Projects
Learn to use projects to collaborate, organize your work, manage billing, and control access to files and executables.

About Projects

On the DNAnexus Platform, a project is first and foremost a means of enabling users to collaborate, by providing them with shared access to specific data and tools.
Projects have a series of features designed to facilitate collaboration, help project members coordinate and organize their work, and ensure appropriate control over both data and tools.
See the User Interface Quickstart for details on how to create a project, share it with other users, and run an analysis.

Managing Project Content

A key function of each project is to serve as a shared storehouse of data objects used by project members as they collaborate.
Click on a project's Manage tab to see a list of all the data objects stored in the project. Within the Manage screen, you can browse and manage these objects, with the range of available actions for an object dependent on its type.
The following are four common actions you can perform on objects from within the Manage screen.

Downloading Files

File objects can be directly downloaded from the system. To download a file:
  1. 1.
    Select its row, then click the More Actions button - the "..." icon - at the end of the row showing the file's name.
  2. 2.
    Select "Download" from the list of available actions.
  3. 3.
    Follow the instructions in the modal window that opens.

Getting More Information on Objects

To learn more about an object:
  1. 1.
    Select its row, then click the Show Info Panel button - the "i" icon - in the upper corner of the Manage screen.
  2. 2.
    Select the row showing the name of the object about which you want to know more. An info panel will open on the right, displaying a range of information about the object. This will include its unique ID, as well as metadata about its owner, time of creation, size, tags, properties, and more.

Deleting Objects

To delete an object:
  1. 1.
    Select its row, then click on the More Actions button - the "..." icon - at the end of the row.
  2. 2.
    Select "Delete" from the list of available actions.
  3. 3.
    Follow the instructions in the modal window that opens.
Note that deletion cannot be undone.

Copying Data to Another Project

To copy a data object or objects to another project, you must have CONTRIBUTE or ADMINISTER access to that project.
  1. 1.
    Select the object or objects you want to copy to a new project, by clicking the box to the left of the name of each object in the objects list.
  2. 2.
    Click the Copy button in the upper right corner of the Manage screen. A modal window will open.
  3. 3.
    Select the project to which you want to copy the object or objects, then select the location within the project to which the objects should be copied.
  4. 4.
    Click the Copy Selected button.

Access and Sharing

Adding Project Members

You can collaborate on the platform by sharing a project with other DNAnexus users. On sharing a project with a user, or group of users in an organization, they become project members, with access at one of the levels described below. Project access can be revoked at any time by a project administrator.

Removing Project Members

To remove a user or org from a project to which you have ADMINISTER access:
  1. 1.
    On the project's Manage screen, click the Share Project button - the "two people" icon - in the top right corner of the page. A modal window will open, showing a list of project members.
  2. 2.
    Find the row showing the user you want to remove from the project.
  3. 3.
    Move your mouse over that row, then click the Remove from Members button at the right end of the row.

Project Access Levels

Access Level
Description
VIEW
Allows users to browse and visualize data stored in the project, download data to a local computer, and copy data to other projects.
UPLOAD
Gives users VIEW access, plus the ability to create new folders and data objects, modify the metadata of open data objects, and close data objects.
CONTRIBUTE
Gives users UPLOAD access, plus the ability to run executions directly in the project.
ADMINISTER
Gives users CONTRIBUTE access, plus the power to change project permissions and policies, including giving other users access, revoking access, transferring project ownership, and deleting the project.

Project Access Levels: Two Examples

Suppose you have a set of samples sequenced at your lab, and you have a collaborator who's interested in three of the samples. You can upload the data associated with those samples into a new project, then share that new project with your collaborator, granting him or her VIEW access.
Alternatively, suppose that you and your collaborator are working on the same tissue samples, but each of you wants to try a different sequencing process. You can create a new project, then upload your sequenced data to the project. Then grant your collaborator UPLOAD access to the project, allowing him or her to upload his or her data. You'll then both be able to use one another's data to perform downstream analyses.

Making a Project Public

If you want to share a project with all DNAnexus users, you can make it public. You might do this if, for example, you've published a research paper and want to make the associated data available anyone who's read the paper. To make a project public, contact DNAnexus Support.

Project Data Access Policies

Users with ADMINISTER access to a project can configure data access policies for the project. These policies restrict ability of project members to copy, delete, and download project data. Special restrictions apply to projects containing data that qualifies as Protected Health Information (PHI).
To view or modify a project's access policies:
  1. 1.
    On the project's Settings screen, scroll down to the Access Policies section, to view or modify the project's policy settings. For a list of settings available, see table below.
  2. 2.
    To view the project's PHI Data Protection setting, scroll down to the Administration section. To set up PHI Data Protection for a project, contact DNAnexus Sales.

