Release Notes: Volume 7, 2025
Welcome to the 7th 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 July 2025.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Notebook Check GA [2025.7.N.1]
Notebook Check is now generally available. This AI-powered feature detects potential issues in any Notebook entry. It is opt-in and can be enabled tenant-wide or for select users. Learn more.
Direct Links to Notebook Sections [2025.7.N.2]
Users can now create links to specific sections or days in Notebook entries, allowing direct navigation to that content.
Publishing Status Filter [2025.7.N.3]
Users can now search templates by their publishing status.
Enhanced Review History [2025.7.N.4]
Enhanced Review Records is an opt-in feature that improves the formatting and metadata of review exports across entries, worksheets, and custom studies. Review history is now separated from scientific content, and for customers using e-signatures, the exports clearly indicate when a formal signature took place.
Multi-Select Field Updates [2025.7.N.5]
Users can now see a unique icon for multi-select fields in Notebook tables and use a “+” button to add more choices.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
CRISPR Vector Permissions Update [2025.7.MB.1]
Users can now access a CRISPR vector only if they have access to the associated sequence in a project or folder.
Fuzzy Match for AA Sequence Features [2025.7.MB.2]
Users can now use regex syntax for fuzzy matching in AA features within feature libraries, helping identify imperfect matches.
Audit Events for Alignment Deletion [2025.7.MB.3]
Users can now see audit events when alignments are deleted due to the deletion of associated AA, DNA, or RNA sequences.
Small Molecule & Other Modalities
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.
Improved Large Molecule Rendering [2025.7.SM.1]
Users can now view very large molecules more clearly. Large molecules are automatically cleaned up during import, ensuring accurate structure display.
In Vivo
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Max Cage Population Increased to 15 [2025.7.IV.1]
Users can now house up to 15 animals per cage to better support litters.
Validation for Preset Measurements [2025.7.IV.2]
Users can now save measurement forms with optional fields left blank, honoring preset input requirements. This supports partial data entry for calculations (e.g., unilateral vs. bilateral tumor measurements) without editing the workflow setup.
Flexible In Vivo Sync Backfill [2025.7.IV.3]
Users can now selectively sync historical In Vivo data by study, item type, and date range. The UI provides progress tracking, event-level outcomes, and options to cancel or retry without affecting live sync.
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.
Increased Plate Map Schema Field Limit [2025.7.RI.1] Users can now add up to 20 schema fields to plate maps, doubling the previous limit of 10.
Insights SQL Writer GA [2025.7.RI.2]
Insights SQL Writer is now generally available. This AI-powered feature allows users to generate Insights queries using natural language prompts. It is opt-in and can be enabled tenant-wide or for select users. Learn more.
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.
Delete Default Responsible Teams [2025.7.W.1]
We've deprecated default responsible teams. So now we allow for users to delete teams even if the team is associated with a default responsible team.
Archive Task Schemas from Archived Flowcharts [2025.7.W.2]
Previously if task schemas were in use in archived flowcharts, they could not be archived. Now users can now archive these task schemas if they are only used in those archived flowcharts.
Assignee Column in Request Documents [2025.7.W.3]
A new column has been added to request documents tables to allow users to view and define an assignee directly in that table..
Navigate a flowchart in a single tab [2025.7.W.4]
Previously when you selected tasks within a flowchart new tabs would be opened to display the tasks. This ended up creating a lot of tabs for users to manage. This change makes it so a single tab opens is used to update the task that's being displayed in the flowchart as you navigate through the flowchart's tasks instead of creating a new tab every time you navigate to a different task in the flowchart.
Benchling Connect
Benchling Connect, formerly Lab Automation, enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Allotropy Updates [2025.7.BC.1]
Users can now access the latest enhancements and fixes in Allotropy, updated through versions 0.1.94 to 0.1.101. See the Allotropy change log for full details.
Bulk Move Datasets [2025.7.BC.2]
Users can now move datasets in bulk to other projects or folders from Global Search and the Projects view.
Liquid Chromatography Connector Updates [2025.7.BC.3]
Added support for multi-unit peak fields in Liquid Chromatography connectors.
Improved Automation File Transform Status Accuracy [2025.7.BC.4]
Status events for automation file transforms are now more accurate, with distinct events for each status type.:
- v2.automationFileTransform.updated.status.running
- v2.automationFileTransform.updated.status.pending
- v2.automationFileTransform.updated.status.succeeded
- v2.automationFileTransform.updated.status.failed
Multi Analyte Profiling Connector Updates [2025.7.BC.5]
Added a new ANALYTE transform to format analyte documents per row and improved error handling for NaN values in statistical and calculated data.
Multi-Select Checkbox for “Required?” in Column Mapping [2025.7.BC.6]
Added support for multi-select checkboxes for the "Required?" field in the dataset column mapping configuration modal within a run,
Flow Cytometry Connector Updates [2025.7.BC.13]
Added support for custom information in Flow Cytometry connectors.
