Welcome to the 10 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 October 2025.

Notebook

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

Updated the styling of the archive/unarchive tooltip [2025.10.N.1]

Updated the visual styling of the archive/unarchive tooltip to match our current UI patterns.

Improved user experience for review process checkboxes [2025.10.N.2]

Updated the user interface to minimize clicks when the user was making the same review stage type selection. Prior to this change, adding a new review stage of the same type would require new configuration.

Structured Table Column audits [2025.10.N.3]

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

Replace terminology updated in "Add from structured tables" [2025.10.N.4]

Renamed the 'replace' option in add from structured tables to 'replace all rows' to clarify the action that will happen

Performance improvements to Lookup table [2025.10.N.5]

Improved lookup table performance by optimizing lookup steps with performance issues.

Data Modifications are now summarized in the footer of structured tables. Change categories include: Added Rows, Modified Rows, Deleted Rows [2025.10.N.6]

This also includes a new audit event and data mod for row deletion - only audited if the row was initially submitted, then archived and then deleted. To view these, Data Modifications must be turned on within the Tenant Admin Console.



 

Improved the language of the review stage audit events [2025.10.N.7]

Updated the new review stage audit events to be more human readable.

Custom well plate sizes supported in Notebook Entries and Worksheets [2025.10.N.8]

Well plates (structured tables), inserted in Notebook Entries and Worksheets, now supports custom sizes. To add a custom size (e.g. 16 rows by 16 columns) contact Benchling Support.

Molecular Biology

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

Map assembly context to schema fields [2025.10.MB.1]

Previously, when a user finalized a combinatorial assembly, they could select a schema for each of their outputs (constructs, primers, amplified fragments) and add them to a worklist. This would set the schema of the newly created entities, but it might still be hard to register them. 

This new feature adds the ability for users to pass context from an assembly to schema fields on those newly created sequences. Specifically, users can set entity links on new sequences by mapping other groups of sequences used in the assembly to schema fields. For example, a user could select a bin of fragments that should map to a specific schema field on the construct. This then preserves the context from the assembly (e.g. what fragment was used to create the construct) and makes registration of sequences easier after assembly. 

Cut sites on DNA sequences in concatenation assemblies [2025.10.MB.2]

Previously, enzyme cut sites weren't visible on DNA or RNA sequence maps when carrying out a concatenation-based assembly. Now, all single-cutter enzymes can be toggled on and off on sequence maps in concatenation-based assemblies.

Small Molecule

The molecule entity in Registry helps users model and interact with chemical compounds throughout the platform.

Removed mentions of "complex polymer" throughout Benchling in favor of oligo conjugates and duplexes [2025.10.SM.1]

Previously, oligo conjugates and duplexes were referred to as "complex polymers” throughout the Benchling. This has been updated everywhere to be more specific as "oligo conjugate" and "oligo duplex".

Bulk update oligo conjugates and oligo duplexes [2025.10.SM.2]

Before, bulk updating oligo conjugates and oligo duplexes in Registry required that all fields were provided. We made a change so that the structure doesn't have to be, allowing users to update fields without updating the complex polymer itself. If any element of the structure is provided in the update, all elements must be (forward offset, components, and connection). However, if no element of the structure is provided, users can make the update without making any changes to the complex polymer structure itself.

Registry and Inventory

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

Container bulk-update api now supports setting roles in bulk [2025.10.RI.1]

The bulk role updates function like the regular ContainerUpdate.

In Vivo

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

SAML setup for Tenant administrators [2025.10.IV.1]

Introduced a self-service capability for tenant admins to configure and manage SAML2 single sign-on (SSO) settings. This empowers admins to update identity provider information without requiring Benchling support, streamlining SSO setup and maintenance.

Delete latest cage food or fluid metric [2025.10.IV.2]

User can now delete the most recent cage measurement. When this happens, any daily food and fluid intake records that were automatically created from that measurement will also be removed.

Contact Benchling Support to enable

Filter by multi-select metadata [2025.10.IV.3]

Now users can filter tables by multi-select metadata fields.

Admin controlled Sample Glossary [2025.10.IV.4]

Benchling In Vivo now supports a tenant-specific sample glossary, allowing administrators to independently manage their own list of sample types, add, edit, archive, assign labels, and set collection details, without Benchling support.

Name cages by group name when recaging [2025.10.IV.5]

When recaging animals based on treatment groups, a new option has been added allowing users to name the newly created cages by group name.

Cage reorder and splitting actions [2025.10.IV.6]

We’ve added new actions on cages to make managing animals more intuitive and aligned with real-world vivarium layouts. Reorder cages directly within the cage list to reflect the physical setup in the vivarium or your preferred workflow order. Split a cage to create a new cage automatically, the new cage retains the same name (with a numerical suffix) and metadata. After splitting, animals can be dragged and dropped between the original and new cages for quick reorganization. These updates help users better mirror how animals are physically housed and streamline daily record-keeping and study organization.

Insights

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

Alert Users when they approach Analysis step limit [2025.10.I.1]

Step counts are now displayed in the Analysis metadata modal window. If step count is approaching 10% of Analysis step limit (default maximum value 600), the user is alerted.

