Projects Guide

What is a project

A project is a collaborative workspace on the DNAnexus platform where you can store objects such as files, applets, and workflows. You can then share your project with other users by giving them access to the project. Within projects, you can run jobs and analyses — executions of apps/applets and workflows respectively. Any user with access to the project can see the history of all executions run in the project. Note: For the remainder of this guide, we will refer to both jobs and analyses as simply "executions."

In short, projects can be thought of as both a "file system" for a set of data and history of executions that you want shared with a group of users.

Project access

You can collaborate on the platform by sharing, giving access to, projects with other DNAnexus users. You can give access to projects to individual users or a group of users within an organization at the levels described in the table below. Access to projects can be revoked at any time by the project administrator.

Project access levels

Access Level Description
VIEW Allows users to browse and visualize data stored in the project, download data to their local computer, and copy the data to further analyze it in their own projects.
UPLOAD Gives users VIEW access, plus the ability to create new folders and data objects, modify 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.

Sharing a project with a user

You can give an individual user access to a project at any of the these access levels by sharing the project with a user.

For example, suppose you have a set of samples sequenced at your lab, and you have a collaborator who is interested in three of the samples. You can upload all the data associated with those samples into a new project and share that new project with your collaborator, granting your collaborator VIEW access.

Alternatively, if you and your collaborator are both working on the same tissue samples but wish to try different sequencing processes. You can create a new project for your collaboration and upload your sequenced data to the project. You can then give your collaborator UPLOAD access to the project so he can also upload his data. Both of you will then be able to use the shared data to perform downstream analyses on the data sets.

To share a project in the UI, please follow the instructions here. To use the CLI, use the instructions here.

Advanced sharing

In addition to sharing projects with a single user, you can grant access to projects to entire groups of users. The following project sharing methods exist on the platform:

  1. Grant access by sharing the project directly with the user
  2. Grant access by sharing the project with an org of which the user is a member

You can be granted access to a project by more than one method. If this is the case, your effective access level to the project will be the greatest level across all the methods. For example, if a project is shared with user-smithj with CONTRIBUTE access, and shared with org-demo_org with VIEW access where user-smithj is a member of org-demo_org, user-smithj will ultimately have CONTRIBUTE access to the project.

For more information and use cases for sharing projects with an org, please see the Organizations Member Guide

Note about public projects: If you wish to make your data available to all DNAnexus users; e.g. making available the data associated with a published research paper, please contact support@dnanexus.com.

Project policies

Users with ADMINISTER access to projects can configure several different project policies for the project which restrict how the data can be modified or copied to other projects.

The following policies exist:

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. Allowed (default) or Not Allowed
PHI Data Protection If PHI Data Protection is enabled for a project, the 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

Users can view or configure policies for a given project on the Settings tab in the project header.

Screenshot of project settings in project header

Project billing accounts and ownership

All storage costs and compute costs associated with executions run in a particular project are invoiced to the project’s billing account. You can bill a project to your own account (e.g. user-smithj) or to an org in which you have permissions to perform billable activities. For more information about orgs and billing, please see the Organizations on DNAnexus guide.

Users with UPLOAD or greater project access level to the project will be able to add more data to the project. All users with CONTRIBUTE or ADMINISTER access will be able to launch new executions and incur charges against the project’s billing account.

Project transfers

You may change the billing account of a project by transferring the project to another user or to an org.

Note: Please note that projects which are sponsored may not be transferred. You must terminate the sponsorship before transferring the project

Note: Projects containing PHI data may only be transferred to org billing accounts which have PHI features enabled

PHI Data Protection

PHI (Protected Health Information) refers to identifiable health information that can be linked to a specific person. PHI Data Protection features in DNAnexus guard the confidentiality and integrity of the data stored in a project in compliance with HIPAA. If a project is marked as containing PHI (a "PHI project"), the project will be subject to the following protective restrictions:

  • Objects in the project cannot be copied to other projects that are not marked as containing PHI ("non-PHI projects")
  • Jobs that run in non-PHI projects will not be able to access any data that can only be found in PHI projects
  • Job email notifications sent from the project will refer to objects by object ID instead of name for extra security, and other information in the notification may be elided. You will need to log in to DNAnexus to view the complete message.

Only projects with billing accounts set to an organization can have be marked as containing PHI. For more information about enabling PHI Data Protection features for your organization, please follow the instructions here. Once you have done so, you can mark any specific project as containing PHI by visiting the project's "Settings" page.

Project sponsorship

Project sponsorship is a feature available upon request which allows a user or org (the "initial Sponsor") to sponsor the storage cost for data objects stored in a project until the sponsorship end date. During the sponsorship period, other users may copy and store the data in their own projects without incurring storage charges.

The sponsorship end date is set at the time of project sponsorship and may be changed by the initial Sponsor at any time. Projects that are sponsored may not be transferred or deleted. If you wish to delete or transfer a sponsored project, you will first need to end the sponsorship by setting the sponsorship end date to a time in the past.

For more information about data sponsorship and request access to sponsorship features, please contact support@dnanexus.com.

Last edited by pmurray, 2017-06-29 21:00:14

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