Welcome to the 5th 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 May 2025.

Notebook

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

Link Icon Now Labeled “Hyperlink” [2025.5.N.1]

The hover text for the link icon now reads "hyperlink" for improved clarity.

Additional Formatting Options for Locked Cells [2025.5.N.2]

Locked cells now support more formatting options, similar to unlocked cells. Some options remain unavailable, such as adding a Vanity URL (a data change) and setting a background color (which conflicts with the locked cell’s default gray appearance).

Sub-Templates Support Table Mapping [2025.5.N.3]

Users can now add Table Mapping when creating a Sub-Template. The mapping is preserved when the Sub-Template is added to an entry.

Sequence Topology in Registration Tables [2025.5.N.4]

Users can now specify sequence topology in registration tables using the topology column. Options include circular and linear.

Improved UX When Editing Submitted Tables [2025.5.N.5]

When making changes to a submitted table, any modified cell is now tagged with a blue dog ear.

Template Publishing [2025.5.N.6]

Templates and Sub-Templates can now be edited in draft mode and published as versions. Each version retains a full edit history and is associated with entries created from it.

To enable reach out to a Benchling Representative

In-Line Editing Optimization for Structured Tables [2025.5.N.7]

Structured tables now render only the rows visible on-screen, improving performance in large tables. Learn more: help article 

Event Triggers for Review Snapshot Status Changes [2025.5.N.8]

Benchling integrations can now receive events when a review snapshot begins or completes generation. This supports automated tracking of reviewed entries.

Structured Table Row Limit Increased to 1,000 Rows [2025.5.N.9]

The maximum row count for structured tables has increased from 500 to 1,000.  Learn more: help article 

Updated Default Limit for Table Rows in Entry PDF Exports [2025.5.N.10]

Notebook entry exports default to a 500-row maximum per table in the exported PDF. If tables are larger than 500 rows, they will not be rendered within the PDF. Instead, these will render as a collapsed table and a CSV file will be included alongside the exported PDF.

Improved UX for collapsed tables [2025.5.N.11]

Collapsed tables that are submitted now show "Submitted" in the collapsed state.

Support for MEDIAN() Formula [2025.5.N.12]

Tables now support the MEDIAN() function to return the middle value of a numeric dataset.

Replicate Column No Longer Required in Non-Parameter Tables [2025.5.N.13]

The replicate column is no longer required in non-Parameter tables (e.g., Registration, Result, Inventory). It remains required for Parameter tables (e.g., Parameter measurement, confirmation, materials, equipment).

Molecular Biology

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

Clearer Error Messages for Large Sequence File Imports [2025.5.MB.1]

Users now see a clear error message when attempting to import a sequence file that exceeds size limits. The message indicates that the file is too large and suggests uploading the data in smaller batches.

Improved Filtering on v3 AA Sequence Endpoint [2025.5.MB.2]

Users can now filter by residues when using the v3 AA sequence API endpoint.

Schema Support for Entities Created via v2 Assembly API [2025.5.MB.3]

Developers can now specify schemas for new entities created through the v2-alpha assembly API.

Fuzzy Matching for AA Annotation Libraries [2025.5.MB.4]

In feature libraries, you can now incorporate regular expressions to allow for imperfect or fuzzy matching. Before, this was supported for DNA features only; now it's supported for AA features, too.

Expanded Codon Optimization Parameters [2025.5.MB.5]

Users now have additional control when performing codon optimization. New parameters and back translation tools have been introduced.

Add AA Sequences to Worklists During Import [2025.5.MB.6]

Users can now add AA sequences to worklists during file import using the global create or project create buttons.

Associate Assemblies with Studies [2025.5.MB.7]

Assemblies can now be associated with a study to support study-based organization of sequence data.

Small Molecule

The molecule entity in Registry helps users model and interact with chemical compounds throughout the platform, enabling users to draw, visualize, store, and search chemical structures.

Detailed Error Messaging for Invalid Leaving Groups [2025.5.SM.1]

Users now see more descriptive error messages when an invalid leaving group is specified in oligo conjugates.

