Welcome to the 11 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 November 2025.

Benchling AI

Benchling's artificial intelligence agents and features.

Compose Links in Entries [2025.11.AI.1]

Notebook Entries created by Compose have a link to the source chat.

File upload in Ask [2025.11.AI.2]

Users can now upload files to Ask Agent which will use them as context to answer its question.

Benchling AI Ask mode can now access help.benchling.com articles [2025.11.AI.4]

Benchling AI Ask mode can now access help.benchling.com articles when answering user questions about how to perform certain actions in Benchling. 

Deep Research with Public Data [2025.11.AI.5]

Users can enable "Deep Research with Public Data" to search over both their Benchling data and the public internet.

This feature is not on by default, it is enabled by admins.

Improved support for larger PDF attachments in Compose Agent [2025.11.AI.7]

Improved support for PDF attachments with many embedded images in the Compose Agent.

BoltzGen initial release [2025.11.AI.8]

The page for BoltzGen under Generative Models now shows all past and ongoing BoltzGen runs. Also, after completing a BoltzGen run, users can see the top-ranked structure in the PDB viewer and download all generated binders by clicking the download button.

Notebook

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

Template naming user experience improvements [2025.11.N.1]

After system-generated version names have been used, the system will now default to controlled version naming. This change prevents users from unintentionally continuing to use the system-generated naming syntax.

Added the ability to generate a worksheet snapshots at the time of review, as well as access it via the API, just like entries [2025.11.N.2]

With this release, users can create PDF snapshots of their worksheet at the time of review and download it for record keeping, as well as access the snapshot via the API.

Structured Table Column audits [2025.11.N.3]

Benchling now audits when a column in a structured table is created or deleted.

Support Data Modification Reasons for Notebook Table Column Edit Audits [2025.11.N.4]

Data Modification reasons are now supported when modifying notebook table columns. This change is only visible if data modification reasons are enabled for a project or organization.

Molecular Biology

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

Connections computed field for oligo conjugates and duplexes [2025.11.MB.1]

Admins can now configure "connections" computed fields on oligo conjugates and duplexes. This allows users to resolve connection points as structured schema fields across Benchling.

New Assembly → Registry & Notebook experience [2025.11.MB.2]

Registering sequences from assemblies used to be painful, users had to recreate context manually and couldn't easily navigate between assembly and Notebook. Now, Benchling carries forward assembly context, streamlining how users capture relationships, register entities, and record their work:

1. [Previously released] Map assembly context to schema fields: When finalizing an assembly, users can now capture key relationships from the assembly in schema fields (e.g. which fragments make up a construct or which primers are paired together). 
2. [Just added] Send assembly outputs to Notebook: Once they’ve been assigned a schema, constructs, primers, and amplified fragments can be sent directly from an assembly to new or existing registration tables in a Notebook entry.

Help article

Registry and Inventory

The Registry and Inventory combine to form an extremely powerful solution for life sciences R&D samples.

Registration Table Validation checks [2025.11.RI.1]

Registration tables can now have validation rules checked prior to being submitted.

In Vivo

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

The In Vivo Sync app overview page no longer contains an option to backfill, instead users are instructed to follow a link to their In Vivo tenant for this action [2025.11.IV.1]

The In Vivo Sync App overview page no longer includes the option to initiate a backfill; instead, users are now directed via a link to perform this action within their In Vivo tenant. 

This change centralizes backfill functionality where users already manage study and sync workflows, providing better context, improved reliability, and enhanced traceability. By moving backfill into the In Vivo environment, Benchling aims to streamline error handling, reduce confusion, and ensure that backfill actions are executed with full visibility into the relevant study data.

Additional APIs to GET samples that have been attached to a request [2025.11.IV.2]

Now users can leverage our GET and LIST request samples API endpoints to retrieve the list of samples that were attached to a specific request in In Vivo.
Help Article

Save measurement form on scanning the next animal ID in Workflow [2025.11.IV.3]

When using an ID scanner through the In Vivo connected devices feature, if the measurement form does not save automatically due to partial completion, simply scanning the next animal will attempt to save the form providing the data is valid.

In Vivo Sync App Version 0.0.16 [2025.11.IV.4]

The In Vivo Sync app has a new version available, this update includes additional fields to map to the Sample Schema including, Sample status, Sample label, Timepoint Value, Timepoint unit and Timepoint ISO duration. Click Upgrade under App listing to update the app and map these fields.

This feature is not on by default, it is enabled by admins.

Workflows

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

Flag to include/exclude execution templates when creating Notebook entries from template [2025.11.W.1]

Customers will now have the ability to include or exclude Notebook templates that are used as execution templates for entry task schemas when creating a Notebook entry from a template. 

To enable this feature, contact Benchling Support

Improved error messaging for when a task schema fields can't be updated [2025.11.W.2]

In addition to in-line messaging, we're now also displaying a specific error message when displaying the red toast in the bottom left of the screen letting the customer know exactly what the issue is that they're racing. 

Insights

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

Improve the performance of analysis templates exports in Config Migration [2025.11.IN.1]

Fix reduces index calculations from O(n^2) to O which significantly speeds up the serialization steps of config migration by 60-75%.

Benchling Connect

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

Updates of Benchling Connect ASM to CSV parsers [2025.11.BC.1]

The following Benchling ASM-to-CSV Parsers have been updated in ValCloud:  

• Binding Affinity Analyzer - add support for multiple device control documents
• Multi Analyte Profiling - separate errors by analyte Plate Reader - add support for peak list
• Solution Analyzer - add support for analyte transform
• Solution Analyzer - add support for multi-analyte document, analyte document custom info 
• Global - fix how Csv Representation is initialized to prevent title/data mismatch 

Please reach out to Benchling Support to inquire about which individual Connectors have out-of-the-box validation packages.

