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Storage Connections

Storage connections are a cloud storage integration for AVITI Systems to transfer sequencing data to a cloud storage bucket. ElemBio Cloud centrally manages the storage connections for all connected systems.

ElemBio Catalyst supports a storage connection that Element hosts and manages on your behalf. The following providers also support storage connections.

Storage Location Data Upload

A sequencing run continuously uploads data from the instrument to a cloud storage bucket. AVITI OS streams data directly to the bucket. If you are using a provider with a full-service solution, such as ElemBio Catalyst or DNAnexus, the bucket is managed for you. If you are using a custom cloud service provider, such as AWS or GCS, you fully own and control your bucket.

The storage connection configuration in ElemBio Cloud provides the permissions to generate temporary credentials that let the instrument communicate with the bucket. If the network connection experiences a disruption, the instrument caches data and retries the upload until it succeeds.

Data Upload Diagram

Storage Connection Locations

Storage connection cards include a storage location link and other details. Information depends on the provider type.

  • Bucket Name: For AWS and GCS, the name of the cloud storage bucket with a link
  • Prefix: For AWS and GCS, the object prefix for the storage location
  • Region: For AWS, the bucket region
  • Project: For DNAnexus, the associated project with a link
  • Run Upload Folder: For DNAnexus, the folder structure in the project for run upload data

Storage Connection Statuses

A badge on storage connection cards indicates one of the following connection statuses:

  • Connected: ElemBio Cloud successfully verifies the connection.
  • Unverified: ElemBio Cloud cannot verify the storage connection and the associated provider credentials. The storage connection is unavailable until the issue is resolved. To resolve, verify the storage connection and review any error messages.

Add a Storage Connection

Before you create a storage connection, you must set up the provider for the storage connection and complete any provider requirements, including credentials. For more information, see the page for your provider:

  1. On the Storage page, select Add Storage.
  2. In the Provider Name drop-down menu, select the provider for the storage connection.
  3. Enter a unique name for the storage connection.
  4. For AWS providers, select the region associated with the bucket in the Region list. If you do not see the region you need, contact Element Technical Support.
  5. For AWS and GCS providers, complete the following fields:
    1. Enter the Bucket Name.
    2. If applicable, enter a Prefix that indicates the folder structure for run data.
  6. For DNAnexus providers, complete the following fields:
    1. Enter the Project ID.
    2. If applicable, enter a Run Upload Folder to indicate a folder structure for run data.
  7. Select a Use for Run Upload setting.
    • If you enable the setting, the storage connection becomes available on instruments associated with your organization.
    • If you disable the setting, the storage connection is unavailable on instruments. You can only use the storage connection for ElemBio Cloud activities, such as verified flows.
  8. Select Save.

Managing Storage Connections

The following buttons on the storage connection cards allow you to manage connections. The available actions depend on your user permissions.

  • Verify: Verifies the permissions for data transfers.
    • If the storage connection is connected, a green success message appears.
    • If a red error message appears, review the error message to address the issue.
    • For additional verification, access the ConnectionTest folder in the storage location and make sure the elembio-read-write.txt file shows a successful verification date.
  • View Associated Runs: Shows a list of runs that use the storage connection for output files.
  • Set As Default: Makes a storage connection the default selection in run setup for AVITI Systems associated with the organization.
    • A badge on a storage connection card identifies the current default selection.
    • If you set a default but want to use a different storage connection for a run, you can manually make the change during run setup.
    • The storage connection default set in AVITI OS can override the default set in ElemBio Cloud.
  • Edit: Modifies the storage connection settings. Changes take effect immediately. ElemBio Cloud restricts editing to the name field and the Use for Run Upload option.
  • Delete: Removes the storage connection from ElemBio Cloud and all associated AVITI Systems.
    • ElemBio Cloud prohibits the deletion of a storage connection in use by an associated system.
    • When prompted, enter the name of the storage connection to confirm deletion. Upon confirmation, ElemBio Cloud deletes the storage connection.

If you disable the Use for Run Upload setting while editing a storage connection, the connection immediately becomes unavailable on associated instruments. Before disabling the setting, make sure that the change does not impact any in-progress instrument activities.