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.
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
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.
Gives users VIEW access, plus the ability to create new folders and
data objects, modify metadata of open data objects, and close data
Gives users UPLOAD access, plus the ability to run executions directly
in the project.
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
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:
- Grant access by sharing the project directly with the user
- 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
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
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:
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
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.
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.
You may change the billing account of a project by transferring the project
to another user or
to an org.
Please note that projects which are
may not be transferred. You
must terminate the sponsorship before transferring the project
Projects containing PHI data
may only be transferred to org billing accounts which have PHI features
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
have be marked as containing PHI. For more information about enabling
PHI Data Protection features for your organization, please follow the
Once you have done so, you can mark any specific project as containing
PHI by visiting the project's "Settings" page.
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
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 firstname.lastname@example.org.