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ElemBio Cloud Release Notes

v3.4.0​

November 14, 2024

New Features​

ElemBio Cloud 3.4.0 introduces Compute Connections, which integrate ElemBio Cloud with provider-specific compute environments encoding the computational resources necessary to execute bioinformatic workflows. Existing flows will be automatically migrated to create connections on your behalf. Compute connections are available for:

  • ElemBio Catalyst
  • AWS, though AWS HealthOmics
  • DNAnexus
  • Seqera Platform

Resolved Issues​

  • Reagent barcodes display the expiry date of the reagent, rather than being blank.
  • When setting up a planned run from ElemBio cloud using a kit compatible with a short-insert custom recipe, the short-insert recipe has been updated to enhance polony density.
  • When an ElemBio Catalyst Analysis bucket is provisioned during setup, the Enabled for Run Upload Setting is blocked for selection.

v3.3.0​

October 25, 2024

New Features​

ElemBio Cloud 3.3.0 introduces Data Explorer, which allows users to seamlessly browse AWS S3 and ElemBio Catalyst buckets registered as storage connections in ElemBio Cloud. Key features include:

  • Browse and Navigate: Explore the folder structure within the bucket for full file visibility.
  • Metadata Display: View key details, such as file size, updated date, and archive status.
  • Search and Filter: Find files quickly with search options.
  • Download: Download files or directories directly to a local environment through CLI commands or a download script.
  • File Selection: When selecting individual files to download using a script, users can select files across folders. A running cart displays a count of the selected files and folders.
  • Mini Views: Browse and download the contents of specific runs and flows on the Run Details page.

Improvements​

  • When users export a table, ElemBio Cloud includes the date and time in the file name.

v3.2.0​

September 25, 2024

Improvements​

  • Indexing Assignment Metrics:
    • If AVITI OS skips onboard demultiplexing for a run, the Indexing Assignment chart displays a message that indicates the reason for skipping demultiplexing.
    • Tooltips for samples in the Indexing Assignment chart display the perfect match and partial match metrics, up to 2 decimal points, along with the sample name or number.
  • Added support for ElemBio Catalyst AWS regions us-east-1 and ca-central-1.
  • When adding an AWS storage connection, additional validations ensure that the input bucket name and prefix conform to the allowed values. Bucket names cannot start with s3:// and prefixes cannot start with a slash (/).
  • In the Advanced Run Settings of the Run Planning form, the Filter Mask field uses additional validations to ensure the entry of a valid base mask.
  • Added an Export button to the All Runs table.
  • Added the ability to verify a flow from the Flows page.

Resolved Issues​

  • When a Bases2Fastq execution through ElemBio Catalyst for a 2 x 300 dataset leads to an out-of-memory (OOM) error, the Bases2Fastq flow supports a memory rollover and autorestart.

v3.1.0​

August 14, 2024

ElemBio Cloud v3.1.0 introduces new data-sharing features for ElemBio Catalyst and AWS providers.

New Features​

  • Data Sharing: This release introduces a new feature that enhances how you share data with external parties from ElemBio Catalyst or your AWS account. With our latest update, you can grant read-only access to specific buckets, ensuring secure and controlled data sharing without the risk of data modifications. The update enables:
    • Simple and secure data sharing with external accounts
    • Instant access to run, FASTQ, or analysis data by your secondary analysis provider of choice
  • The data sharing feature includes:
    • A new Data Management section on the storage connection edit form, where you can add up to 10 external AWS principals (IAM role, IAM user, or AWS account) to grant read-only access to an external party. Only Administrators can add or remove principals to grant access.
    • Updated visuals on the storage connection card that display a count of the connected principals.
    • Updated requirements for AWS credential permissions that are required to enable data-sharing features on your AWS storage connections.
  • Added functionality saves browser navigation states, ensuring the browser Back button restores your previous navigation seamlessly.

Improvements​

  • On the Active Runs page, fields are reorganized for improved visibility, including adding a Sequencing label in the header and moving the Started field to the field list.
  • Bases2Fastq version 2.0.0, released July 19, is available for use in ElemBio Catalyst flows and is the latest version assigned.
  • When creating a planned run, the Run Planning form displays the compatible instrument type (AVITI or AVITI LT) in addition to the compatible AVITI OS version.
  • Read Order is removed from the Planned Runs list view due to the deprecation of V1 chemistry.
  • In the Planned Runs table, the run name links to the edit form for the planned run. You can still edit the planned run through the Actions menu.

