Welcome to the 12 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 December 2025.

Benchling AI

Benchling's artificial intelligence agents and features.

Enhanced Deep Research Tool Call UI [2025.12.AI.1]

The end-note citations and activity items in Deep Research for warehouse queries now render the query and the table of query results with more user-friendly and consistent UI elements for code entry and for table rendering.

Compose and Data Entry Agent now visible in AI Usage chart [2025.12.AI.2]

Compose and Data Entry Agent are now visible in the AI Usage chart in Tenant Admin Console under the AI Settings tab.

Enhancements to suggested questions in Benchling AI side-panel view [2025.12.AI.3]

Additional suggested questions (prompts) are added to the list of possible suggested questions in the Benchling AI side panel.

Support Saving Multi-Section Draft Documents to Entries and Templates [2025.12.AI.4]

Draft documents created in Compose can now include multiple sections/entry days and retain that full structure when saved to an entry or template, with correct date handling based on configuration and the user’s local date.

Multi-Sequence Highlighting [2025.12.AI.5]

When viewing a multimer structure prediction on an AA sequence, users can now highlight a subsection of the sequence map and see the corresponding section highlighted across all copies of the sequence within the 3D Structure viewer.

Allow users to run All Models [2025.12.AI.6]

This feature adds a button allowing a user to run structure prediction for an AA sequence using all models available to them.

Add Generative Models tab to AA Sequences [2025.12.AI.7]

When enabled, this feature allows users to see generative models for binder design. Currently limited to BoltzGen.

Notebook

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

Customize structured table single input fields [2025.12.N.1]

Single input fields in editable structured tables can now be customized to improve table readability and layout, making template design more flexible. Field width can be adjusted by clicking and dragging the right edge of a field, and fields can be reordered by dragging the handle located to the left of the field name. These improvements apply across Notebook entries and worksheets.

New functions within tables [2025.12.N.2]
Notebook tables now support additional functions to enable more robust calculations and error handling:

• IFERROR — Simplifies formula logic by allowing fallback values when a calculation results in an error, improving formula reliability and readability. Learn more
• PI — Enables easy reference to the mathematical constant π, supporting more precise and readable scientific and mathematical calculations. Learn more
• EXP — Supports exponential calculations using the natural base e, making it easier to model growth, decay, and other scientific formulas. Learn more
• DAYS — Calculates the number of days between two dates, enabling clearer time-based analysis and comparisons within tables. Learn more 

Security Enhancement: File Upload Restrictions [2025.12.N.3]

To maintain a secure environment, additional file upload restrictions have been implemented. The following executable file types can no longer be uploaded:

• .exe (Windows application executable)
• .dmg (macOS disk image installer)
• .ps1 (PowerShell script)
• .vbs (Visual Basic script)
• .sh (Shell script used on Linux and macOS)
• .cmd (Windows command script)
• .com (Windows command script)
• .bat (Windows batch file)
• .dll (Windows dynamic link library)
• .iso (Disk image file)
• .jar (Java application archive)
• .msi (Windows installer package)
• .sys (Operating system system file)

Added spell check support for fill-in only text boxes [2025.12.N.4]

Spell check is now supported for text boxes in a fill-in only entry.

Updated Notebook-related Warehouse documentation [2025.12.N.5]

Now the Notebook-related Warehouse documentation includes coverage for entry_template_version. This change also improves the consistency of the documentation.

Audit Events for Notebook Table Locking & Unlocking [2025.12.N.6]

When locking and unlocking Notebook Tables, these actions are now audited and show up in Benchling's audit log.

Timestamp attribution improvements [2025.12.N.7]

Before this change, submitting an entry for review would update the timestamp and its attribution to the submitting user. With this change, the timestamps and user is preserved. 
Note: While most users will have this turned on automatically, a few select accounts and accounts with Bioprocess have not yet been enabled. If you have questions please reach out to Benchling Support. 

Molecular Biology

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

Consolidated AA sequence create and import modals [2025.12.MB.1]

From global or project create, when users created "New AA sequences" or "Import AA sequences", we previously opened different modals. Now, these modals are consolidated into one with different tabs. That way, the user can choose any import method when creating new AA sequences, regardless of their starting point.

