Welcome to the 6th 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 June 2025.

Notebook

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

Performance Monitor Now Available for All Users [2025.6.N.1]

The Performance Monitor is now generally available and enabled for all users. This tool provides visibility into table performance metrics. Use it to quickly identify and resolve performance issues. To disable this feature or limit access to Org Admins, contact Benchling Support.

Table Formulas Support LOWER() [2025.6.N.2]

Table formulas now support the LOWER() function, which converts text to lowercase.

Example: LOWER("Benchling") → "benchling"

Table Formulas Support UPPER() [2025.6.N.3]

Table formulas now support the UPPER() function, which converts text to uppercase.

Example: UPPER("Benchling") → "BENCHLING"

Improved Image Resize Discoverability [2025.6.N.4]

When an image has no annotations, you can now resize it without clicking first. This update improves usability after the introduction of image annotations.

New Version History Panel [2025.6.N.5]

A redesigned version history panel is now available across entries, templates, worksheets, and sub-templates. It improves visual consistency throughout the product.

Edit and Undo Image Annotations with Version History [2025.6.N.6]

Users can now edit image annotations without starting over. Simply select ‘Edit’ on any annotated image saved after this release to move arrows, update text, or adjust shapes. All edits are versioned and auditable.

New Audit Event for Deleting Archived Rows [2025.6.N.7]

Deleted archived rows in structured tables are now logged as audit events. Previously, these deletions were not captured in the audit trail but were instead captured in the notebook version history.

Clickable Section Tabs: Projects and Template Collections [2025.6.N.8]

The Projects and Template Collections tabs in the sidebar are now clickable. Selecting either tab returns you to the root level of that section—no need to use breadcrumbs.

To enable this feature, contact a Benchling representative.

Molecular Biology

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

Monomer Size Limits in Monomer Library [2025.6.MB.1]

Monomers in the monomer library are now limited to a maximum of 300 atoms. This update maintains platform performance and ensures appropriate usage for monomers, such as nucleotide modifications.

In Vivo

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

Track Food and Fluid Intake at the Cage Level [2025.6.IV.1]

Users can now track food and fluid intake directly at the cage level in Benchling In Vivo. This feature enables real-time data capture during workflows, automatically calculates daily per-animal averages (g/day), and supports graphing, exporting, and study randomization.

Optimized for group-housed animals, this update simplifies intake tracking in metabolic and obesity studies, improving data quality and operational efficiency.

To enable this feature, contact your Benchling representative.

Flexible and Scalable In Vivo Sync Backfill [2025.6.IV.2]

 The Sync Backfill feature allows users to selectively sync historical data from In Vivo to Benchling by study, item type, and date range. Users gain full visibility into sync progress and event-level outcomes.

Track, cancel, or retry backfills directly from the UI—without disrupting live sync operations.

To enable this feature, contact a Benchling representative.

Set Task Durations and Reschedule Individual Tasks [2025.6.IV.3]

The Timed Tasks feature introduces support for specifying start and end times for tasks, improving scheduling accuracy and operational flexibility.

Users can now reschedule individual tasks without affecting the rest of the task series. Updated calendar views reflect precise task timing, enabling better planning and workload management for In Vivo teams.

To enable this feature, contact a Benchling representative.

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.

Required Fields for Inventory Metadata [2025.6.RI.1]

Admins can now require users to enter key metadata when working with inventory. Required fields are strictly enforced across location, box, plate, and most container schemas.

Note: Container “well” schemas (used in fixed plate schemas) are not currently supported.

Workflows

 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.

Create Tasks for Submitted Requests [2025.6.W.1]

Users can now create tasks within requested task groups even after a request has been submitted (status:’Sent’). 

 Responsible Parties [2025.6.W.2]

We’ve rolled out the Responsible Parties feature across all tenants, replacing the older Responsible Teams field. This update enables task-level assignments to individuals and teams, triggers email notifications, and supports audit logging. 

View Assignees in Request Documents [2025.6.W.3]

Users can now add an Assignee column to request documents to define who is responsible for each item. 

Insights

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

Performance Boost for Large Table Blocks in Insights Dashboards [2025.6.IN.1]

We’ve improved performance and responsiveness for large table blocks in Insights Dashboards. Tables now load faster, use less memory, and are paginated 100 rows at a time—enhancing usability and consistency with Analysis tables.

Benchling Connect

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

Allotropy Library Updated [2025.6.BC.1]

The Allotropy library has been updated through three sequential versions, introducing various improvements and fixes:

• v0.1.91 – Released May 22, 2025
• v0.1.90 – Released May 21, 2025
• v0.1.88 – Released May 14, 2025

Refer to the Allotropy changelog for full release details.

