Welcome to the 9 volume of our 2025 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 September and October 2025.

Benchling AI

Benchling’s artificial intelligence agents and features.

Entry inline formatting is now recognized by Notebook Check [2025.9.AI.1]

Notebook Check and other AI features are now able to be made aware of inline formatting in your entry, for example any strikethroughs, or highlights.

View structure predictions [2025.9.AI.2]

You can now view a list of your structure predictions and start a new one form the 3D structure tab of your amino acid entities

Contact Benchling Support to enable

Gemini support [2025.9.AI.3]

Google Gemini is now listed as a supported Benchling AI model in the Tenant Admin Console for customers with model selection enabled.

SQL Writer rename [2025.9.AI.4]

"SQL assistant" has been renamed to "SQL Writer".

Notebook

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

Insignificant table cell value changes now require submission [2025.9.N.1]

Previously mathematically “insignificant” edits (e.g., adding trailing zeros 15.0 → 15.00 or manually switching scientific notation 0.0123 → 1.23e-2) did not require re-submission. Now any edit to a cell value will now be treated as a change. These edits will appear as unsubmitted and all modifications will be audited in the table audit log.

Enable Author and Sender Reviewers via Review Process Configuration [2025.9.N.2]

Administrators can now configure whether review process stages allow authors and review senders to be reviewers through new checkbox controls in the Review Process configuration interface. 

New capabilities: 

• Allow author reviewers
• Control whether the entry author can review their own work in specific stages
• Allow sender reviewer
• Control whether the person who initiated the review can serve as a reviewer 

These settings provide more granular control over reviewer participation in notebook review workflows, enabling organizations to implement more flexible governance policies while maintaining proper separation of duties when required.

Worksheet Reviews is now generally available [2025.9.N.3]

Now customers using worksheets can require them to be reviewed and approved, just like entries. To get started, reach out to support to enable. You will then need to have at least one review process set for the project that contains the worksheet.

Contact Benchling Support to enable

Close hover tooltips immediately when mouse leaves hover target [2025.9.N.4]

Previous tooltips would have a delay is disappearing when the mouse left the hover target

Updated consistency of disabled colors to grey for form inputs based on common platform to make them more accessible [2025.9.N.5]

This will not apply to form input controls that are based on other platforms or custom built, but most form inputs should now have accessible colors in the disabled state.

In-App Audit Trails Limited Availability [2025.9.N.6]

You can now view immutable audit trails directly in Benchling, making it easier for QA and compliance teams to review records in-app and stay inspection-ready. Exports remain available for offline review.

Contact Benchling Support to enable

Schema display precision is now better applied on tables [2025.9.N.7]

You now view the schema display precision in the column header tooltip. Additionally, the display precision is now applied after entering a value, not just after submission. 

For fields without schema display precision, scientific notation will now be preserved (previously scientific notation was dropped in registration tables but was kept in result tables).

Contact Benchling Support to enable

Rapid barcode scanning for structured tables [2025.9.N.8]

Using a barcode scanner is now more reliable for inputting values into Registration, Inventory, and Lookup tables

Improved template migration validation [2025.9.N.9]

Added a validation check to prevent importing templates with section-like content into tenants where Sections are disabled. Invalid templates will now be flagged during migration.

In Vivo

Manage in vivo studies with modern software designed for data capture, collaboration, and insights.

In Vivo Sync in tenant activity and error tracking [2025.9.IV.1]

We’ve upgraded the infrastructure behind Benchling In Vivo’s real-time data sync. This release improves reliability, transparency, and scalability of the sync. Admins and users can now view detailed sync activity, filter by entity or status, and retry failed syncs directly from the In Vivo Tenant, increasing visibility into the data flow between In Vivo and core Benchling tenants.

Contact Benchling Support to enable

Improved Experience for In Vivo Updates [2025.9.IV.2]

Version update notifications in Benchling In Vivo have been improved to reduce workflow interruptions. Previously, a popup required users to either refresh immediately or skip the update, which could disrupt in-progress tasks like data capture. 