Resolved Issues​

  • When a run uses the Individually Addressable Lanes add-on, the Primary Analysis Metrics on the Run Details page correctly reports the Lane 2 thumbnail, rather than reporting the Lane 1 thumbnail.
  • When setting up an ElemBio Catalyst Free Trial, the start button is enabled for administrators.

Known Issues​

  • The Team Members page can be slow to display a long list of users.

v3.0.0​

July 18, 2024

ElemBio Cloud v3.0.0 is a sustaining update to the software frameworks used by ElemBio Cloud, including overall experience updates to improve consistency and performance.

New Features​

  • When setting up a planned run, the Run Manifest upload uses a drag-and-drop. You can continue to browse and select to upload a run manifest.

Improvements​

  • On the Executions page, the Flow Name links to the flow edit form.
  • When using the data browser, the display uses pagination rather than an infinite scroll.
  • Planned runs no longer support version 1 chemistry.
  • Updated the naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ kits.

Resolved Issues​

  • When adding a new storage connection Seqera is no longer selectable as a provider. Seqera is not a compatible storage partner.
  • When a run manifest contains > 768 index pairs or sequences, the Indexing Assignment chart on the Run Details page displays the same notification as AVITI OS. The notification indicates that onboard demultiplexing cannot be completed.
  • On the Run Details page, the PhiX Error Rate chart reports the lane-level %PhiX Assigned metric when a run uses the Individually Addressable Lanes add-on.

Known Issues​

  • The Team Members page can be slow to display a long list of users.

v2.2.1​

June 27, 2024

ElemBio Cloud v2.2.1 introduces features that support AVITI OS v2.6.0.

New Features​

  • When setting up a planned run with a compatible sequencing kit, you can apply Advanced Run Settings, including Custom Recipes, Filter Mask, and Polony Density (also known as Expert Mode HD). Access to these settings requires an add-on.
  • The Cloudbreak UltraQ sequencing kit is available in the Run Planning form, including the following kit:
    • AVITI 2x150 Sequencing Kit Cloudbreak UltraQ

Improvements​

  • When adding an AWS HealthOmics Bases2Fastq flow, an additional validation ensures the execution role is a properly formatted ARN input.

v2.1.0​

May 2, 2024

New Features​

  • The FASTQ Files tab on the Run Details page includes the following improvements:
    • The data browser links to logs in the provider console for AWS, DNAnexus, and Seqera flows.
    • When a flow execution fails, a banner displays the failure reason from the provider.
  • ElemBio Cloud displays a cookie use and consent notification for first-time visitors.
  • When a team member reexecutes a flow, the Executions table and FASTQ Files tab identify the team member in the Executed By field.

Improvements​

  • Bases2Fastq flows support Bases2Fastq v1.8.0 and use it as the latest available version.
  • ElemBio Catalyst region names include the cloud storage provider (e.g., AWS) and the geographic region (e.g., Oregon), in addition to the bucket region (e.g., us-west-2).
  • Storage connection cards and edit forms display the name of the associated provider.
  • Storage connection cards display a Settings field with detailed setting information, such as the availability for run uploads on instruments.

Resolved Issues​

  • Cloudbreak Freestyle sequencing kits display the High, Medium, or Low output value on the Run Details page.
  • Values for total run times in ElemBio Cloud use the Time Started value as the start time, rather than the Time Created value. This change better estimates the total run time and aligns it with the run time in AVITI OS.
  • On the Run Details page, the Primary Analysis charts retain selections, zoom level, and other interactive settings during data updates, rather than repeatedly resetting the chart.
  • Executions of Bases2Fastq flows correctly display the Bases2Fastq version on the FASTQ Files tab.

v2.0.0​

March 27, 2024

ElemBio Cloud v2.0.0 introduces features that support AVITI OS v2.5.0.

