Welcome to the GenomeQuest Documentation Wiki
My GenomeQuest NGS
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 your sequence database and reference sequence databases like Genbank, genomes and tracks.
Overall the My GenomeQuest page (Fig 1.) has three areas.
- The Header. At the top of the page, are a few important links in the header
- The GenomeQuest logo at the left is a link back to the My GenomeQuest page from any other page.
- The Send Feedback link to send feedback back to GenomeQuest.
- The Documentation link that link to the help pages.
- The other drop-down is your user name. From here, you can log out or change your account settings such as your password and manage your teams.
- The Left Panel has
- a search box at the top for looking through your results by name or do other filtering on your results.
- a folder listing like a Windows explorer to show your folders and allow other operations
- an area for managing your uploaded reads files
- Two drop down menus - Import Data to add new data to your account and Analyze to launch new workflows to analyze your datasets.
- The Main panel on the landing page has two subpanels
- The left panel is for recent samples that shows you the newest data you've uploaded and imported into GenomeQuest with a Import More button on the bottom.
- The right panel shows the recent analyses you've conducted and their results. These could be from your own analyses or they could be results that were shared with you from others on your team.
Clicking on the icon similar to the one labeled "1" in the image above will bring you to a more detailed view of your work shown below.
Clicking on any of the links like the one labeled "2" will take you to the next analysis step.
Using the menu button at the top of the Left Panel called Analyze to see all of the available workflows:
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 in the "Recent Analysis Results" sub-panel as shown in Figure 1 above.
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,
- Select the results you want to move by clicking the checkboxes next to them.
- Click the Move to Folder button at the top.
- On the pop-up dialog, select the folder you want to move the results into.
- Click OK.
Deleting results and folders
Deleting results is similar to moving them into folders.
- Select the results you want to delete.
- Click the Delete button at the top.
- 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
- Mouse over to the parent folder.
- Click the drop down menu at the right end of the line. This menu is called the Folder Operations menu.
- Click Create folder.
- Give the folder a name in the pop-up dialog.
- Notice your folder created in the left panel.
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:
- When you are viewing a list in the main panel, you may be seeing results as well as folders.
- Now click on the share tab.
- Here you have the same two levels of sharing: readable and writeable.
In both ways of sharing, you can:
- Keep the folder or result private so that only you, the owner, has access to it. This is the default status.
- 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.
- 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.
- 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
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:
- Create a team by clicking the "Add Team" button.
- Select the team members from the pop-up window by checking the box next to their name.
- You can also add pre-existing teams as a component of this new team by checking the box next to the team's name.
- Hit OK.
- Edit a team (change its composition) by clicking the "Edit link next to it.
- This brings up the same pop-up window with team members' names already checked.
- Remove a team member by unchecking the box next to their name and add members by checking the box next to their name.
- Hit OK.
- Delete a team by clicking the Delete link next to it's name and agree to the pop-up by hitting OK.