# Managing Trusted Research Environments

{% hint style="info" %}
Apollo and Trusted Research Environments licenses are required to use Trusted Research Environments on the DNAnexus Platform. [Contact DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}

A Trusted Research Environment (TRE) is a secure, configuration-driven framework for sharing sensitive biomedical data. It enables data providers to organize, manage, and share data with authorized researchers while maintaining full ownership and control.

As a TRE Admin, you manage the full lifecycle of secure environments — from initial setup to ongoing maintenance and data releases. This includes configuring data governance policies, organizing versioned data resource inventories, and managing multi-step access review workflows. For the researcher and reviewer perspective, see [Explore Trusted Research Environments](/user/trusted-research-environments.md).

## Setting Up a New TRE

Setting up a new TRE is a sequential process. Start with [planning your research environment](/admin/trusted-research-environments/planning-a-tre.md) to make the decisions that are hardest to change later:

* How many review steps your governance pipeline needs and who reviews each step
* Which data access restrictions to enforce on researcher projects

You also need to prepare four inventory assets before you can configure the TRE: the Tabular Data Inventory, Data Showcase, File Inventory TSV, and Data Collections JSON. Contact [DNAnexus Professional Services](https://www.dnanexus.com/professional-services) for guidance on preparing these assets.

TRE visibility — whether to restrict access to a defined list of authorized users or make the environment publicly discoverable to all users on the DNAnexus Platform — can be configured during initial setup or adjusted at any time after publishing.

Once your inventory assets are ready and your decisions are made, you can [create and publish the environment](/admin/trusted-research-environments/creating-a-tre.md).

## Configuring an Active TRE

After publishing, you can continue adjusting the TRE configuration:

* Control who can discover and access the environment by [managing TRE membership](/admin/trusted-research-environments/configuring-tre-membership.md).
* Add or remove individual reviewers from existing review steps by [configuring reviewers](/admin/trusted-research-environments/configuring-review-workflow.md).
* Set and adjust the restrictions enforced on all researcher projects using [data access policies](/admin/trusted-research-environments/managing-tre-lifecycle.md#update-data-access-policies), which work similarly to [project data access controls](/getting-started/key-concepts/projects.md#project-data-access-controls).

## Lifecycle Operations

A TRE moves through three states that determine what configuration is possible at each stage.

{% @mermaid/diagram content="flowchart LR
Start((Start)) -->|Create| Draft\[Draft]
Draft -->|Publish| Active\[Active]
Active -->|Deactivate| Maintenance\[Maintenance]
Maintenance -->|Reactivate| Active
Draft -->|Delete| End((Deleted))
Maintenance -->|Delete| End

%% Styling
classDef lifecycleBoundary fill:#60F299,stroke:#1F519D,stroke-width:2px,color:#000
classDef draftState fill:#66C9F9,stroke:#1F519D,stroke-width:2px,color:#000
classDef activeCycle fill:#1F519D,stroke:#1F519D,stroke-width:2px,color:#fff

%% Apply classes
class Start,End lifecycleBoundary
class Draft draftState
class Active,Maintenance activeCycle" %}

In **Draft** state, you have full configuration access: TRE details, membership, resource inventory, data access policies, and review steps. Once you publish to the **Active** state, the resource inventory structure and review pipeline lock. You can still update membership, adjust policies, and manage reviewers within existing steps.

When you need to update the inventory to a new data version, transition to **Maintenance** state. The TRE remains visible to researchers but is marked as under maintenance, and new access requests are suspended. Once the updated inventory is ready, reactivating returns the TRE to the **Active** state.

For all state transition procedures, see [managing TRE lifecycle states](/admin/trusted-research-environments/managing-tre-lifecycle.md).


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://documentation.dnanexus.com/admin/trusted-research-environments.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.