New Features​

Analysis Platforms in ElemBio Cloud​

ElemBio Cloud v2.0.0 introduces support for native and integrated analysis solutions. Using one of the available cloud service providers, data streamed from an AVITI System to cloud storage can generate FASTQ data automatically upon run completion. The platform lets you connect to secondary analysis partners, simplifying the process for secondary analysis.

This release makes the following cloud service integrations available:

  • ElemBio Catalyst: This release introduces ElemBio Catalyst, a subscription-based native data storage and analysis platform on ElemBio Cloud. With ElemBio Catalyst, Element acts as your cloud service provider, managing data storage and compute on your behalf. Sequencing runs sent to ElemBio Catalyst storage automatically generate FASTQ files upon run completion, which are accessible in Elembio Cloud. With ElemBio Catalyst, you can:

    • Stream data from the AVITI directly to an AWS S3 bucket that Element manages, with the data still owned by yourself.
    • Manage a flow to automatically generate FASTQ files upon run completion.
    • Browse and download generated FASTQ data in the ElemBio Cloud interface.

  • DNAnexus: ElemBio Cloud integrates with DNAnexus, a comprehensive cloud-based platform to manage and analyze omics data. Using DNAnexus, you can:

    • Stream data from the AVITI directly to a DNAnexus project.
    • Connect a custom workflow to automatically generate FASTQ data upon run completion.

  • Amazon Web Services (AWS): This release expands the capability of connections with AWS beyond AWS S3 buckets to support analysis integrations with Amazon HealthOmics. Using AWS, you can connect to Amazon HealthOmics Ready2Run Bases2Fastq workflow to automatically generate FASTQ files upon run completion.

  • Seqera Platform: ElemBio Cloud integrates with the Seqera platform to enable a verified Bases2Fastq flow. The flow orchestrates a Bases2Fastq workflow to automatically launch in your connected Seqera workspace upon run completion. The pipeline generates FASTQ files through a Google Cloud Platform or AWS account connected to your Seqera instance.

This release also introduces the following features and changes:

  • A new Integrations section replaces the existing Storage section. The new section includes the following subsections:

    • Providers: A provider represents the single source of reusable credentials that securely connect ElemBio Cloud to a cloud service provider, such as AWS, Google, DNAnexus, and Seqera.
    • Storage: Storage connections use a provider credential to set up a cloud storage integration. The integration lets AVITI Systems transfer sequencing data to the cloud storage bucket.

  • A new Analysis section connects FASTQ generation flows from ElemBio Cloud to providers that support analysis, including ElemBio Catalyst, DNAnexus and AWS. The new section includes the following subsections:

    • Flows: Flows are cloud-hosted workflows that process AVITI System data for analysis, file conversion, and other post-sequencing activities. This release introduces the verified Bases2Fastq flow that generates FASTQ files automatically upon run completion for ElemBio Catalyst, DNAnexus, and AWS providers.
    • Executions: Executions display records of current and historical flow executions.

  • Data Management features allow you to access and manage the output files from sequencing runs and flow executions for ElemBio Catalyst and AWS S3 cloud storage.

    • On the Run Details page, navigate through the sequencing run or Bases2Fastq output directory.
    • Download files individually or programmatically using temporary access granted through presigned URLs or AWS CLI.
    • Reexecute a Bases2Fastq flow with an updated Run Manifest or input parameters.

Planned Runs​

  • The Third Party library type is available on the run planning form, supporting Cloudbreak Freestyle sequencing, including the following kits:

    • AVITI 2x75 Sequencing Kit Cloudbreak Freestyle Medium Output
    • AVITI 2x75 Sequencing Kit Cloudbreak Freestyle High Output
    • AVITI 2x150 Sequencing Kit Cloudbreak Freestyle Low Output
    • AVITI 2x150 Sequencing Kit Cloudbreak Freestyle Medium Output
    • AVITI 2x150 Sequencing Kit Cloudbreak Freestyle High Output
    • AVITI 2x300 Sequencing Kit Cloudbreak Freestyle Medium Output
    • AVITI 2x300 Sequencing Kit Cloudbreak Freestyle High Output

  • When setting up a planned run, the Low-Diversity High-Multiplex option is available for all Cloudbreak and Cloudbreak Freestyle sequencing kits using Adept or Third Party library types, instead of only 2x300 Cloudbreak kit runs. Planned runs that use this setting are only compatible with AVITI OS 2.5.0 or later, except for 2x300 Cloudbreak kits, which retain prior compatibility.