Updated Connectors for Liquid Chromatography Instruments [2025.6.BC.2]

Liquid chromatography parsers now support capturing run log data, enhancing data traceability and analysis for chromatography workflows.

FACSDiva Connector Now Available [2025.6.BC.3]

Benchling now supports integration with BD FACSDiva. For setup details, see the FACSDiva Configuration Guide.

FlowJo Connector Now Available [2025.6.BC.4]

Benchling now supports integration with BD FlowJo. For configuration steps, refer to the FlowJo Configuration Guide.

Improved Accuracy for automationFileTransform Status Events [2025.6.BC.5]

Status events for automationFileTransform are now more accurate. Previously, the v2-beta.automationFileTransform.updated.status event could incorrectly report a RUNNING status instead of PENDING due to race conditions.

This has been resolved by introducing distinct events for each status:

• v2.automationFileTransform.updated.status.pending
• v2.automationFileTransform.updated.status.running
• v2.automationFileTransform.updated.status.succeeded
• v2.automationFileTransform.updated.status.failed

These updates ensure more reliable tracking for custom automation transforms.

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.

Schema Descriptions Now Supported [2025.6.SCH.1]

Entity Schemas now support an optional description field. Admins can add a summary (up to 1,000 characters) to help users understand the schema’s purpose.

Note: This field is not yet available via the API.

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.

 Legacy Admin Dashboards Disabled for New Tenants [2025.6.AC.1]

The legacy Organization Admin dashboards—including the Activity Log—are now disabled by default for new tenants. These dashboards were previously accessible via the View Activity link in the Tenant Admin Console.

If you’d like to enable or disable these dashboards for your organization, contact Benchling Support.

 Audit Events for Team Deletion on Org Deletion [2025.6.AC.2]

When an organization is deleted, all associated teams are automatically deleted as well. These team deletions are now recorded as audit events for improved traceability.

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

Improved Dropdown Validation in Config Migration [2025.6.CC.1]

Resolved an issue where dropdown updates in Config Migration could trigger a KeyError. The system now better handles cases involving multiple object matches, improving reliability during configuration changes. 

Faster Config Migration Exports [2025.6.CC.2]

Optimized the Config Migration list endpoint to retrieve only the necessary data, significantly improving export page load times and reducing overhead.

Clearer Error Messages for Snapshot Conflicts [2025.6.CC.3]

Enhanced Config Migration error reporting when changes are blocked due to dependent snapshot fields. Error messages are now more informative, helping admins resolve issues more efficiently.

Improved workflow matching behavior in config migration [2025.6.CC.4]

Improved workflow matching behavior in config migration increasing accuracy by avoiding duplicates

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.

PipeBio<>Benchling integration v2 (Alpha Release) [2025.6.DP.1]

We’ve begun rolling out the v2 integration between PipeBio and Benchling. This version allows users to register sequences from PipeBio into Benchling and offers greater flexibility by supporting more formats beyond the limited schemas used in the previous version.

To enable this feature, contact a Benchling representative.

Improved Naming for Numbered Alignment Results [2025.6.DP.2]

Numbered alignment documents no longer include square brackets in their names. This change improves naming clarity and consistency across results.

 PipeBio API Now Returns a Single Organization Object[2025.6.DP.3]

The PipeBio API response now reflects that users belong to a single organization. Previously, the orgs field returned an array containing one organization, which implied support for multiple organizations. This field has been updated to org and now returns a single object instead of an array.

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.

Parallel Execution [2025.6.BP.1]

Users can now perform all condition replicates for a given Unit Operation within a single Worksheet—eliminating the need to switch between tabs. 

Procedures tables promoted from draft to beta [2025.6.BP.2]

The Procedures warehouse tables were promoted from draft to beta

Naming Templates for Recipe Runs [2025.6.BP.3]

Users can now define naming templates for Recipe and Assay Runs. These templates support concise, human-readable names—such as Sample ABC or unique IDs like S-100100—making it easier for scientists to identify and track experimental work for execution, review, or analysis.

PipeBio

PipeBio / Benchling Integration helps scientists work faster by linking sequence design with data management. Updates make it easier to register and connect sequences, configure schemas, import large datasets, and ensure workflows and APIs remain consistent.

PipeBio<>Benchling integration v2 alpha release Improved naming of numbered alignment results [2025.6.PB.1]

Start of v2 integration rollout between PipeBio and Benchling. This version allows users to register sequences from PipeBio in Benchling with support for more flexible formats compared to the limited schemas previously available.

To enable this feature, contact a Benchling representative.

