GenomeQuest 7.0 represents major upgrades across the board. It provides new data management capabilities, major new NGS analysis capabilities, upgrades in content, upgrades in underlying technologies and speed, and upgrades in large file transfers. This page has an overall description of the major new upgrades to GenomeQuest in GQ7.

1. Data Management Upgrades. A folder system to place your work inside of folder structures that you define. You can also search for results inside folders and share them.
2. NGS Analysis Capabilities. We have greatly improved the underlying GenomeQuest engine, moving to Biofacet 9 which contains a large set of new innovations.
3. Content Upgrades. INcluding adding your proprietary genomes and adding arbitrary tracks on them.
4. IT and Network Upgrades. Including support for Aspera and better Queueing control for jobs.

For more details on these abilities, click here.

Contents 1 FAQ on Folders and Sharing in GenomeQuest 7.0 1.1 What are folders? 1.2 How do I make folders? 1.3 How do I reach the My GenomeQuest page? 1.4 How do I launch workflows? 1.5 Where do my new results go? 1.6 How do I move result(s) into a folder? 1.7 Where are my old results? 1.8 What about my alerts under GQ5? 1.9 How do I share folders? 1.10 Can I share individual items without putting them in folders? 1.11 Levels of Sharing

FAQ on Folders and Sharing in GenomeQuest 7.0

The introduction of folders is the single biggest change in GQ7 which gives you a lot more power than before but could also disorient you a little with the changes. Please read through the following FAQ and also read the documentation on the new GQ7 My GenomeQuest page.

What are folders?

Folders hold other entities including workflow results, sequence databases and other folders. The top level folder is called My Data. Your searches may be in this folder but you can organize the results anyway you like by creating folders and sub-folders.

How do I make folders?

The top level of your results is called "My Data". This is your home folder. You can create folders in this home folder or can make subfolders within other folders.

To make a folder,

1. Mouse over the parent folder (or My Data) in the Left panel under which you want to make the folder.
2. Click the down arrow at the right to open a menu.
3. Select Create folder.
4. Give the folder a name in the pop-up dialog and click OK.

How do I reach the My GenomeQuest page?

Simply click the GenomeQuest logo on any other page to go back to the My GenomeQuest page. Of course, when you login, you will be in the My GenomeQuest page to begin with.

How do I launch workflows?

This is quite similar to the way you do it currently. Specifically, there are two ways.

1. When you login, you will see buttons for your most common actions. For example, if you are an IP user, you will see a button called Run IP Search. To launch a new IP search workflow, click this button and it will take you to the IP search launch page.
2. When youa re within the My GenomeQuest page, click the Launch Workflows button in the left panel and choose the workflow that you want to launch.

Where do my new results go?

By default, results from all launched workflows go into your home folder i.e. My Data. From there you can organize your results into any folders - or leave them in the My Data folder.

How do I move result(s) into a folder?

Click the check-box(es) next to the result(s) you want to move to a folder. Then click the Move to Folder button at the top. In the pop-up dialog, choose the folder into which you want to move the result(s).

Where are my old results?

Your old results should all be under the My Data tree.

1. For a start, we have created folders like "Blast Search", "IP Search" and "GQ5 results" so that the results organization resembles what you are familiar with. However, these folders are now very dynamic and you can move results among them or into brand new folders.
2. Any new searches you do will end up in the My Data top level folder.
3. For those who had results from GQ5, those are in the folder called GQ5 results.
4. Project folders you had under GQ5 are now back. They are under the folder called "My Projects"

It is important to reiterate that these folders are there only as a starting point. They are dynamic; you can move results among them and into newly created folders.

What about my alerts under GQ5?

If you had search alerts set under GQ5, the results from those alerting runs are ported over and you can see them. However, the alert itself is not ported. In order to reactivate the alert, simply set a new alert on one of those results.

How do I share folders?

You cannot share the My Data "folder" But all other folders can be shared. To share a folder

1. Mouse over the folder you want to share in the left panel.
2. Click the down arrow at the right to open a menu.
3. Click share.
4. Follow the instructions in the pop-up dialog.

Can I share individual items without putting them in folders?

Yes. When you click the name of an item, it typically opens.

1. Just mouse over an item in the main panel - the line highlights in yellow.
2. Click somewhere on the line but not on the name.
3. This opens the details of the item.
4. Now click the "Share" tab and follow the instructions there-in.

Levels of Sharing

1. Keep a folder or item private i.e. only you can access it.
2. Share it with your group (i.e. all users from your organization can access it).
3. Share it with specific users in your organization by selecting their name in the pop-up.
4. Share it with a team. If you want to share with multiple specific users in your organization,
   1. Create a team with those users, by clicking "Add New" in the drop-down menu on the pop-up dialog.
   2. Create a team with the users in this team.
   3. Now share the folder with that team.

NOTE: Once you create a team, it is available for future use. If you need to share another item with this same team, it is available right on the pop-up dialog.

Apart from the users, there are also two levels of access control in your sharing.

1. Read Privileges. These team members can only read and view the result.
2. Write Privileges. These team members can read and also create sub folders inside shared folder. But they can't change the name of the folder, nor can they delete/move/share it.