In Vivo

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

Observation tasks can be created without selecting any pre-defined observations [2025.12.IV.1]

Previously, users were required to select at least one observation type when recording observations. Now, this field can be left empty to support ad-hoc observations that weren’t defined when the task was created.

Record normal observation in workflow [2025.12.IV.2]

In Workflow, users can now add a timestamped ‘Normal’ observation with a single click and automatically advance to the next step, reducing the number of clicks needed to complete clinical observations.

Contact Benchling Support to enable

Save Default Analysis summary table settings [2025.12.IV.3]

Users can now save the summary table settings in the Analysis tab. This is saved for that study so that all users viewing this page will see the default summary table without needing to configure it fresh each time.

Maintain dosing history on animal move [2025.12.IV.4]

When animals are moved to another study, their dosing history is now preserved. The original treatment records remain linked to the previous study and are read-only, but they are not included in the new study’s design.

Alert actions [2025.12.IV.5]

Users can now define the next step to be performed after an alert is triggered in the alert settings.

[Beta] Planned animals and Sample plans [2025.12.IV.6]

Plan your complete in vivo study before animals arrive with new animal and sample planning capabilities. Create placeholder animal IDs, assign them to treatment groups, and define all metadata during study design—then seamlessly convert them to registered animals when ready.

Build comprehensive sampling plans that specify sample types, timepoints, volumes/weights, and metadata, assigning collections to groups or individual animals. Generate planned samples ahead of collection for pre-labeling tubes and container preparation, then collect samples in bulk with automatic status updates from "Planned" to "Collected." These integrated features enable complete study design upfront, eliminate manual data entry during execution, and maintain full traceability from planning through collection.

Contact Benchling Support to enable
Learn more: Help Article

[Beta] Sample collection from plan [2025.12.IV.7]

Collect samples efficiently with new bulk collection workflows. Select multiple planned sample groups from your sampling plan and collect all associated samples in a single action, applying the same collection date, time, and comments across the entire set. Planned samples automatically convert to "Collected" status upon collection, preserving all sample IDs, metadata, and container links. 

Optionally exclude specific animals from bulk collections when needed. Samples that won't be collected can be manually cancelled in bulk or are automatically cancelled when studies are completed or animals become deceased, with the ability to uncancel if needed. All collection and status changes sync in real-time to Benchling Registry, ensuring downstream teams have immediate access to newly collected samples and accurate sample status.

Contact Benchling Support to enable
Learn more: Help Article

Workflows

Workflows are a sequence of processes that are performed to answer a research question or synthesize new material.

Ability to click definition of a task schema field [2025.12.W.1]

Users can now click into the definition of a task schema field to view the definition of that task schema field (in the same browser window).

Insights

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

Redesign of Views within Analysis [2025.12.IN.1]

Redesign of Views within Analysis. The update modernizes the Views interface with enhanced flexibility and clearer terminology. Users gain new capabilities like:

• Copying of top-level views
• Wider right sidebar with repositioned Save/Cancel buttons at the bottom and ability to apply transformations via sidebar
• The interface moves from "table"-centric to "source/view"-centric language for better clarity 
• Second-tier views can now be flagged without editing,
• Warnings are consolidated directly on affected items with tooltips 
• Child views now have the same button options as parent views, plus a "promote view to top-level" option 
• Tables and charts now consistently extend across the full viewport 
• Chart views have uniform buttons across all interfaces and no longer display the source table

• Prevent showing stale data when filters are running or have failed, ensuring users only see current, accurate results.

Add X-Axis Min/Max range configuration to Scatter charts [2025.12.IN.2]

Add configuration of X-Axis minimum/maximum range to Scatter charts in Analysis

Enable generating read-only Results outputs from Analysis/Analysis Templates [2025.12.IN.3]

Add configuration checkbox ("Lock results table") to Create Outputs modal of Analysis. By clicking on "Lock results table", Results table will be created as read-only and are uneditable in Notebook Entry. Users can perform this functionality on a single Analysis and save configuration settings as an Analysis template. 

