Welcome to the fifth volume of our product release notes in 2021! We’ve been working hard to bring you some much requested features. Read along to learn more about our new product features and enhancements released April 2021 - May 2021.

Notebook

Benchling’s Notebook helps users log their experiments, create protocols, and capture results against their samples.

Insert rows on structured tables

Users can now insert rows above or below a selected region within a structured table. You can also highlight multiple rows for bulk insertion.

Molecular Biology

Benchling’s Molecular Biology suite is a cutting-edge in-silico design tool that supports the latest scientific workflows.

New entity support for RNA oligos

Benchling now supports a new entity type: RNA oligos. This allows users to more easily create, register, and model RNA oligos. Existing API support for oligo endpoints have been deprecated in favor of specific DNA-oligo and RNA-oligo endpoints. Contact support@benchling.com to enable this feature. Check out the Spring Product Bulletin to learn more.

Update amino acid residues when “Updating Entities” from CSV

Benchling now supports bulk updating of amino acid residues on protein sequences via the “Update Entities from CSV” workflow.

Find sequence parts using Ctrl-F

Users can now search for filled parts on sequence maps when using Ctrl-F search.

Faster auto-annotating of AA feature libraries

Previously, auto-annotations of AA features were much slower than DNA features. Users can now bulk annotate AA-based feature libraries at a much faster rate.

Ability to rename AA alignments

Users are now able to rename amino acid alignments.

Registry and Inventory

Benchling Registry and Inventory combine to form an extremely powerful solution for life sciences R&D samples. The Registry can be used to model and log any biological entity, while the Inventory provides an interactive digital window into the physical storage system of your lab.

Enforce lineage for entity relationships

Previously, no restrictions existed on entity linkages other than schema type. Now, users can restrict what values are considered valid for a given entity link to enforce lineage between entities with parent links. Contact support@benchling.com to enable this feature.

Schemas

Utilize floats for subtraction computed fields

Computed fields now support floats for subtraction.

Use boolean fields in results

Result schema fields now support boolean-type fields.

Insights

Benchling Insights enables users to query, visualize, and share high-quality, structured data that resides in Benchling.

SQL templating is now available

The SQL templating feature is now available on all industry environments.

Update naming in “Add block” menu

Naming within the Insights “Add block” menu has been updated as follows:

  • TEMPLATES -> BLOCK TEMPLATES

  • Entity -> List of entities

  • Custom SQL query -> SQL query

Lab Automation

Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.

Use Lab Automation UI for run configs

Run schemas can now be configured through the UI, reducing the need for custom JSON configuration. Users can use the UI for configuring run fields and input file configs. Contact support@benchling.com to enable this feature.

Process plate shapes in runs

Data formatted in a plate schema shape (e.g. a 96-well plate) can now be transformed into new columns, allowing the data to be processed by Lab Automation runs.

New run edit permissions

Users now have more control over run editing in the UI. You can edit runs in the UI if they were created via API. Users can also disable the run edit button after a run has been created, an input file has been generated, or an output file has been processed. Contact support@benchling.com to enable this feature.

Performing timezone calculations in output file configs

Lab Automation runs including a date or datetime column mapping will include a timezone picker at runtime.

Allow skipping wells in WELLS lookup steps

Benchling Lab Automation Run schemas now support a “Skip Wells” parameter that allows users to choose which individual wells to skip.

Application Platform

Benchling's Application Platform helps provide a unified experience for our users and makes it easy to work across the Benchling applications seamlessly.

New Validated Cloud badge icon

Validated cloud environments now have a visual indicator on user avatar icons.

View tenant version and environment in validated cloud environment

In a modal view, users on a Validated Cloud tenant can now view the version of Benchling and the unique name of the tenant.

Disable email address changes

Users can no longer change the email address associated with their account. Note: This was released in the Volume 3 feature releases.

Developer Platform

Our developer platform is fundamental to centralizing and standardizing all your R&D data. Benchling’s APIs and Events are built to match the flexibility and speed of modern life science R&D.

Developer capability now in Capability Management

Tenant Admins can give users access to the Developer Platform via capability management. Enabling the Developer Platform capability will give a user access to the API and Warehouse.

Old API reference documentation deprecated

We have removed the old API reference documentation. It will now automatically forward site visitors to the new documentation site at benchling.com/api/reference.

View new API guides

We have published new online API tutorials and guides that cover filters and pagination, registering entities, and schemas and schema fields.

Request specific return fields in plates API

The Plates API now allows users to request specific return fields, resulting in faster performance.

Use GET and LIST endpoints for request task schemas

Users can now access GET and LIST endpoints for request task schemas.

Sequence search endpoints released in beta

Sequence search endpoints are now live for all customers that have beta API’s enabled, which can be accessed at https://benchling.com/api/v2-beta/reference#/.

New filtering options for LIST endpoints

Additional options to the archiveReason LIST endpoint have been added that allow greater filtering capabilities. This includes the ability to filter by archive reason, include unarchived items, or return both archived and unarchived items.

Dropdown options can now be archived and unarchived via the API

This new endpoint allows users to archive or unarchive options within a dropdown via the API. Please reference the documentation linked here for additional information.

Greater consistency with formatting for POST and PATCH endpoints for schema fields

Previously, creating runs and results with schema fields via the API required different formatting than other schema API objects. The POST and PATCH run schema fields and POST result fields are now consistent with other schema objects in the API. The old formatting is still accepted, however we recommend developers migrate to the new format when possible.

Improved API schema view

API reference documentation now includes longer form descriptions and improved UX for the “schema” view on endpoints.

Added a “copy public link” button to the API docs

Users can now copy a public link when navigating tenant-specific API docs.

Users with the “Copy API ID” setting enabled can now copy the ID of runs

Users can now use the “Copy API ID” feature to quickly copy the ID of runs. For instructions on how to enable this feature, please refer to this link.

More improvements to the API documentation

We’ve made several changes to descriptions and examples within the Benchling API documentation:

  • Added the full type of CustomFields

  • Added an enum for AIG/AOP status

  • Added an enum for containableType

  • Completed the type of schemas and schema fields (archiveRecord, mixture, numericMin, numericMax, etc.)

Bug Fixes

The following bugs were fixed in this release:

Molecular Biology and Chemistry

  • Spreadsheet import CSV headers are optional when importing oligos

Notebook

  • Fixed issue where blob links in registration & transfer tables did not create attachments when exporting notebook entries

  • Fixed issue where adding a highlight to a cell in a template caused the row to be skipped when filling in rows via ‘Add from Structured Table’

  • Fixed issue preventing cloning entry versions when a mixtures table is present

Lab Automation

  • Missing lookup values are now automatically set to [None] in output files to prevent crashing

  • Spec validation no longer crashes when Unicode values are included in error messages

  • Run saving errors caused by orphaned lookup steps left by deleted input file config have been resolved

  • Benchling now ensures user preferences for per-run folder and location pickers are unique

  • CONSTANT lookup step can now set fields in destinationInfo to populate a dropdown field

  • The raw time-parsing from Excel files with no date information has been fixed

  • Benchling can now handle setting empty values in a CONSTANT step

  • Benchling now prevents users from selecting a non-containable entity as content of a container

  • An error no longer appears when the TRANSFER_VOLUME_AMOUNT column is empty but FINAL_VOLUME_AMOUNT is specified

  • An error message no longer appears when the name is missing from the output file config

  • Benchling can now handle invalid values in FILTER processing steps

Application Platform

  • When users are now added to an organization or team and provisioned their capabilities, Benchling now syncs the provisioned capabilities with the user preference flag

  • A name truncation has been added to dropdowns so dropdown fields and menus are no longer broken by long names and descriptions

Developer Platform

  • Race condition on setting entry schema now allow single entry events to be delivered

  • Assay Schemas endpoints now have stable ordering and pagination for schemas that were created at the same time

  • Alpha Python SDK codegen models now properly deserialize nullable properties that are unset

  • Users are no longer required to login when browsing public docs

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