Frequently Asked Questions

How are data organized in Orion, starting with release 2021.1.1?

Project Data Page

The new data organization system implements familiar concepts of paths and folders to organize and access data in Orion.

Users will still create projects, and the data will remain in the Project Data organizational structure. Now, users can organize the data the way they would like to share data among team members in a project. In addition, there are controlled data sharing capabilities among members in the project. To achieve these objectives, the following objects are available to users.

My Data

The data in this location are private and only accessible by the user. However, these data still can be shared by moving the data to a Shared Space.

Team Data

The data in this location are available to all project members.

Shared Spaces

The data in this location are available to project members selected by the user. Most operations on folders are available with shared space. See Shared Spaces for more information

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Video tutorial about project data

For more information on the use of the project data facilities, see Data Organization in Orion.

Tutorial video about discussion boards

The discussion board is a new feature that facilitates collaboration about data:Introducing Discussion Boards

You can see further information in this training video:Using Discussion Boards.

For more information about discussion boards, see Discussion boards.

What actions do I need to take if I had an account on a previous version of Orion?

In this new data organization, users will need to take some action on the shared data from previous Orion versions.

  1. Decide how to organize the data.

  2. Move all previously shared items into the appropriate folders.

  3. Assign collections to a project.

As an admin user, can I still share datasets and collections with the entire organization?

Yes, the Organization Data space still allows for admin users to share datasets and collections with the entire organization.

How can I create a new subfolder?

To create a new subfolder, first select the place (My Data, Team Data or Shared Spaces) where you want to create a new subfolder. Then, click on the folderplus icon next to the path (example: My Data). In the pop-up window, enter the folder name and click OK. A new subfolder will be created with the specified name in the selected path.

Do I need to create a subfolder before uploading data or running a floe?

No, a new folder or subfolder can be created in the same window you use to upload data or when starting a Floe run.

To do this, select the path and then enter the name of the subfolder you want to create. A green bar will appear with Create a new folder, next to the subfolder name you just entered. Click on Create a new folder. A new folder or subfolder will show up on the path specified.

Can I move a subfolder to another path or location (another project, main folder, or subfolder)?

Yes, subfolders can be moved to another path or location. To do this, select the folder you would like to move, and click either the bi-directional line icon on top or the ellipsis icon, and select Move. Then, choose the destination or path and click the Move button. The subfolder (and its contents) will be moved to the specified destination or path.

Can I move data between projects, folders, or subfolders?

Yes, data (datasets, files and collections) can be moved between projects, folders or subfolders. To do this, select the data you would like to move and click the bi-directional line icon or the ellipsis (...) icon and select Move. Then, choose the destination or path, and click the Move button. The selected data will be moved to the specified destination or path.

Note

Multiple datasets can be moved at once.

Can I specify a path when launching a Floe run?

Yes, a path or location can be specified in the job submission form. When launching aFloerun, you will see an Output path property field. The default path will be Project Name/My Data. To go up a directory, click on the up arrow or use the backspace key to move up one directory. Finally, select the path you want.

How do I upload a file in this new data organization system? Can I specify a path?

Yes, a path can be specified when uploading a file into Orion. To specify a path, select the folder or subfolders as applicable. Alternatively, you can go up a directory by clicking on the up arrow or using the backspace key. Also, you can create a new subfolder by entering the name and then clicking on Create a new folder.

How can I quickly access a subfolder I created?

To quickly access a subfolder, you can mark it as a favorite by clicking on the star next to the folder, and it will be added to the Favorite Folders area in the left side column.

Can I still add tags to datasets?

Yes, you can still add tags to datasets. The tags will remain the same as in the previous version of Orion.

How can I search for datasets in this new system?

You can still search for datasets by entering a tag or resource name in the search bar. Select the main folder or space you would like to search. Next, enter the tag or resource name and click on that name. Then, the results will be shown at the bottom of the page. In addition, you will be able to see the path where this data can be found.

How can I share data? How can I set the permissions?

To share data, we have created the Shared Spaces main folder (or space). You can start by creating a workspace in Shared Spaces. Click on the + icon next to the path. A pop-up window named Workspace name will appear. Enter the name of the workspace you want to create and click OK. A new subfolder with the specified name will show in the Shared Spaces. If you click on this workspace, then you will have the option to add members you want to share the data with. Click on the orionpeople icon and then click on Edit Users. Enter the name of the user/project member you want to add. In this window, you will have the option to set the permissions (write, delete) you want for that user to have. All the data in this workspace will be shared with the selected users/project members.

Alternatively, if you would like all project members to have access to the data, save this data in the Team Data space.

How can I delete data? (and multiple selection of datasets)

To delete data, first select the data you want to delete by clicking on the square box on the left side to the folder or subfolder name. Next, click the trashicon icon on the far right or in the top menu. Multiple data can be selected and deleted at once. Then, these data will be moved to the Trash space. The items in the trash will be automatically deleted after 30 days.

Can I delete a subfolder?

Yes, a subfolder can be deleted. To do this, select the subfolder you want to delete and click on the trashicon icon. The subfolder and all the contents in this subfolder will be moved to the Trash space. The items in the trash will be automatically deleted after 30 days.

How has 3D Modeling changed?

  • The list on the 3D Viewer was moved to a record focused list.

  • Badges to identify molecules, proteins, and other components were added in the list.

  • Protein editing tools (for example, change protonation states, mutate residues, delete sequence, etc.) were added in the 3D Modeling page. An edited protein can be saved as a new dataset.

  • More options to save edited molecules are now available.

  • A discussion board was added for collaboration and replaces Saved Views.

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Tutorial video about new 3D features

There are new badge and list features on the 3D Modeling page. Here is an introduction: Badges and Lists in Orion.

There are several more new videos about 3D modeling at Orion Video Tutorials.

What has changed on the Workfloe Page?

  • Job cost alerts can be set globally for all Floe runs in the Profile section. Users can modify Job cost thresholds in the Job form before launching a Floe.

  • Promoted Parameter Grouping

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