Access Policy Options

Policy
Description
Options
Copy Policy
Dictates whether project members can copy data to other projects or use data as input to executions in other projects. If not allowed, no users can copy data to other projects.
Allowed (default) or Not Allowed
Delete Policy
Dictates whether project members with CONTRIBUTE access to the project can delete data from the project. If not allowed, only members with ADMINISTER access to the project can delete data.
Contributors & Admins (default) or Admins Only
PHI Data Protection
If PHI Data Protection is enabled for a project, data in the project will be considered protected health information (PHI) and will be subject to additional restrictions to ensure security and compliance.
Not Enabled (default) or Enabled

Apollo Database Access

Apollo customers can limit access to project databases by project members with VIEW access, by using dx-toolkit to set the project's databaseUIViewOnlyflag to "true." Members with VIEW access will only be able to access project databases via the Cohort Browser.
This feature is only available to customers with an Apollo license. Contact DNAnexus Sales for more information.

Restricting Access to Executables

A project admin can configure a project to allow project members to run only specific executables as root executions. The list of permitted executables is set by entering the following command, via the CLI:
1
$ dx update project project-xxxx --allowed-executables applet-yyyy --allowed-executables workflow-zzzz [...]
Copied!
Note that by entering this command, you will overwrite any existing set of permitted executables.
To unset the list, and thus permit project members to run all available executables as root executions, enter the following command:
1
$ dx update project project-xxxx --unset-allowed-executables
Copied!
Note that executables that are called by a permitted executable are permitted to run, even if they are not included in the list.

Billing and Charges

On the DNAnexus Platform, running analyses, storing data, and egressing data are billable activities, and always take place within a specific project. Each project is associated with a billing account, to which invoices are sent, covering all billable activities carried out within the project.

Transferring Project Billing Responsibility

Transferring Billing Responsibility to Another User

If you have ADMINISTER access to a project, you can transfer project billing responsibility to another user, by doing the following:
  1. 1.
    On the project's Settings screen, scroll down to the Administration section.
  2. 2.
    Click the Transfer Billing button. A modal window will open.
  3. 3.
    Enter the email address or username of the user to whom you want to transfer billing responsibility for the project.
  4. 4.
    Click Send Transfer Request.
The user will receive an email notification of your request. To finalize the transfer, he or she must log onto the Platform and formally accept it.

Transfer Billing Responsibility to an Org

To transfer project billing responsibility to an org, follow the instructions in the Org Member Guide.

Cancelling a Transfer of Billing Responsibility

You can cancel a transfer of project billing responsibility, so long as it hasn't yet been formally accepted by the user in question. To do this:
  1. 1.
    Select All Projects from the Projects link in the main menu. Open the project in question. You'll see a Pending Project Ownership Transfer notification at the top of the screen.
  2. 2.
    Click the Cancel Transfer button to cancel the transfer.

Accepting a Transfer Request

When another user initiates a project transfer to you, you’ll receive a project transfer request, via both an email, and a notification accessible by clicking the Notifications button - the "bell" - at the far right end of the main menu.
Note that if you did not already have access to the project being transferred, you'll get VIEW access, and the project will appear in the list on the Projects screen.
To accept the transfer:
  1. 1.
    Open the project. You'll see a Pending Project Ownership Transfer notification in the project header.
  2. 2.
    Click the Accept Transfer button.
  3. 3.
    Select a new billing account for the project from the dropdown of eligible accounts.

Projects with PHI Data Protection Enabled

If a project has PHI Data Protection enabled, it may only be transferred to an org billing account which also has PHI Data Protection enabled.
Ownership of sponsored projects may not be transferred without the sponsorship first being terminated.

PHI Data Protection

Protected Health Information (PHI) is identifiable health information that can be linked to a specific person. On the DNAnexus Platform, PHI Data Protection safeguards the confidentiality and integrity of data in compliance with the Health Insurance Portability and Accountability Act of 1996 (HIPAA).
When PHI Data Protection is enabled for a project, it is subject to the following protective restrictions:
  • Objects in the project cannot be copied to other projects that do not have PHI Data Protection enabled ("non-PHI projects").
  • Jobs that run in non-PHI projects cannot access any data that can only be found in PHI projects.
  • Job email notifications sent from the project refer to objects by object ID instead of by name, and other information in the notification may be elided. If you receive such a notification, you can view the elided information by logging onto the Platform and opening the notification and accessing it in the Notifications pane, accessible by clicking the "bell" icon at the far right end of the main menu.
Only projects billed to org billing accounts can have PHI Data Protection enabled.
For more information about enabling PHI Data Protection for a project, contact DNAnexus Sales.

Project Sponsorship

A user or org can sponsor the cost of data storage in a project for a fixed term. During the sponsorship period, project members may copy this data to their own projects and store it there, without incurring storage charges.
On setting up the sponsorship, the sponsor sets it end date. The sponsor can change this end date at any time.
Billing responsibility for sponsored projects may not be transferred.
Sponsored projects may not be deleted, without the project sponsor first ending the sponsorship, by changing its end date to a date in the past.
For more information about sponsorship, contact DNAnexus Support.

Learn More

See the Org Management page for detailed information on projects that are billed to an org.
Learn about accessing and working with projects via the CLI:
Learn about working with projects as a developer: