Release Notes: Volume 10, 2023

  • Updated

Welcome to the tenth volume of our 2023 product release notes! We’ve been working hard to bring you performance improvements that add value to your work. Read on to learn about the product enhancements and bug fixes released in October 2023.


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

Audit logs now include attachment names [2023.10.N.1]

Users can now more easily understand audit log entries as audit logs now use attachment names instead of Warehouse IDs.

Small Molecule

The molecule entity in Registry helps users model and interact with chemical compounds throughout the platform, enabling users to draw, visualize, store, and search chemical structures.

V3000 MolFile and RDKit Upgrade [2023.10.SM.1]

Users will benefit from the V3000 MolFile support and the RDKit upgrade, which bring several enhancements. These include improved stereochemical support, support for larger molecules, enhanced molecule rendering, support for polymer repeat notation, and more robust uniqueness validation of molecules.

Monomer management APIs are now in stable [2023.10.SM.2]

The following endpoints have been promoted from alpha to stable: create, update, archive, unarchive.

Registry and Inventory

The 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 entities while the Inventory provides an interactive digital window into the physical storage system of your lab.

Improved language consistency for report exports [2023.10.RI.1]

When exporting a selection as a .csv, the language is now consistent whether Export selection to CSV is enabled or disabled. Both options display the same text, and when disabled, the text is gray and non-selectable.

Location metadata page [2023.10.RI.2]

Users can now view and edit a location’s metadata by opening the location metadata page. To open it, click the gear icon on the location and click Open location.

Inventory table search is limited to selected container type [2023.10.RI.3]

The search functionality in an Inventory table now only searches for containers of the container type selected when inserting the table.

Delete columns in Update Inventory table [2023.10.RI.4]

Users can now delete unlocked columns in the Update Inventory table.

Update locations via spreadsheet import [2023.10.RI.5]

Users can now update location metadata via the Update location spreadsheet import option, similar to updating containers, boxes, or plates.

Add actions to Update Inventory table [2023.10.RI.6]

Users can now take the following actions on a container directly from their execution surface:

  • Move a container to a new location
  • Reserve, check in, or check out a container
  • Update concentration
  • Update schema field values


Workflows are a sequence of processes that are performed to answer a research question or synthesize new material. For example, synthesizing a new set of proteins from supernatants, or improving the transduction process.

Email notifications for task creation via Responsible Parties [2023.10.WF.1]

Responsible Parties is a Task Level system field that is a collection of users or teams. All responsible parties are emailed on task creation. Reponsible Parties replaces Responsible Teams.

Config option to execute tasks from the dashboard [2023.10.WF.2]

When this Routers configuration option is enabled, users can view tasks executed from the dashboard in order of execution within the task group.

To enable this feature, contact a Benchling representative.

Benchling Connect

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

Benchling Connect [2023.10.BC.1]

This release includes several significant features, such as a point-and-click API configuration, file-based instrument integrations, 12 commonly used instrument adapters across 7 categories, management and monitoring of instrument connections, auto-result schema creation, and open source industry-standard/data converters (Allotropy).

Added an audit event for run schema notebook preference [2023.10.BC.2]

Added an audit event for object type = run_schema, property = allow_create_run_from_notebook. An audit event is now recorded when setting the run schema notebook preference to allow creating new runs from the notebook.

Added an audit event for allowing inserting runs from the inbox [2023.10.BC.3]

Added an audit event for object type = run_schema, property = allow_insert_run_from_inbox. An audit event is now recorded when setting the run schema notebook preference to allow inserting runs from the inbox.

Add timestamps to all datetimes in generated Allotrope files [2023.10.BC.4]

When creating or updating a connection, a new field, "Default Timezone," is added to timestamps in a vendor file if they are not already set. The default value is UTC.

Option to remove the trailing "_step#" when generating an input file [2023.10.BC.5]

Users can choose whether input files with transforms start from "_step0" as the initial file without a suffix on the final transform file or have suffixes on all transform files.

To enable this feature, contact a Benchling representative.

Updates to Retrieve Data Modal via Connect [2023.10.BC.6]

Users can define default data types when configuring a run schema, skipping the conversion file selection during run processing via the retrieve data modal.

Windows Installer UI Update - Download and Token generation [2023.10.BC.7]

The gateway download workflow within the Instrument Gateways page has been updated with two new options:

  • Download Gateway
  • Generate New Installer Token

This enables gateway installation via a Windows installer, replacing the existing PowerShell-based installation.