Improved naming of numbered alignment results [2025.6.PB.2] 

Updated the naming of numbered alignment results. Square brackets are no longer included in document names, improving clarity.

PipeBio API returns users as having exactly one org [2025.6.PB.3]

Refined the PipeBio API to return a single "org" object instead of an array, aligning the response with actual usage, as users only ever belong to one organization.

Bug Fixes

Notebook

• Fixed bug where table mapping failed in sub-templates.
  
   
• Fixed bug where filters could not be added to a Lookup Table within a sub-template.
  
   
• Fixed bug where dropdown fields could not be specified.
  
   
• Fixed bug where result tables displayed a persistent blue mark stating "This value was updated after the table was last submitted."
  
   
• Fixed bug where zooming in or out in the browser caused table rows to disappear.
  
   
• Fixed bug where editing long formulas was difficult due to scrolling failures.
  
   
• Fixed bug where using arrow keys in row 1 caused the view to snap unexpectedly.
  
   
• Fixed bug where complex polymer registration tables appeared blank and did not support copy/paste.
  
   
• Fixed bug where complex polymer registration tables did not support cell references.
  
   
• Fixed bug where review process comments failed to expand when clicking "Show more."
  
   
• Fixed bug where @mention links did not resolve correctly due to missing usernames; updated logic to resolve using email instead.
  
   
• Fixed bug where note parts linked across tenants rendered as if the items were deleted.
  
   
• Fixed bug where the plate map "fill by pattern" modal did not resize or support scrolling.
  
   
• Fixed bug where notebook entries and templates failed to load due to missing complex polymer component columns.
  
   
• Fixed bug where creating entries via the v2-alpha endpoint required a schema ID unexpectedly.
  
   
• Fixed bug where PDF export for GxP customers blocked the revision history under the header.
  
   
• Fixed bug where worksheet exports rendered incorrectly—analysis charts were blank and result tables were cut off.
  
   
• Fixed bug causing a red toast error when archiving procedures from the procedure editor.
  
   

Molecular Biology

• Fixed bug where create_part_and_replace unexpectedly cleared modifications and partially deleted multi-region features.

Small Molecule

• Fixed bug where UT flexibility was not supported in the complex polymer map.
  
   
• Fixed bug where schema fields were not properly audited when archiving linked units.
  
   
• Fixed bug where oligo duplexes could not be registered without a required component.
  
   

In Vivo

• Fixed bug where users could not print cage cards for cages not part of a study due to colony permissions.
  
   
• Fixed bug where Excel exports displayed a ' character in front of negative numbers.
  
   
• Fixed bug where the In Vivo sync app converted mL values to µL without updating the units, leading to data integrity issues.

Registry and Inventory

• Fixed bug where a UniqueViolation error occurred due to duplicate barcodes on storable registry items.
  
   
• Fixed bug where the search sidebar did not update after renaming an item.
  
   
• Fixed bug where the "Add a constraint" modal clipped its dropdown menu. 

Workflows

• Fixed bug where legacy workflow entry snapshots failed to generate.
  
   
• Fixed bug where users could not create a task from an existing request task.
  
   
• Fixed bug in mapping destination wells that caused errors.
  
   
• Fixed bug where tasks created from Insights failed for schemas with dropdown fields.
  
   
• Fixed bug where initiating a request from a structured table did not work as expected.
  
   
• Fixed bug where the Create Workflow dropdown extended off-screen.
  
   
• Fixed bug where the Bulk Scheduled on Date modal failed to appear in search.

Insights

• Fixed bug where the dynamic_pivot SQL function broke after the 2025.2 upgrade.

Benchling Connect

• Fixed bug where CSV imports added unexpected text.
  
   
• Fixed bug where specific Excel formatting introduced hidden line breaks that caused Analysis errors.
  
   
• Fixed bug where column mapping in Connect → Analysis used a static analysis template input table.

Schemas

• Fixed bug where users could remove interface fields used in name templates.
  
   
• Fixed bug where the Lookup modal failed to query tag schemas correctly.

Application Core

• Fixed bug where line numbers displayed incorrectly in the Benchling Insights Console.
  
   
• Fixed bug where the Results UI failed due to snapshot fields, blocking migration.
  
   
• Fixed bug in the POST /users endpoint that caused unexpected errors.
  
   
• Fixed bug where users could not delete a team due to an error stating that suspended users cannot be added to a group.
  
   
• Fixed a bug where objects with invalid archive reasons did not appear in search results
  
   
• Fixed bug causing export issues.
  
   
• Fixed bug where FileTable study item associations failed to sync to the warehouse.

Bioprocess

• Fixed bug where the date picker overflowed in the TransitionRunModal.