Improved Connection Drawing in Oligo Conjugates [2025.5.SM.2]

When drawing connections in oligo conjugates and duplexes, molecule components now auto-space to prevent overlap. Users no longer need to manually reposition components when adding attachments.

Associate Molecules with Studies [2025.5.SM.3]

Molecule entities can now be associated with a study for improved data organization.

Monomer Size Limits in Monomer Library [2025.5.SM.4]

Monomers in the monomer library are now limited to 300 atoms. This update helps maintain performance and aligns with typical use cases for nucleotide modifications.

In Vivo

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

Search for Cages Using the Search Bar [2025.5.IV.1]

Users can now search for specific cages in Workflow by entering a cage name or cage catalog number (the barcode on printed cage card labels) in the search bar.

Monitor Task Completion Status [2025.5.IV.2]

When a task is marked as "Done," the timestamp and user who completed the task are now displayed on the task.

Move Individual Animals Across Studies with Different Presets [2025.5.IV.3]

Users can now move individual animals—not just entire cages—between studies with different presets. During the move, users can map measurement fields to maintain data continuity. A study history section on the animal profile and updated audit logs ensure full traceability.

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.

Archive Option Disabled for Fixed Well Plates [2025.5.RI.1]

The archive option is now disabled when a fixed well plate is set as the primary container.

Select All Wells in Plate Maps [2025.5.RI.2]

Users can now use a "Select all" button to quickly select all wells within a plate map.

Preview Well Roles Defaulted to On in Contents View [2025.5.RI.3]

When viewing the Contents tab of a plate map, the Preview well roles toggle is now enabled by default.

Print Labels from Inventory Tab [2025.5.RI.4]

A Print labels button is now available on the Inventory Tab, allowing users to print labels directly.

Default to Barcode in CSV Export When Container Name Is Blank [2025.5.RI.5]

When exporting containers to CSV, if a custom container name is blank, Benchling now defaults to using the container barcode in the Name column.

Use Plate Designs in Templates [2025.5.RI.6]

Users can now include plate designs in templates, not just in entries. This enables creation of plate records directly from predefined designs within Notebook entries.

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.

Flowchart ID Column Added to Task Group Search Results [2025.5.W.1] 

The Flowchart ID is now shown as a column in the Task Group search overview.

Tooltips for Workflow Task Schemas[ 2025.5.W.2]

Users can now configure tooltips for both task and output fields in workflow task schemas to provide additional context to end users.

Create Workflow Tasks from Insight Blocks [2025.5.W.3]

Users can now create workflow tasks directly from Insight blocks.

Right-Click to Filter Workflow Search Results [2025.5.W.4] 

Users can now right-click on items in workflow search results to apply filters based on the selected item.

Data Modifications Visible in Workflows [2025.5.W.5]

When Data Modifications are enabled, changes to task and output fields are now displayed in workflows.

Updated Create Tasks Modal [2025.5.W.6]

An updated modal is now shown when creating workflow tasks from search, tables, or Insights. Users can select which fields to use for task creation. Previously, field mapping was automatically inferred with no way to adjust it.

Task Names Shown in Collapsed Side Panel [2025.5.W.7]

When viewing workflow tasks in a collapsed side panel, task names are now shown instead of human IDs.

All Blocking Tasks Displayed When Archiving Task Schema [2025.5.W.8]

Previously when archiving a task schema Benchling displayed up to 4 tasks that prevented the archival of the task schema. Now all tasks that block the archival of a task schema are displayed for clarity.

Insights

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

Rename Analysis Templates [2025.5.IN.1222]

Users can now rename Analysis Templates directly from within Template Collections. This feature can be enabled in the Tenant Admin Console.

Multi-Select Show/Hide Columns in Analysis [2025.5.IN.2]

Users can now show or hide multiple columns in Analysis using a multi-select dropdown, reducing the number of clicks needed to manage column visibility.

Deprecation of Legacy Warehouse Metadata Tables [2025.5.IN.3]

Over the coming months, access to select PostgreSQL metadata tables within information_schema and pg_catalog will be removed. The aim of this change drives ongoing improvements to the Benchling Insights platform allowing for increased efficiency, long-term scalability and reliability. The removal of these tables impacts a small number of users. To review the list of supported tables moving forward, please refer to the developer documentation. For questions please reach out to Benchling support or your representative.