Collapse a dataset table in a run based on a flag value [2025.7.BC.15]
Dataset tables in a run will now automatically collapse if the row count exceeds a set threshold. This feature must be enabled—please contact Benchling Support to adjust the threshold from the default setting(25 rows).
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.
Entity Schema Descriptions [2025.7.SCH.1]
Users can now add and view Entity Schema descriptions across the platform. Descriptions can be entered on the Entity Schema configuration page and are accessible in the V3 API, the Warehouse, and Configuration Migration. In the Notebook, descriptions appear as tooltips when hovering over the schema name in a registration table.
Improved Error Messages for Risky Field Type Changes [2025.7.SCH.2]
Users will now see clearer warnings when changing a field type. If a change could cause data loss (e.g., datetime to boolean), the system will explicitly notify the user.
New Entity Types in Schema and Fieldset Configuration [2025.7.SCH.3]
Users can now select newly available Entity Types when choosing the entity definition for a link field.
Updated Entity Types in Schema Configuration [2025.7.SCH.4]
Complex Polymers (Oligo Duplex, Oligo Conjugate) and Equipment are now listed as separate Entity Types, rather than custom entity checkboxes. Existing schemas will reflect this change in the UI. The V2 API will still use Custom Entity, while the V3 API has dedicated endpoints for these new types.
System Name Replaces Warehouse Name [2025.7.SCH.5]
The label “System Name” now replaces “Warehouse Name” to better reflect its use across the V3 API and Warehouse, while keeping the underlying value unchanged.
Updated Naming Template Dropdown [2025.7.SCH.6]
The naming template dropdown on the schema configuration page now better sorts and organizes available options into submenus.
Access Management
Access management is the way customers control who is able to access which resources, and includes things like project permissions, access policies, and admin roles.
Folder-Level Permissions GA [2025.7.AM.1]
Folder-level permissions are now generally available and will be supported in GxP in the next release. This feature does not yet apply to Warehouse or Insights Dashboards, so folder-level access will not grant visibility in those areas. A new Tenant Admin Console page allows admins to enable or disable folder permissions for their tenant. Learn more.
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.
Custom Email for Suspended Users with SAML SSO [2025.7.AC.1]
When SAML SSO is enabled, suspended users who attempt to log in will now see a custom email address (if configured) instead of “your admin” in the error message. Please reach out to Benchling Support to configure this feature.
Search Support for Oligo Duplex, Oligo Conjugates, and Equipment [2025.7.AC.3]
The Type dropdown in Search now includes Oligo Duplex, Oligo Conjugate, and Equipment as selectable entity types.
Units Support in Config Migration [2025.7.AC.4]
Users can now migrate the unit dictionary, including unit types and individual units, using Config Migration. This ensures consistency across environments and reduces manual setup.
Point-in-Time Capture for User & Name Fields in Audit Logs [2025.7.AC.5]
The “Name” and “User” fields in audit logs are now snapshotted at the time of capture, ensuring exports reflect historical values.
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.
App Admin Role for All Non-GxP Customers [2025.7.DP.1]
Non-GxP customers can now assign the “App Admin” role to individual users, granting permissions to create, install, and update Benchling Apps without requiring full tenant admin access.
Review Data in Warehouse [2025.7.DP.2]
For improved operational reporting, users can now access worksheet and entry review data in the warehouse. The review and reviewer tables in the warehouse are now in Alpha stability. These are meant to replace custom mapped review columns in the worksheet table.
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.
Notification Schedules Disabled Without Workflows [2025.7.BP.1]
If workflows are not provisioned, notification schedules for custom studies will not be available because workflow tasks cannot be created.
Improved PD Studies [2025.7.BP.2]
Users can now plan, manage, and analyze multiple recipe runs within a single study.
Default Recipe Run Name Templates [2025.7.BP.3]
Recipe runs now default to the format Date – Recipe Name – Run ID. The template can be edited, but the Run ID is always required.
New Warehouse Table for Unit Operation Links [2025.7.BP.4]
A new table records links between unit operations in multi-run Process Development studies.
New V3 API Endpoint for Unit Operation Links [2025.7.BP.5]
A new V3 API endpoint lets users create, retrieve, list, and delete links between unit operations in multi-run Process Development studies.
Add Conditions During Recipe Execution [2025.7.BP.6]
Users can now add conditions to recipe or assay runs after creation. This update also includes an improved worksheet header, human-readable worksheet IDs, and a new worksheet naming convention.
Worksheet exports will now also show the ID of the Worksheet [2025.7.BP.7]
Users can now view worksheet IDs in exported worksheet files.
Unique Worksheet IDs [2025.7.BP.8]
To make worksheets easy to uniquely identify, there are now unique IDs that will initially appear as a column in various search results and on the chips that link to worksheets such as from the study. All new worksheets will have a human-readable IDs. Existing worksheets will not be backfilled with human readable IDs.
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.
Automatic Linking of AA & DNA Translations [2025.7.PB.1]
AA and DNA sequences registered via the Add-to-Benchling tool are now automatically linked when there is an AA match.
