you to specify a name for the new project. Enter a name for your new project. Under the Project Name prompt is another entry showing the intended file folder where the project will be located. The Project Name is also the default name of the new folder that will hold all of the project data. Every project has its own folder.

    To change the Project Location (the parent folder that will contain the new project folder), click on the Browse button and designate the new location in the Browse For Folder dialog window. Press OK when done to return to the New Project dialog.

    Notice that the project name is automatically appended to the project location that was previously specified. It now becomes a new folder on your system. To complete the project creation process, click the Create Project button.

    A new project has now been created and is displayed in the Project Navigator.

    A new folder has also been created at the location you specified. This folder stores all the data files associated with the project and a project file (.ghp), which holds important information about your project. The .ghp file is the file to select when you want to re-open this project at a later date.

  • Open Existing Project: If you already created a project you can choose from a list of recently opened projects or click on Open Existing Project to browse to your existing Golden Helix, Inc. Project file (*.ghp). You can also open an existing project by choosing File > Open Project, or File > Recent Project Files.
  • Example Projects: Several completed tutorial projects are available and can be downloaded by clicking on Example Projects. These projects can be used to familiarize yourself with the software or to test out new methods on a range of different types of data, such as those used in haplotype analysis or regression and more.
Community Resources

A variety of tools are available to help you become more proficient with the software and extend the utility of your data.

  • Add-on Scripts: Python scripts written by Golden Helix, Inc. and its customers can be downloaded and used to enhance the usability of the software. Enhancements range from simple data transformations to completely automated workflows and integration with other packages.
  • Webcasts: Golden Helix, Inc. hosts webcasts periodically presented by its staff and customers to discuss new methods, new products and relevant research within the community.
  • Knowledge Base: A knowledge base is available online providing answers to a range of frequently asked questions about the software and its methods.
  • Tutorials: More in depth tutorials are available on our website covering a variety of topics, ranging from basic getting started operations to more complex analysis workflows.
  • Manual: The manual provides context sensitive help for every aspect of the software.

Community resource tools can also be accessed from the Help Menu in the Welcome Screen and Project Navigator.

Support

The Golden Helix, Inc. Support Team is here to help. Whether you have a question about how to use the software or if you need to find a technical paper, the experts at Golden Helix, Inc. will have the answer you need. We are committed to providing you with legendary support.

License Information

This section 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.

More detailed license information is available by choosing Help > About SVS.

Modules

This section lists all the modules you have active for your license. If a module has a check beside it, the module is active. If it has an ‘X’ beside it, the module is inactive.

The Menu Bar

All but two of the menu bar items (Tool > Current Project’s Options and Tool > Update Software) are also available from the Project Navigator. They are described in detail in the Project Navigator section.

Global Product Options

Setting program level options is done prior to opening or creating a project. Any changes to the options set before a project is open will be applied to all future projects and to the operation of the program. An individual project’s options can be changed after that project has been opened.

To set program level options, choose Tools > Global Product Options from the welcome screen. The window for the global product options is displayed in Figure 4.

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Figure 4: SVS Global Product Options Window

The tabs available are:

  • Application
    • Default Genome Map
    • Menu and Navigator Defaults for New Projects
    • Custom Paths
    • Memory Usage
    • Python Settings
  • Network and Updates
    • NetAffx Login for Library Files and Marker Maps
    • Proxy Settings
  • Genotype Association
    • Genetic Model or Tests
    • Test Statistic or Method
    • Missing Values
    • Multiple Testing Correction
    • Additional Outputs
    • Principal Component Analysis (PCA)
    • Genomic Control of Output Data for Stratification
  • Numeric Association
    • Test Statistic or Method
    • Multiple Testing Correction
    • Additional Outputs
    • Principal Component Analysis (PCA)
  • Principal Component Analysis
    • Principal Components Source
    • Principal Components
    • Output
    • Data Centering
    • PCA Marker Normalization
    • Genetic Model for PCA
    • PCA Outlier Removal
  • Genotype Statistics
    • Generic Marker Statistics
    • Count Tables
    • Additional Output

  • CNAM Segmenting
    • Chromosome Segmenting Options
  • Runs of Homozygosity
    • ROH Options
    • Output Options
  • Haplotype Estimation Options
  • Haplotype Analysis Options
    • Haplotype Block Definition
    • Haplotype Estimation Options
    • Multiple Testing Correction
    • Haplotype Association Tests
    • Addition Outputs
  • QA Filtering
    • Filter Genotype Columns
      • General Statistics Filtering
      • Hardy Weinberg Equilibrium (HWE) Filtering
    • Actions
    • Additional Output
  • SNP Block Detection
    • Block Defining Algorithm
    • General Options
  • Numeric Regression
    • Selection Parameters
    • Regression Options
    • Full Model Covariates
    • Reduced Model Covariates
  • Numeric Regression Outputs
    • Multiple Testing Correction
    • Additional Outputs
    • Detailed Output

  • SNP PBAT Phenotype and Haplotype Options
    • Phenotype Parameters
    • MFBAT (Multi-Marker/Multi-Phenotype) Test Parameters
    • Analysis and Algorithm options
    • Perform Analysis for Haplotypes
  • SNP BPAT Test Statistic and Computational Options
    • Tests Statistic Parameters
    • Screening Type
    • GFBAT
    • Computational Parameters
    • Output Format
    • Computational Details
  • CNV PBAT Phenotype and Haplotype Options
    • Phenotype Parameters
    • Algorithm options
  • CNV PBAT Test Statistic and Computational Options
    • Test Statistic Parameters
    • GFBAT
    • Computational Parameters
    • Output Format
    • Computational Details
  • PBAT Distributed Options
    • Run On
    • General Options
  • IBD Estimation Options
    • Allele Counts
    • Identity by Descent Estimation
    • Additional Outputs
Update

When updates are available for the software there will be a link on the Welcome Screen indicating that an update is available. To manually check for updates, go to Tools > Update Software and follow the prompts from Golden Update.

If additional modules were added to the existing license the program will need to be completely closed and restarted for the changes to the license to take effect.

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