User Interface

• This menu item gives a reminder message to upload files by dragging and dropping them onto the destination folder in the directories or files and subdirectories panels.
• For step-by-step instructions see the Upload Data to GenomeSpace recipe.

Import from URL

(File menu only)

• Enter or drag-drop the file URL in the provided textbox.
• Select the destination folder from the provided directory structure.
• Edit the name of the imported file.

• Creates a subfolder within the selected directory. Enter a name for the subfolder.

• Displays the highlighted URL address of the file/folder that you can copy by keyboard shortcut or right-click menu.

• View and edit the share setting for the file/folder with individual users, groups, or the public.
  • To create groups, see instructions for Manage>Groups below.
• To confirm a username exists, click on the magnifying glass (Screenshot, circled in red).
• Revoke permissions by clicking on the red X next to the shared user/group name.
• Checking Allow public access for a file/folder places an alias of the file/folder in the Public directory within a folder with your username. Within your user directory, the file/folder icon displays green people () to indicate public sharing.
• Read more in the Share Data section.

• Add or remove tags to file(s)/folders.
• Folder tags apply only to the folder and not to contents.
• The search bar matches search terms within the file name and tags, tool name, tool description, tool tags and tag descriptions.
• To tag tools, see Customizing the interface.

• Compress or expand file/folder in ZIP, TAR.GZ, or TAR format with option to edit name. At the directory level, ZIP and TAR.GZ compression are recommended.
• Archiving creates a secondary compressed file and leaves the original file/folder intact.
• Similarly, expanding an archive creates a secondary expanded folder and leaves the archived files intact.

• The original file/folder name is displayed for editing.

• Select the destination folder for the copied or moved file/folder.
• Edit the file/folder name. An error occurs if a file/folder of the same name already exists in the destination folder so be sure to edit the name if copying to the same folder.
• Progress is shown at the bottom of the browser and a dialog box informs you of completion.

• Delete file(s) or a folder with contents from the main files & subdirectories area.
• To delete from the directories panel, the folder must be empty.
• Refresh your browser window to reflect the change.

• Disconnects linked account. Browser refreshes automatically to reflect change.

• Displays the highlighted URL address of the file/folder that you can copy by keyboard shortcut or right-click menu.

• View the share setting for the file/folder. These folders do not allow editing of share settings.

• Archive a file or folder and its contents or expand an archive to the User directory. Move the archived file or expanded folder to the desired linked account afterwards.
• Supported compression formats are ZIP, TAR.GZ, and TAR and you can edit the name of the resulting file/folder.
• Archiving creates a secondary compressed file and leaves the original file/folder intact.
• Similarly, expanding an archive creates a secondary expanded folder and leaves the archived files intact.

• Select the destination folder for the copied or moved file/folder.
• Edit the file/folder name. An error occurs if a file/folder of the same name already exists in the destination folder so be sure to edit the name if copying to the same folder.
• Progress is shown at the bottom of the browser and a dialog box informs you of completion.

• Disconnects linked account. Browser refreshes automatically to reflect change.

• View the selected text-based file up to the first 5 kilobytes in a new window.
• Depending on file type, you may see an additional tab labeled Heatmap. Click to switch to Heatmap view created by jHeatmap. If the file is large, the heatmap may take a while to load.
  • Scroll within the heatmap to zoom view.
  • Click on a datapoint in the heatmap for column, row, and value.
• Read more in the Preview & Heatmap section.

• Create a new file containing selected columns and selected consecutive rows.

• View the selected text-based file up to the first ten rows in spreadsheet format.
• Use the Save as field to change the file name. GenomeSpace automatically appends the term .slice between the original file name and extension.
• Select consecutive rows by entering start row and end row numbers. Leave end row field blank to include all remaining rows.
• Select tab, comma, space, or semicolon delimiter with option to treat consecutive delimiters as one.
• Select columns by checking boxes at top of columns. Scroll bar at bottom to display additional columns.
• Click on Toggle all columns to invert selections.
• See the Extract file rows & columns section for additional details.

• Convert files into data formats used by popular bioinformatic tools. Within your account, go to Help>Fomat Converters to see the most current list of supported conversions. For more instruction see Convert file formats.
• Select a single file and Convert.
• Select the conversion format from the drop-down menu.
• Download to your desktop or save to your GenomeSpace account by selecting Convert on Server.
• The original file remains intact and the converted file saves as a new file.
• Some tools will automatically convert compatible formats for you when launched on files.

• Download files to your local machine.
• For multiple files, check the files and use File menu>Download.
• Alternatively for a single file, you can right-click on the item and select Download.

• Opens the folder the search result item is found in.