Benchling Connect

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

Sidebar Indicator Only Displays for Unsubmitted or Incomplete Runs [2025.5.BC.1]

Runs now display the blue sidebar indicator only when unsubmitted or incomplete. The indicator is removed once the run is submitted, consistent with behavior across the platform.

"Allow Attachment" Option in Run Schema Configuration [2025.5.BC.2]

Users can now configure run schemas to allow file attachments per run. If this option is not enabled, the attachment modal is not shown during run execution.

Files Linked in Run Blocks [2025.5.BC.3]

Files imported through Benchling Connect are now linked within run blocks, making it easier to navigate to parsed files.

Connection Audit Logs Track Field Changes [2025.5.BC.4]

Connection field changes are now tracked in the instruments service, and audit logs reflect changes based on the updated service state.

Liquid Chromatography Connector Updates – Run Log Capture [2025.5.BC.5]

Connectors for the Liquid Chromatography instrument class now support capturing run log data through the chromatography parsers.

Clearer Input File Generator Audit Logs [2025.5.BC.6]

Audit logs for input file generators now provide clearer tracking of state changes. Updates include:

• RUNNING → SUCCEEDED/FAILED now logged as input_file_generator: Finished
  
  
• File creation logged as input_file_generator: Generated
  
  

Plate Reader Connector Update – Group File Aggregation [2025.5.BC.7]

Refactored aggregation logic for Group file CSVs in Plate Reader connectors to account for group IDs and non-unique sample IDs.

Plate Reader Connector Update – Unique Column Label [2025.5.BC.8]

Connectors now generate unique column labels in Group file CSVs when multiple calculated data columns come from the same group.

Allotropy Integration Updated to v0.1.87 [2025.5.BC.9]

Benchling's integration with Allotropy has been upgraded to version 0.1.87. See the Allotropy v0.1.87 changelog for details.

Improved Folder Configuration for Run Schemas  [2025.5.BC.10]

Users can now configure run schemas with no default folder, allowing destination folders to be selected per file. When Registry is restricted to project use, Registry folders are hidden from run schema and run folder pickers.

To enable reach out to a Benchling Representative

Plate Reader Connector Update – Unique Column Labels [2025.5.BC.11]

Generated Group file CSVs now include distinct column labels for multiple calculated data columns from the same group.

Plate Reader Connector Update – Group File Aggregation [2025.5.BC.12]

Refined the aggregation of Group file CSVs to better handle group IDs and duplicate sample IDs in Plate Reader connectors.

Liquid Chromatography Connector Update – Empower Field Capture  [2025.5.BC.13]

Updated ASM-to-CSV conversion for Liquid Chromatography connectors to reflect changes in Empower custom field capture.

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.

New "Add Field" Button on Entity Schema Field Table [2025.5.SCH.1]

Benchling has created a new "Add field" button at the bottom of the field table on Entity Schemas. This is an improved experience for customers with large sets of fields, allowing them to choose to add a new field without have to always scroll up and click the "+" button to add a new field.

Boolean Field Definitions for Entity Schemas [2025.5.SCH.2]

Entity schemas now support fields with a Boolean field definition.

New Filtering Options on Entity Schemas List Page [2025.5.SCH.3]

Users can now filter the Entity Schemas list page by Entity Type, Fieldset, and Validation Status. These filters help narrow results to specific schema types (such as Custom Entities or DNA Oligos), locate schemas using a particular fieldset, or identify schemas with validation errors.

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.

Renamed Config migration "Errors" section [2025.5.AC.1]

The "Errors" section in Config Migration has been renamed to "Issues" to reflect that both errors and warnings are displayed in this section.

Improved Access Denied Page [2025.5.AC.2]

The message shown when users attempt to access a restricted page has been updated for clarity. The layout has also been modernized for better display across screen sizes.