New Connectors [2025.11.BC.2]

• Release Cytiva Biacore T200 Evaluation Connector: Configuration Guide
• Release Luminex INTELLIFLEX Connector: Configuration Guide

Update Allotropy to 0.1.111 [2025.11.BC.3]

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

Roche BioHT Connector - Add support for mM (millimolar) units [2025.11.BC.4]

Roche BioHT Connector - Extend parsing support of Roche BioHT export files containing mM unit strings. Units will be reported as mmol/L to follow Allotrope unit standard.

Populate the Condition Replicate column in the Run Results Table within the Worksheet [2025.11.BC.5]

When working in a Multi-batch procedure, a run can now display a Condition Replicate column in the results table within Worksheets. The run automatically includes this column when it is configured in the Run Schema column mapping. In contrast, runs viewed in Notebook entries continue to follow existing Results Table behavior and do not display the Condition Replicate column. This maintains consistency with the current Notebook results-viewing experience.

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.

Sync Project Descriptions to warehouse [2025.11.DP.1]

Project Descriptions are now available in the Warehouse.

Schemas

Schemas are the structural foundation for how your information is categorized in Benchling. They are categories created specifically for your tenant that can represent materials, data, storage methods, and tasks.

Enable Display Precision configuration for fields during Entity Schema creation [2025.11.SCH.1]

Users previously were able to set display precision on decimal entity fields for created schemas, but not during schema creation. This update now enables display precision during schema creation.

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.

New scrollable, search, overflow functionality in Benchling sidebar menus [2025.11.AC.1]

New navigation overflow behavior and new create menu scroll/search behavior. Customers can opt-into these features early prior to auto-enablement in December 2025

Revamped In-Progress spinner [2025.11.AC.2]

Updated progress spinner UI to have a new, modern, consistent version across the product

Updated config migration to match units on name by default [2025.11.AC.3]

When config migrating units, if there is not already a relationship established between the source and destination units we'll match on name before creating a new unit.

Replace old loading spinner with new spinner [2025.11.AC.4]

The horizontal throbber have been replaced with a redesigned spinner for loading screens.

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.

Bulk export entries as separate PDFs [2025.11.CC.1]

Entries can now be bulk exported as individual PDFs in a ZIP file, making large exports more reliable and easier to navigate.

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.

Allow users with limited study permissions to use study overview shortcuts [2025.11.BP.1]

Previously for users who only had permission to assign items to a study (e.g. creating Notebook entries under that study, or associating entities with that study) but did not have edit access to the study itself, the object creation shortcuts on the custom study overview page was disabled. Now users with this permission set have access to these shortcut buttons.

PipeBio

Benchling's cloud-based bioinformatics software for antibody/peptide screening & drug development. Conduct BCR, TCR, VHH, scFv, or peptide sequence analysis and integrate your workflows with Benchling's core platform.

Improved AA Barchart legends [2025.11.PB.1]

Amino acid barchart legends have historically included all amino acids. Now the legend is limited to amino acids represented in a given chart.

Faster parsing of FASTQ files at import [2025.11.PB.2]

The speed up parsing & importing of large FASTQ files has been improved. For smaller files, this will have limited / no improvements.

Bug Fixes

Benchling AI

• Resolved a bug where saving a Deep Research response to Entry would fail in some cases

Notebook

• Fixed an invalid review error message
• Fixed an issue with some column names not appearing in Notebook table exports
• Fix errors following closing an Entry
• Fixed an issue where at-mentioned users on worksheets weren't emailed
• Table Submission Checkmark Stays After Row Archive
• Fixed a bug when navigating away from editing a protein or sequence
• Fixed a small visual bug impacting the Project and Template Collections titles
• Fixed issue where review dropdown was not scrollable on small screens
• Fixed issue where Intermediary stage approval comments were not captured in audit trail
• Fixed missing user and timestamp in worksheet step popover

Molecular Biology

• Fixed issue with attaching primers
• Fixed bug with translation region visualization on sequence maps
• Fixed bug with Lookups from part, translation, or transcription link fields

Small Molecule

• Fixed bug in oligo duplex/conjugate registration tables

In Vivo

• Fixed bug with entities failing to Sync if dropdowns contained encoded characters
• Fixed issue found after recaging, when cages failed to delete if deleted animals had previously been in that cage
• Fixed an issue where tasks were being shifted by a day due to daylight savings
• Fixed a bug that prevented audit logs being exported when a forbidden character was included in file name

Registry and Inventory

• Fixed a bug where data modifications (reason for change) was not triggering in some scenarios when unarchiving a registered entity

Insights

• Fix issue with creating dataset from a result with legaltext dropdown
• Fixed error when hovering over a interpolation step in flowchart
• Fixed bug where Analysis Template with Lookup Step were Failing Due to Referenced Column Break

Benchling Connect

• Resolved issue with reading reduced data blocks containing empty rows in the SoftmaxPro connector

Schemas

• Fixed issue with being unable to correctly migrate Assay metadata
• Fixed incorrectly validating a False value of a required Boolean type field on Entry Schema
• Fixed issue when configuration migration was errantly identifying an unchanged unique constraint as changed
• Fixed bug where large schema field type changes would fail

Application Core

• Fixed issue in updating schema fields via config migration
• Fixed issue including all collaborations in permissions report
• Fixed issue where updating team name caused errors in large tenants
• Fixed a bug where Units were mapping incorrectly after an initial Config migration

Compliance Controls

• Updated Audit logging to say "Display Precision" instead of "Decimal Precision"

Developer Platform

• Fixed error code returned when calling the create_team_membership API

BioProcess

• Fixed bug that prevented procedures from being migrated when using single input columns
• Fixed bug that would prevent unpublished procedures from being updated on import