My GenomeQuest is like your home page. From this page you can

• Launch new workflows
• View a listing of all your results
• Organize your results into folders / subfolders
• Tag your results or folders of results
• Share results with other users (on a read-only or a read-write basis)
• Start browsing reference sequence databases like Genbank, genomes and patents.

Contents 1 Overall Layout 2 Launching workflows 2.1 The most common operations are accessible through buttons 2.1.1 Changing buttons available for you 2.2 All Workflow launch pages are available through the Launch Workflow button 3 Operations on Workflow Results 3.1 Accessing your results 3.2 Moving results into folders 3.3 Deleting results and folders 4 Operations on Folders 4.1 Creating New folders 4.2 Renaming Folders 4.3 Sharing Folders and Results 4.4 Operations on teams 4.4.1 To Create a Team From the Share tab 4.4.2 Managing teams from the Account Settings Panel

Overall Layout

Overall the My GenomeQuest page (Fig 1.) has three areas.

1. The Header. At the top of the page, are a few important links in the header
   1. The GenomeQuest logo at the left is a link back to the My GenomeQuest page from any other page.
   2. The Support drop-down at the right has two entries for sending feedback to GenomeQuest and a link to the help page.
   3. The other drop-down is your user name. From here, you can log out or change your account settings (more on this later.
2. The Left Panel has
   1. a search box at the top for looking through your results by name or do other filtering on your results.
   2. a folder listing like a Windows explorer to show your folders and allow other operations
   3. an area for managing your uploaded reads files
3. The Main panel on the landing page has
   1. a few buttons for commonly done operations.
      1. If you choose the IP interface this includes launching IP search, Blast search and Browsing patents.
      2. If you choose the NGS interface, it is for uploading a file, processing your reads and running analysis workflows.
      3. Note: You can choose which interface you prefer as shown below in Account Settings section
   2. Your recent results. These could be from your own searches and workflows or they could be results that were shared to you by a colleague.
      1. This is a good place for accessing your most recent results. Note however, that this is not a comprehensive list that is shown later.

Fig 1. Overall Layout of the My GenomeQuest page for NGS users. (If you are an IP user, the buttons may be for operations you commonly do - see Fig 2 below.

Fig 2. Overall Layout of the My GenomeQuest page for IP users.

Launching workflows

There are two ways to launch a workflow.

The most common operations are accessible through buttons

For IP users, the most common operations are available through buttons on the landing page as shown in the figure below.

1. Launch IP Search button links to the launch page of the IP workflow.
2. Align two sequences links to a page allowing you to aligning two sequences.
3. Keyword Search links to a page allowing you to do keyword searches in patents and public reference databanks.

For NGS users, a different set of buttons are available as shown in the figure below:

1. Upload data button links to the page for uploading NGS reads
2. Prepare reads links to the Reads Processing workflow
3. Analyze Reads links to a page that has a listing of all available analysis workflows with links to their launch pages.

Changing buttons available for you

As mentioned above, the most common operations are available to you through the three prominent buttons available on your landing page. You can change these buttons through changing your account settings. Specifically, you can choose whether to have the IP set or NGS set of buttons. TO do this:

1. Drop down the menu with your name at the top right and choose Account Settings:
   
2. Next click the Interface Preferences tab and choose the set you would prefer:
   

All Workflow launch pages are available through the Launch Workflow button

Using the button at the top of the Left Panel called Launch Workflow launch pages of all workflows are available:

Operations on Workflow Results

All newly launched workflows create their results in your top level i.e. My Data folder. However, you can then re-organize them in anyway.

Accessing your results

Your most recent results are in the main panel of the My GenomeQuest page just below the three buttons.

All your results are accessible through the folders in the left panel. Click the appropriate folder's name to populate the main panel with results from that folder. By default all newly launched workflow results go into the My Data folder.

The main panel then gets populated by the results in that folder.

Moving results into folders

To move result(s) into a specific folder,

1. Select the results you want to move by clicking the checkboxes next to them.
2. Click the Move to Folder button at the top.
   
3. On the pop-up dialog, select the folder you want to move the results into.
   
4. Click OK.

Deleting results and folders

Deleting results is similar to moving them into folders.

1. Select the results you want to delete.
2. Click the Delete button at the top.
3. Accept the pop-up dialog by clicking OK.

This same procedure can be used for deleting folders as well.

Operations on Folders

Creating New folders

All folders are created as subfolders of another folder, called the parent folder. A top level is a subfolder under the My Data folder. To create new subfolder

1. Mouse over to the parent folder.
2. Click the drop down menu at the right end of the line. This menu is called the Folder Operations menu.
   
3. Click Create folder.
4. Give the folder a name in the pop-up dialog.
   
5. Notice your folder created in the left panel.

Renaming Folders

To rename a folder, choose Rename from the Folder Operations menu of that folder.

Sharing Folders and Results

To share a folder, one way is to go to the Folder Operations menu of the folder you want to share - as described above. Then choose Share. On the pop-up window, select the sharees at two levels of sharing: Readable and "Writeable".

Note that you can only share items (results and folders) that belong to you. For example, if someone has shared a folder with you, you can further share that folder with someone else.

There is another way which works for both folders and other results:

1. When you are viewing a list in the main panel, you may be seeing results as well as folders.
   
   1. If you click on the name of a folder, you will be taken to a list of the contents of the folder. Name of a result will take you to that result.
   2. However, if you click on the line of the result but not on the name hyperlink, this will open up the details of that folder.
      
2. Now click on the share tab.
   .
3. Here you have the same two levels of sharing: readable and writeable.

In both ways of sharing, you can:

1. Keep the folder or result private so that only you, the owner, has access to it. This is the default status.
2. Share it with your whole group by clicking the group name on the drop-down menu. Here all members of your group (typically your company or organization) will have access to it. Of course they will have to be GenomeQuest users. This is dynamic sharing i.e. as new members enter your group, they automatically get access to the folder or result.
3. Share with a specific user. You can choose a specific (single) user that you would like to share the result of folder with by clicking on their name.
4. Share with a specific team. You can choose to share with a team of multiple specified users by choosing the name of the team. (Don't have the proper team? You can create one as described below). This is also dynamic sharing in that you can modify the members of the team in your account setup page (as described below) and the changes will cascade into all results or folders shared with that team.

Operations on teams

A Team is defined as multiple specified users in your organization. They are usually created to provide an easy way to share your results and folders with multiple colleagues. Since you can create a team yourself, you can choose any combination of users from your organization

To Create a Team From the Share tab

You can quickly create a team, by clicking the quickly create a team link on the share tab.

You can also create a team from the account settings portion of your page, as described below in managing teams. But in either way, you see a pop-up window that shows all users and groups from your organization.

Select any combination of team members or pre-existing groups by checking the box next to them.

Then hit OK to create the team. The team name is now available on all sharing operations.

Managing teams from the Account Settings Panel

Account settings panel (briefly described above) is the place you go to manage the teams you have created. As described above, click on your login name at the top right and choose Account Settings. Next select the Manage Teams tab.

From this tab you can:

1. Create a team by clicking the "Add Team" button.
   1. Select the team members from the pop-up window by checking the box next to their name.
   2. You can also add pre-existing teams as a component of this new team by checking the box next to the team's name.
   3. Hit OK.
2. Edit a team (change its composition) by clicking the "Edit link next to it.
   1. This brings up the same pop-up window with team members' names already checked.
   2. Remove a team member by unchecking the box next to their name and add members by checking the box next to their name.
   3. Hit OK.
3. Delete a team by clicking the Delete link next to it's name and agree to the pop-up by hitting OK.