Benchling Connect

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

New Connectors: [2025.10.BC.1]

• Release Cytiva Biacore Insight Connector. Configuration Guide
• Release Cytiva Biacore T200 Evaluation Connector. Configuration Guide
• Release Luminex INTELLIFLEX Connector. Configuration Guide

Updates of Benchling Connect ASM to CSV parsers [2025.10.BC.2]

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 lists
• Solution Analyzer - add support for analyte transform
• Solution Analyzer - add support for multi-analyte document, analyte document custom info
• Global - fix how CsvRepresentation 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.

Update Allotropy to 0.1.108 [2025.10.BC.3]

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

Change Log

Schemas

Schemas define how information is categorized within Benchling.

Setting units on Entity Schemas and Fieldsets is now audited [2025.10.SCH.1]

Fields on entity schemas and fieldsets can be configured with Units. The actions associated with configuring / updating units are now audited.

Application Core

The Application Core provides central capabilities for a smoother Benchling experience.

GA release for simple validation rules [2025.10.AC.1]

We now support customers configuring simple validation rules on entity schema fields like integers and strings. 

Improved Config migration changelog generation performance [2025.13.AC.2]

The changelog is generated after the import of a config migration file is imported and processed into a destination tenant

BioProcess

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

Prevent recipes from being created or moved to a personal template collection [2025.10.BP.1]

Benchling has removed the ability for recipes to exist in personal collections. This work is part of a broader set of work that Benchling is doing to improve the foundation recipes and enable new capabilities in the future such as pipelines that can be directly configured in a recipe.

Added the ability to generate a worksheet snapshots at the time of review, as well as access it via the API, just like entries. [2025.10.BP.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

Contact Benchling Support to enable.

Editing or updating a step in a worksheet now updates the modified_at timestamp for worksheets. [2025.10.BP.3]

Previously editing or updating an individual step within a worksheet did not change the modified_at timestamp of the worksheet itself. This has been updated so that whenever a step is edited or changed, the worksheet's modified_at timestamp is updated.

PipeBio

PipeBio provides cloud-based bioinformatics for antibody, peptide screening, and drug development.

Experimental pair job improvements [2025.10.PB.1]

Experimental functionality has been added to enable the pair job to pair large documents of millions of sequences. This is controlled by Benchling and disabled by default. If you'd like access, please reach out to support@pipebio.com and share your use case.

Re-align alignments [2025.10.PB.2]

It's now possible to run alignment jobs on alignment documents. That could be all sequences in an alignment document or just some. Use cases include re-aligning with a different alignment algorithm or extracting a subset of aligned sequences into a new alignment

Deduplicate raw sequence reads after merging [2025.10.PB.3]

We've added experimental support for optionally deduplicating merged reads. To enable this feature, check the checkbox in Flash dialog advanced options. Reads having the same nucleotides after merging are deduplicated and the number of matches are recorded in a column "SequenceCount". Downstream tools clustering and comparisons have been modified to understand this column and use it in calculations. Other tools (charts and other jobs) are not yet supporting this feature so read counts will be incorrect. Therefore please be careful when using this new tool and reach out to us (support@pipebio.com) should you need assistance.

Minor annotation pipeline improvements [2025.10.PB.4]

We've improved progress updates for the annotation job and added some improvements for cases where jobs might have failed previously.

Bug Fixes

Notebook

• Access Denied message when adding step with sub-template
• Cannot Export tables in protocols
• Prevent editing any archived rows during table submission
• Fix Button Spacing Issue in Template Collection Page
• API raises HTTP500 for GET /entries when there is an invalid review state present
• Corrected Templates not found on causing warehouse integrity check failures
• Undo/Redo not functioning in Recipe Editor
• Template collectible type filter doesn't have correct display value for all types
• Export failing with tombstoned parameter in table (possibly in orphaned document)

Small Molecule

• Error importing csv into monomer library

In Vivo

• Corrected In Vivo Sync Not Working for Treatments
• Fixed bug when multiselect dropdowns fail to sync from In Vivo
• Fixed bug with Recaging Group Number Ordering
• Prod regression - Cage metric cursor goes to food in instead of food out first
• DataTables: Calculation of Average (not all inputs required) fails to include all measured values
• Fixed bug with Volume Calculations Use Incorrect Length

Insights

• Can create results in Analysis with only READ schema access
• Updated Mabtech adapter to support Apex 2.0 files

Workflows

• Corrected bug where next task in flowchart is not initiated because last task completed in merge did not have outputs
• Fixed bug showing duplicate name error when creating flowchart

Schemas

• Fixed being unable to delete fields when re-registering under different schema
• Fixed bug required Boolean field treats FALSE as null
• Fixed bug blocking users from changing the field's link type if it's used in a computed field

Workflows

• Maintain study url when refreshing study search page
• Updating Input table missing Location and Position columns

Application Core

• Fixed bug where Feature settings menu unexpectedly closing in SND environment

Developer Platform

• Fixed bug where Old App Name Showing up in Entity’s Audit Logs

BioProcess

• Fix duplicating step does not copy contents

PipeBio

• Corrected export to genbank/name scheme issue