Now, update alerts appear as a non-blocking banner in the top-right corner, allowing users to continue their work uninterrupted and refresh at a convenient time, ensuring a smoother experience during active study tasks

Benchling Connect

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

ZIP file support for S3 gateway input processor [2025.9.BC.1]

Users can now send ZIP files to the S3 gateway via the Connect Run input file processor.

Support for multiple contents in Add Column and Input File Source/Destination LookUps in connect runs [2025.9.BC.2]

Users can now use lookup functionality in connect run to retrieve all contents from containers instead of erroring when multiple contents exist. This enables looking up all contents and then filtering down

Schemas

Schemas are the structural foundation for how your information is categorized in Benchling.

New option to edit a schema field's tooltip when it is managed by a Fieldset [2025.9.SCH.1]

Previously, users were not able to edit any attribute of a schema field that is managed by a Fieldset. When this feature is enabled by Benchling Support, Benchling allows the schema field tooltip to be edited even if it is managed by a fieldset. 

Contact Benchling Support to enable

Improved error messaging for unarchiving fields [2025.9.SCH.2]

When trying to unarchive a schema field dependent on an archived dropdown, users would get a generic error message telling them to contact support. Now, the user will get a more informative message, "Please unarchive "dropdown" in order to unarchive "dropdown field"

Units are now supported on Fieldset fields [2025.9.SCH.3]

Users can now set units on Fieldset fields. For the appropriate field, the user can click on the gear icon, then select "Set unit..."

Units on Result Schema are now supported with Configuration Migration [2025.9.SCH.4]

Users that configure units on Result schema fields can now migrate them using configuration migration.

Corrected the labeling of decimal precision to be display precision. [2025.9.SCH.5]

Previously, Benchling had labeled a setting on Fields as "Decimal Precision". This did not accurately reflect the purpose of the setting. The purpose of the setting was to configure the Display Precision. This is an important distinction because the setting does not alter the value. It just alters what is displayed.

For registry schemas, when updating a decimal field, the user has a configure (gear) icon available. When selecting that, the user now has the option to "Set display precision". For result schemas, the user has the ability to configure a schema field by choosing to "Edit as JSON". The JSON editor now provides a setting called "displayPrecision".

Application Core

To create a seamless Benchling experience, our platform must be consistent, compliant and predictable.

Support for units config migration [2025.9.AC.1]

This release enables migration of the unit dictionary - including unit types and their individual units using Config migration.

RDKit upgrade in Search [2025.9.AC.2]

A few months ago, we updated RDKit, which powers the molecule entity, to the most recent version. We now have updated RDKit in search, which means that molecules are now better kept in sync across Search and Registry.

BioProcess

Our Bioprocess offering helps with process development studies, including non-In Vivo workflows.

Visualization of Process Development Studies [2025.9.BP.1]

This adds a visualization tab to Process Development studies that visualizes all Recipe Runs and their Unit Operations in an easy-to-digest format. The visualization shows the sequence of Unit Operations within a Recipe Run and the connections created between Unit Operations across Recipe Runs.

PipeBio

Benchling’s cloud-based bioinformatics software for antibody / peptide screening & drug development.

Link to Benchling registry schemas from PipeBio Benchling settings [2025.9.PB.1]

PipeBio Benchling integration settings now include links to the Benchling registry schemas as a helpful tool to move between the platforms quickly when configuring the integration between the 2 platforms.

PipeBio jobs table links to all entities registered in Benchling from a given job [2025.9.PB.2]

There is now a helpful link in the sidebar for add-to-benchling jobs that enables you to easily find all registered sequences in Benchling from a given PipeBio job. This is helpful when you want to do downstream operations such as add all sequences / complexes to a worklist.