Updated Compare Configuration Button in Config Migration [2025.5.AC.3]

The Compare configuration button in Config Migration has been updated. The icon has been removed, and the button label has been revised for clarity.

Removed Top-Level Warning Icons in Config Migration Summary [2025.5.AC.4]

Top-level warning icons are no longer shown after a successful Config Migration import. These icons are now replaced with green checkmarks for imported objects.

Auto-Load Config Migration History Records [2025.5.AC.5]

Users can now view a new Config Migration history record immediately after a successful import. A manual page refresh is no longer required.

Improved Manage Access Modal UI [2025.5.AC.6]

The Manage access modal now extends to full screen height to reduce scrolling when working with a large number of collaborators.

Improved Add Collaborators UI [2025.5.AC.7]

When searching for collaborators to add, users already added are now grayed out in the search results for better visibility.

Search items on Benchling with API IDs [2025.5.AC.8]

Users can now search for items in Benchling using their API ID.

Import Config migration Validate + Export button [2025.5.AC.9]

The Validate + Export button in Config Migration is now consistently visible and no longer gets cut off.

Improved Error Message for Invalid API Keys [2025.5.AC.10]

Error messages related to API key issues now include more specific details instead of a generic message.

‘Converted From’ Fields Removed from Config Migration [2025.5.AC.11]

Fields labeled ‘Converted From’, which were generated by a legacy tool, are no longer migrated during Config Migration.

Align Export and Import UX in Config migration [2025.5.AC.12]

The user interface for Export and Import in Config Migration has been aligned to have consistent sizing and layout.

Removed Product Limit on Registry Revalidation in Config Migration

[2025.5.AC.13]

The Config Migration product limit that blocked imports requiring registry revalidation for more than 100,000 entities has been removed.

CSV Export in Tenant Admin Console Respects Filters [2025.5.AC.14]

CSV exports of users from the Tenant Admin Console now only include users who match the applied filters.

Improved Reporting of Referenced Object Changes Config Migration [2025.5.AC.15]

Referenced objects with changes in Config Migration are now identified by API ID instead of internal IDs.

Improved Name Conflict Error Messages in Config Migration [2025.5.AC.16]

Error messages for display name conflicts now specify the object type to help users locate the conflict more easily.

Feature Settings Side Panel Now Always Expanded by Default [2025.5.AC.17]

The Feature Settings side panel now always opens in an expanded state, regardless of side panel settings on the home screen.

Custom Language for Email Subjects from Tenants [2025.5.AC.18]

Admins can now configure custom text to append to email subject lines sent from a Benchling tenant. This helps distinguish emails across environments. For example, subjects may include “Test environment” or the tenant subdomain.

To enable reach out to a Benchling Representative

Improved Error Messages on User Creation [2025.5.AC.19]

Error messages shown during user creation now include more detail to clarify the affected user and the underlying issue.

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.

v3 API documentation now live[2025.5.DP.1]

The v3 REST API documentation is now publicly available at 

https://benchling.com/api/v3-beta/reference and 

https://benchling.com/api/v3-alpha/reference.

Note: Access to use the v3 APIs still requires enablement by Benchling Support.

Canvas webhooks include userId [2025.5.DP.2]

All Canvas webhooks now include the userId field in the payload. Previously, only one of the three webhooks included this information.

Required Fields in Canvas Blocks [2025.5.DP.3]

Developers can now set Canvas input fields as required. The Canvas will prevent submission if required fields are not filled and will indicate where input is missing.

File Upload UI Block in App Canvas 2025.5.DP.4

Developers can now add File Upload blocks to App Canvases. The block allows configuration of accepted file types and quantity. The Canvas API returns a download link for uploaded files

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.

Update Study Schema system ID [2025.5.BP.1]

Users can now update the system name of a Study Schema. The updated name is reflected in the data warehouse.

Custom Studies [2025.5.BP.2]

Users can now model studies using the Custom Studies framework. Previously, studies were modeled as custom entities or projects, without a unified view of study-wide data.

Recipes Warehouse Tables (Beta) [2025.5.BP.3]

The warehouse tables supporting Procedures in Recipes are now available in Beta.