• Analysis / Unlocked - Create an analysis. - Click "Create outputs". - Configure a table to be output as results. The "Lock result tables" checkbox should appear. - Do not check the checkbox. In the entry, you should be able to edit values in the table. 
• Analysis / Locked - Create an analysis. - Click "Create outputs". - Configure a table to be output as results. The "Lock result tables" checkbox should appear. - Check the checkbox. In the entry, you should not be able to edit values in the table. You should, however, be able to archive results and add lookup columns. 
• Analysis Template / Unlocked - Create an analysis. - From the overflow menu, click "Save as analysis template". - Configure a table to be output as results. The "Lock result tables" checkbox should appear. - Do not check the checkbox. Create the template. - Apply the template. In the entry, you should be able to edit values in the table. 
• Analysis Template / Locked - Create an analysis. - From the overflow menu, click "Save as analysis template". - Configure a table to be output as results. The "Lock result tables" checkbox should appear. - Do not check the checkbox. Create the template. - Apply the template. In the entry, you should not be able to edit values in the table. You should, however, be able to archive results and add lookup columns.

Benchling Connect

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

Enhanced Excel Stylesheet Error Handling [2025.12.BC.1]

Expanded our handling of stylesheet-related Excel parsing errors to ensure more spreadsheets import successfully. These improvements help ensure that spreadsheets with unusual styling or formatting load successfully

Update Chromeleon Connector for Chromeleon v7.4 [2025.12.BC.2]

Update Chromeleon Connector for Chromeleon v7.4 and verify support for new Chromeleon version

Update Allotropy to 0.1.112 [2025.12.BC.3]

Reference Change Log for comprehensive list of updates to Allotropy Connectors: Change Log 

Application Core

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

Removed mapping details from Config migration update messages [2025.12.AC.1]

Removed information about provenance URI from customer-facing UI as it's not a customer-facing concept.

Updated Config migration review page message for constraints [2025.12.AC.2]

Updated language around constraints to make changes more clear to users of config migration.

BioProcess

Our BioProcess offering helps with process development studies, including non-In Vivo workflows. It includes tools for tracking, managing, and analyzing experiments like process development studies, recipes, and studies.

Automatic PD Charting [2025.12.BP.1]

When clicking on Analyze within a PD Study or Recipe Run, now in addition to the tables previously generated, new line charts, bar charts, and summary tables are automatically created. 

No configuration or templates is required to use this feature. These charts are created based on the shape of the data within the experiment. This does not prevent users from doing their own analysis but aims to save time by creating typical types of views. 

Bug Fixes

Benchling AI

• Fixed a datetime parsing error in Data Entry Agent

Notebook

• Fixed horizontal scroll bar issue in entries
• Fixed template filter to only show provisioned types
• Fixed analysis templates to show up in Contextual Templates user interface
• Fixed deleted team entry review rendering issue
• Fixed reassignment review process issue
• Improved the loading time for templates
• Fixed an issue that could occur when doing Config Migration for Templates
• Fixed an issue where the send to PatentSafe button was missing

Small Molecule

• Fixed a Monomer stereochemistry bug
• Oligo conjugate/duplex bug fix

In Vivo

• Clearing a field in In Vivo did not clear the corresponding field in Benchling Core tenant.
• Navigation of cages in workflow did not adhere to the user defined order in the Cages page
• Fixed a bug where metadata fields were not visible in Samples export
• Fixed an issue where the summary statistics under graphs were not displaying correctly

 Registry and Inventory

• Fixed a bug where some validation happened on import/registration rather than upfront before registration

Workflows

• Fixed bug for legacy requests spreadsheet import flow
• Removed filter results functionality for unsupported direct entry tasks
• Fixed a styling bug in the flowchart configuration transitions menu

Application Core

• Fixed issue with workflow templates being incorrectly shown as "missing" in some circumstances
• Fixed issue with validation rules being incorrectly exposed on Results schemas
• Fixed issue with valcloud patch version not showing the patch number
• Fixed issue where bulk results were created via bulk-create endpoint however Run had previously been archived in the Notebook Entry. 
• Fixed issue mapping access policies with identical names in tenant comparison report
• Removed "Box" tab from tenant comparison report as it contained information about Box instances rather than Box schemas

Developer Platform

• App name in dev console now reflects latest installed version

BioProcess

• Fixed a bug that would prevent locking of columns in [unstructured] tables in Recipes and Assays

PipeBio

• Improved import of uploaded files
• Small update aimed at improving the app load more reliably
• Filtering improvement to handle Null within columns
• Structure view selection improvements