Support to add-to-benchling from PipeBio Alignments [2025.9.PB.3]

It's now possible to register ungapped sequences (and their annotations & metadata) from PipeBio alignment documents.

Bug Fixes

Notebook

• Fix issue where users were unable to use the "Add from structured table" or "Add from worklist" option if the destination column was single input.
• Removed ellipsis function on table column headers when hovering or editing formulas. Previously this caused part of the column name to be cut off.
• Fix bug when pasting data that had line endings from older Mac programs (such as JMP), where it would not paste into each row and would instead paste into one cell.
• Fixed a bug with table cells, where typing a single character then clicking out of the cell, caused the new newly typed value to be lost.
• When cutting and pasting a structured table (other than results) in the same entry, it was treated as a new table and the old table audit log was no longer available without viewing an old version of the entry. Now, the full table audit log and ID stay.
• Corrected handling of Pasted Links.
• "Registered In" feature is now working for entities registered from a request.
• Fixed incorrect "last modified" dates on notebook entry templates.
• Removed "Superseded" option from publishing status search filter.
• Enhanced link validation in Notebook.
• Preserve point-in-time user name/handle on exports.
• Fixed Team Member Reassignment.
• Fixed a bug where Review EventBridge Events weren't firing after Reverting Project Settings.
• Fixed bug caused when, double clicking a cell and then hitting escape incorrectly cleared the cell..
• Fixed a bug where MP4 video attachments were not previewable.
• Fixed Bug to prevent unintended Template Version Creation.
• Fixed issue where Entity link inputs in mixture prep tables lost borders.
• Fixed intermittent upload failures to Box file sharing.
• Prevent mixture tables from being inserted into mixture instructions.
• Fixed issue where Location History Report creation audit event was missing when locations created via bulk import tool.
• Prevent Runs from being pasted in inappropriate contexts.
• Improved reliability of worksheet exports with many attachments.
• Entity rename was failing for customers with Data mods enabled.

Molecular Biology

• Fixed homology bug in combinatorial assembly.
• Fixed feature library bug.

Small Molecule

• Fixed monomer library bug.

In Vivo

• Resolved an issue with food intake recorded at date when users account timezone didn't match the browser timezone.
• Workflows ID have truncated when being displayed.
• Resolved an page state issue when changing the workflow setup date mid session.
• Added missing validation to ensure preset calculation inputs start with a letter.

Registry and Inventory

• Added missing tool tip when required field checkbox is disabled.
• Fixed a bug causing registration timeouts in some cases.

Workflows

• Fixed bug that caused task execution to timeout.
• Bug preventing creation of a request from a lookup table.

Insights

• This fixes a bug that caused the wrong data to be drawn in a chart when running multiple regressions at once.
• This change fixes an issue with regression chart generation, so it can correctly handle partially failed regression with partition. For the failed partition, there won't be regression lines and only the scatter points will be shown.

Benchling Connect

• Fixed issue where column updates were not reflected in Run Schema UI.
• Fixed issue where lab auto run with "use contents of source container" configuration fails with "value is missing" error.
• Resolved issue that blocked the Output Generator from starting automatically from the Input File Generator.
• Fixed issue where unsupported timezone formats were converted to UTC in Connect Runs.

Schemas

• Fixed Schema descriptions that were truncating.
• Fixed race condition during field type changes.
• Fixed a bug with some Organizations being blocked from creating schemas.

Application Core

• Clarified error message for archived dropdown options with config migrating templates.
• Fixed issue where global create was cut off on smaller screens.
• Fixed a bug where Execution templates were displayed in Config migration with "Missing Collections".

BioProcess

• Fixed bug with config migrating parameters.
• Changes to the units of parameter definitions are always audited, even if setpoint of the parameter is null.
• Fixed a bug that would cause issues if reserved prefixes were used.
• Fixed issue where users lost the ability to insert row above/below in Bioprocess configuration.

PipeBio

• Fix broken import of tabular data caused by tabs in key fields.