Policy Statement Dependencies for Recipes [2025.5.BP.4]

The Recipes item type has been updated to include dependencies on policy statements from key Benchling modules—Notebook, Studies, and Workflows. This enhancement ensures more robust governance and traceability by enforcing the appropriate compliance and procedural checks when working with Recipes in regulated environments.

Custom Studies [2025.5.BP.5] 

Custom Studies is now generally available. Users can model studies and view data across multiple experiments.

Direct Hyperlinks to Worksheet Steps [2025.5.BP.6]

URLs in hyperlinks for Unit Operation Tasks opened the Flowchart of an Experiment execution, which required additional manual steps to open a Worksheet Step

Bug Fixes

Notebook

• Fixed an issue where updates to Custom Fields in legacy Result tables weren’t recorded in the audit log.
  
  
• Template Collection description changes are now properly captured in audit events during config migrations.
  
  
• Resolved an issue where cell highlighting in unstructured tables would disappear until the page was refreshed.
  
  
• Improved clickability of sub-menu options in lookup configuration modal when overlapping the menu border.
  
  
• Addressed header/footer overlap issues in Result tab tables, which were obscuring data.
  
  
• Fixed view jump that occurred after submitting table data in worksheets.
  
  
• Resolved issue where dropdowns in the last cell failed to render the editor if horizontal scrolling was triggered.
  
  
• Fixed disappearing share links for entries under review.
  
  
• Enabled interactive inputs inside pop-ups triggered via modals.
  
  
• Updated @mention behavior to show email when no username is set, matching the resulting mention chip.
  
  
• Fixed formula reference errors caused by deleting the first row in tables with single inputs.
  
  
• Corrected incorrect incrementing of single input cell references in parallel execution worksheets.

Molecular Biology

• Corrected the structure in API documentation for v2 assembly endpoints.
• Resolved an error with v2 assembly API when start/end positions weren’t provided for concatenation.
• Additional improvements to v2 assembly API documentation.
• Fixed a bug that cleared modifications or removed regions in RNA/DNA sequences when creating parts from the sequence map.
• Prevented autofill of RNA parts from erroneously removing modifications.

In Vivo

• Audit logs now correctly reflect that no reason is recorded when the “Reason for Change” setting is disabled.
• Fixed validation error that occurred when using follow focus—values now register properly.
• Prevented errors when attempting to edit completed tasks.
• Enforced integer-only filtering for animals by latest measurement.
• Supported exponential values in numeric disease metadata fields to prevent errors.
• Resolved issue with task scheduling forms failing to save if days were entered before a condition was selected.
• Fixed errors encountered when editing observations after glossary removal.
• Corrected baseline misalignment for % dT/dC and % Inhibition calculations in summary analysis—Tracking Date is now used correctly.

Registry and Inventory

• Fixed incorrect incompatible units error for source containers with different concentration units.
• Prevented invalid schema field changes in container naming templates.

Insights

• Corrected filter logic for text columns—numeric-like strings now properly compared with equals/does-not-equal filters.

Benchling Connect

• Fixed saving issue for Notebook Entry Templates when connections were added to runs.
• Resolved dropdown selection bug where identical case-insensitive options returned None.
• Addressed UI overlap in the run schema configuration page due to narrow window widths.

Schemas

• Enhanced error reporting for schema field issues by including the schema name for better clarity.
• Fixed issues with migrating property updates (e.g., system/display names) on computed fields of complex polymer schemas.
• Updated audits to consistently refer to “Fieldset” instead of “Schema Interface.”
• Resolved a blocker that prevented modifying entity links from schemas to fieldsets.
• Fixed UI freezing when archiving child schemas that were linked from a parent schema.

Application Core

• Addressed multiple crashes during configuration migration caused by incorrect schema and reference handling.
• Prevented unnecessary differences from being flagged for unchanged objects.
• Resolved errors during execution template migrations.
• Fixed team/org settings not refreshing after updates.
• Fixed profile picture removal issues at org/team levels.
• Corrected use of reasons for archival in study schemas and related definitions.
• Ensured global create menu repositions correctly when window is resized.