See the two previous sections above for details.

• Launch a selected tool or data source. If you have selected a file, you can launch a tool on that file.
• The drop-down menu lists all available tools and data sources alphabetically described in Tools.
• Alternatively, drag-drop selected files on the tool displayed in the Toolbar.
• For step-by-step instructions see the Send Data from GenomeSpace to a Tool recipe.

• Refresh current directory refreshes the directory currently in your view.
  • The alternative browser refresh resets the directory view
• Recent uploads displays files most recently queued for upload to your GenomeSpace User account.
  • This differs from the User>History list
• Customize toolbar displays the same toolbar manager as clicking the blue + button on the left of the toolbar. Using the displayed toolbar catalog, add or remove tools, tag tools, and search tools. You can  rearrange the display order of tools either in the catalog or directly on the toolbar. For more details, see Customizing the interface.

• Dropbox (links take you to service provider websites)
• Amazon S3 (1) public S3 data buckets on the Public S3 Bucket tab and (2) private S3 buckets from the Read/Write S3 Bucket tab.
• Google Drive

Connection to these three commercial cloud storage systems are supported for access from GenomeSpace and enabled tools. Select the storage to connect from the menu and the permissions granted, read only or read and write, and follow directions from the service provider. Once connected, drives appear as folders in the left directories panel (1). You can connect multiple drives at a time.

1. For Amazon public S3 data buckets, enter the bucket name in lowercase, e.g. 1000genomes or human-microbiome-project.
2. Connecting a private Amazon S3 bucket is a multistep process to verify you have access to the Amazon Web Services (AWS) account.
   • Read only or read & write permissions are granted by the bucket owner. To enable writing to a bucket from a browser, from your AWS console, select the S3 bucket Properties>Permissions>Add CORS Configuration. Copy-paste the following custom script over the sample CORS configuration and save.

<?xml version="1.0" encoding="UTF-8"?>
<CORSConfiguration xmlns="http://s3.amazonaws.com/doc/2006-03-01/">
    <CORSRule>
        <AllowedOrigin>*</AllowedOrigin>
        <AllowedMethod>PUT</AllowedMethod>
        <AllowedMethod>POST</AllowedMethod>
        <AllowedHeader>*</AllowedHeader>
    </CORSRule>
    <CORSRule>
        <AllowedOrigin>*</AllowedOrigin>
        <AllowedMethod>GET</AllowedMethod>
    </CORSRule>
</CORSConfiguration>

• Follow the connection instructions provided by GenomeSpace using the provided links to specific AWS console pages to perform steps.
• Note that leading or trailing spaces in textboxes, leftover from copy-pasting, will give errors in connecting the bucket. Go back to each field and remove the spaces and submit again.

One advantage of accessing data in these drives from your GenomeSpace account is that GenomeSpace links preserve 3-letter file format extensions required by many bioinformatic tools to recognize file types, e.g. the IGV tool, which may not be the case when the files are accessed directly from the connected storage system.

• Select Groups to create groups of GenomeSpace users.
  • Select a group under Group Names to view, edit members, or delete the group.
  • Members with administrator priviliges are shown with a red icon and other members in blue.
• Private Tools opens a window that allows you to add private tools to your toolbar or to share with your groups.
  • Press Add new and fill in the form.
  • To display more instruction, click the ? icon on the right.

• View GenomeSpace Recipes of which there are three groups in a new browser tab:
  • Loading data into GenomeSpace
  • Moving data between tools via GenomeSpace
  • Analyzing data with GenomeSpace tools
• Recipes are step-by-step instructions of two types: (1) they outline how to perform tasks in GenomeSpace such as loading or moving data, and (2) show how to perform specific integrative bioinformatic data analyses using GenomeSpace tools.

Menu items link to the following:

• User Guide (GenomeSpace Help)
• Tools listing (Tool Help) where you can find support information by clicking on a specific tool
• a popup box listing supported Format Conversions
• System Status page to check for changes in the system that impact using GenomeSpace
• GenomeSpace Support page for our help email, links to forums, and to sign up for email lists.
• What's new popup box featuring news highlights and excerpts and links to the blog
• email the GenomeSpace team (Contact us) opens your desktops default email app
• About GenomeSpace gives information about the origin, funders, and participating labs of GenomeSpace.

• Change the associated email address
• Change account password
• Make your user name unsearchable by others or searchable (default)
• Check the amount of storage you are using against the quota

• Search and view your account activity log by date range
• Toggle and sort column headers of time, action, and files

• Logs you out of your GenomeSpace account.
• To open multiple different accounts at the same time from the same machine, use a private instance of the browser or different browsers, i.e. Firefox and Chrome.