Access Management

Access management is the way customers control who is able to access which resources, and includes things like project permissions, access policies, and admin roles.

Tenant invitations now expire after 14 days [2023.10.AM.1]

Invitations to organizations or projects now expire after 14 days. Expired invitations are no longer valid.

Application Core

To create a seamless Benchling experience, our platform must be consistent, compliant and predictable. The Application Core provides the central capabilities platform to create a smoother user experience.

New UI blocks in App Canvas [2023.10.APP.1]

Users can now access 3 new UI blocks in the App Canvas. These blocks offer additional options for drop-down menus, search inputs, and selectors.

Support ingestion of localized Excel files [2023.10.APP.2]

Users can now upload localized Excel files with support for localized dates and numbers, if they’re interpreted as such in the file.

Compliance Controls

With Compliance Controls, gathering required information for compliance is simple, intuitive, and performant. The team’s primary focus is on our auditing platform but we also own exporting and archiving.

Container history report [2023.10.CC.1]

Users can now trace the complete lifecycle of a sample with container history reports. These reports include detailed records of container creation, modification, inventory location, stored sample entities, user information, and associated activity.

Deliver successfully exported files via email when a subset fails [2023.10.CC.2]

When executing a large export, users will now receive an email identifying any failed files within the export. The email also includes a hyperlink to download the successfully exported files. Previously, the entire export was considered failed if even one file failed.

Large registry exports chunk entity files into a zipped folder [2023.10.CC.3]

Large registry exports now chunk files into multiple zipped folders to ensure larger registry exports succeed.

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.

nextToken addition [2023.10.DP.1]

GET /dna-oligos returns "nextToken" by default when used with the "returning" parameter; this improves the developer experience by making it more intuitive.

Updated the generic 500 errors [2023.10.DP.2]

This change adds the API endpoint in error reports.

Bug Fixes

The following issues were resolved this month:


  • When a URL was linked directly in a notebook entry, it was clickable in the .pdf, but when it was linked within text it wasn’t clickable.
  • Add API Pending Values results button remained active in some cases
  • Unable to send entry for review if table submissions were blocking for Inventory tables with archived rows
  • Inventory table contents incorrectly referenced with = in other cell

In Vivo

  • Admins couldn't use Change role to administrator
  • Data table didn't refresh to update state after a column was moved

Registry and Inventory

  • Users were unable to assign a container to a box or matrix plate grid position if that position previously held a container
  • Error in printing the quantity unit: "x10^N cells" on a label template. Now, users can use "E" to represent "x10^N" e.g. E9


  • The Studies column no longer shows up in the Task table when fixing failed Workflows mappings
  • When configuring a Router node, the Delete edge icon could appear in the middle of the configuration  modal
  • Require all transitions that go through the same Router to map from the same source schema (all from the Task or all from the Output)


  • Choosing a drop-down field type in the Registry-based dataset creation method appended an API ID to the value in the drop-down menu

Benchling Connect

  • The datetime displayed on the Connect retrieve data window for time of 'last sync' was shown in UTC instead of local time
  • A run raised the error that the “Output file is too large to process without "Skip rows with errors" enabled.” The expected behavior was that a run automatically selects "Skip rows with errors" without options to deselect for a large enough data set. 
  • Fixed a bug for using field name instead of displayName when guessing col types in SetColumnsMapModal
  • Fixed a bug with runs inserted through subtemplates
  • Allow to use custom extension for input file if there is a custom transform applied

Access Management

  • The owner field was hidden on personal ownables when personal ownables were disabled for a tenant - now it displays if the ownable is not owned by the org
  • "Other" item types (Enzyme lists, Feature libraries, and Ladders) were allowing users without the Admin policy statement granted to edit collaborators or other admin settings
  • The backend for the legacy workflow template was checking "Write" instead of "Admin" access (the UI was correctly enforcing permissions)
  • In new LA permissions UI, tenants with multiple orgs would have registry permissions set on one org applied to the other orgs as well
  • Missing audits for permissions changes when users were logging in using Google Auth for the first time as a previously unverified user and had pending invitations to projects
  • Missing audits for permissions changes when users were resetting their password as an unverified user with pending invitations to projects
  • In new LA folder permissions UI, new users could not be invited from the collaboration search box
  • Missing audit for password reset events

Application Core

  • The App Activity page was previously not filtering results correctly

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