  • When setting up a planned run, individual cycle length maximums no longer apply for all cycles (R1, R2, I1, I1). The maximum total number of cycles for the kit remains enforced. Planned runs using this setting are only compatible with AVITI OS 2.5.0 or later.

  • When you set up a planned run that is not compatible with an older AVITI OS version, a warning displays to indicate planned run compatibility.

Resolved Issues​

  • Responsive issues on chart rendering are resolved for smaller screen sizes and zoom levels.
  • When uploading a run manifest with an invalid name to a planned run, ElemBio Cloud identifies and displays the error, instead of allowing the planned run to proceed without a run manifest.

v1.7.0​

January 16, 2024

Improvements​

  • Updated the Plan a Run form as follows:
    • Added safeguards to Cycles fields that prevent exceeding the maximum number of cycles for any kit configuration.
    • Added requirement to complete fields in order.
    • Reordered fields to reflect the order for run setup.
    • Renamed Low-Diversity Amplicon Library field as Low-Diversity High-Multiplex.

v1.5.0​

November 13, 2023

New Features​

  • When you plan a run with the Adept Workflow and a 2 x 300 kit, the Low-Diversity Amplicon Library option becomes available.

v1.4.0​

October 26, 2023

ElemBio Cloud v1.4.0 introduces features that support AVITI OS v2.4.0.

New Features​

  • When a run uses AVITI OS v2.4.0 and a run manifest that enables onboard demultiplexing, the expanded Indexing Assignment Chart on the Run Details page displays a Top Unassigned Sequences table.
  • The Plan a Run form includes additional information on kit availability for the Element AVITI System LT.

Improvements​

  • When adding a storage connection for AWS S3, you can select Asia-Pacific regions in the Region list.

Resolved Issues​

  • An invitation status correctly updates to Expired after 7 days, rather than remaining as Pending.

v1.3.0​

September 21, 2023

ElemBio Cloud v1.3.0 introduces features that support AVITI OS v2.3.0.

New Features​

  • Planned Runs: Run planning lets team members remotely create and manage runs in ElemBio Cloud for use on any connected instrument. The feature shortens setup time on the instrument and provides full sample and run manifest validation, which can simplify debugging and prevent issues during on-instrument run setup.
    • Select a planned run during run setup on any connected instrument. To use planned runs, an instrument must have AVITI OS v2.3.0 or a later version.
    • All users can create and edit planned runs. ElemBio Cloud tracks changes to enable auditing.
    • After a planned run starts on an instrument, you can remotely monitor the run in ElemBio Cloud.
  • Add-Ons: An Add-Ons page displays the add-ons for your organization, including expiration dates and a history of any previous add-ons.
    • Add-ons apply to connected and offline instruments that have AVITI OS v2.3.0 or a later version.
    • ElemBio Cloud lets you download a product key for the installation of add-ons on offline instruments.
  • The Team Members section is renamed to Organization and contains both Team Members and Add-Ons pages.

Resolved Issues​

  • The y-axis for the % Q30 chart adjusts to display the full range of values for each cycle, rather than values < 90%.
  • The Top Samples with Mismatch table displays samples in descending order by default, rather than randomly.

v1.2.0​

September 7, 2023

New Features​

  • The Run Setup card displays updated field names and adds a Library Pools field.

Resolved Issues​

  • The y-axis of the Indexing Assignment chart displays the percent assigned value of each sample, rather than displaying only values > 2%.
  • The % Assigned Reads metric in the Indexing Assignment chart includes perfect and partial match rates, rather than assigned reads with perfect matches only.

v1.1.0​

July 13, 2023

Feature Updates​

AVITI OS v2.2.0 launched July 11, 2023. Customers who upgrade to AVITI OS v2.2.0 can access metrics and charts in ElemBio Cloud for the following data:

  • Base composition
  • Image thumbnail
  • Percent passing filter (PF)
  • Percent PhiX-aligned

v1.0.0​

June 16, 2023

Initial release of ElemBio Cloud with the following components:

  • Remote run monitoring
  • Cloud storage connections
  • Team member management
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