Schema-Specific Naming Strategies [2025.7.PB.2]
Users can now set different naming strategies for each schema in the PipeBio Benchling settings page, instead of a single global strategy.
AWS Import Supports More Than 1K Rows [2025.7.PB.3]
The AWS import dialog now supports infinite scrolling, more than 1,000 rows, and includes a prefix search to quickly find AWS data.
Autosave for Add-to-Benchling Settings [2025.7.PB.4]
Settings in Add-to-Benchling now save automatically after each change—no save button required.
Create New Folder Helper Text [2025.7.PB.5]
Added helper text to clarify the purpose of the “Create New Folder” field.
Improved Rendering for Large Nested Schemas [2025.7.PB.6]
The Add-to-Benchling settings page now loads and renders faster for tenants with deep schema hierarchies.
Workflow Naming Improvements [2025.7.PB.7]
Workflows can now optionally generate cleaner names in large workflows and avoid unnecessary file name postfixes from the merge tool. Editable by PipeBio staff only—contact support@pipebio.com for details.
Improved Synchronization with Benchling Schemas [2025.7.PB.8]
Enhancements include automatic schema refresh, change detection to prevent outdated configurations, and monitoring of new, modified, or deleted fields.
PipeBio API Org Field Update [2025.7.PB.9]
Previously the PipeBio API would list "orgs" for a user in response objects, implying a user could have more than one organization. The response object was an array with one value; the user's org. In practice users only ever had one organization. This change updates the API response object to imply that; "orgs" becomes "org" and the object is the org itself, rather than an array with a single org inside.
Document ids (entity ids) are now strings [2025.7.PB.10]
For internal reasons, we've changed entity ids (document ids) from numeric, serial ids (like `1234`) to string nano ids (like `ent_582Z2tSfuMxRcPhV`). - The change is backwards compatible meaning that any linked entity ids (stored in bookmarks, PDFs etc) will continue to work. Numeric serial ids will continue to be supported for queries. - All new entity ids will be new string nano ids and our API will return string ids for all entities.
Bug Fixes
Access Management
- Corrected 500 error from beta API endpoint.
- Added audit event for enabling/disabling the Admin Dashboard for Organization Admins.
Application Core
- Fixed issue preventing deletion of internal teams.
- Corrected snapshot versioning logic causing StageEntry snapshots to fail.
- Moved workflow template matching to the server.
- Generating a historical Entry Snapshot no longer includes full review change history.
- Fixed pagination issues with relevant templates when archived templates were present.
- CM Importer: Archived objects now respect relevant authorization checks.
- Fixed MigrationImportError created without object_id or unattributed error source.
Benchling Connect
- Fixed issue where multiple events were generated with different IDs for Connect custom transforms.
BioProcess
- Limited the number of studies in the metadata studies list.
In Vivo
- Fixed issue where admins could not see doses on the doses page.
- Fixed issue where next_URL in multi-page API responses returned non-secure links.
- Fixed inability to clear treatment metadata fields after treatment creation.
- Fixed regression causing animal alerts issues in workflows.
- Added draft_id to study create payload.
- Fixed regression where cage metric forms from previous cages were shown incorrectly.
Molecular Biology
- Fixed Geneious file import issues.
- Corrected case sensitivity for primers in the combinatorial assembly tool.
- Fixed issue where feature library read-only banner displayed for all org-owned libraries.
- Locking a project now also locks oligos in its folders.
- Fixed issue where unlocking sequences in a project was not saved.
- Fixed double overlap sequence in Gibson assembly.
- Fixed missing react slices in alignment PDF export preview.
- Fixed permissions bug causing CRISPR vector read endpoint errors for registry items.
Notebook
- Fixed issues with Boolean fields.
- Corrected Excel compatibility issue for files downloaded from Benchling tables with square brackets.
- Fixed text truncation in structured tables during entry export.
- Fixed resubmission/re-sync errors for Results Table.
- Fixed error message in Preview Tenant when importing mixture ingredients.
- Fixed issue where sub-templates with table mapping were not updated via config migration.
- Fixed request task table mapping errors.
- Added scroll bar to Notebook Entry Review Assignee list.
- Fixed email notifications incorrectly sent to large teams when first review step was reassignable.
- Fixed double-click expand behavior for structured table columns with asterisks.
- Fixed bug allowing fill-down and multi-row paste into read-only cells.
- Fixed issue where table names with ! could not be used in formula references.
- Fixed copy/paste and spreadsheet import for translation link fields.
- Fixed PNG images not copying over.
- Added missing audit for review_criterion: Updated status events.
- Allowed admins to search review processes and create projects even if some review processes are inaccessible.
- Fixed Review TargetClosedError errors in headless pipeline.
- Fixed incorrect counters in “My Worksheet Todos” section.
PipeBio
- Fixed synchronization not updating modified values.
- Fixed crash when tabular import contained newline characters or tabs.
- Fixed delete label dialog not closing.
- Fixed extract job filter mismatch issues.
- Improved usability of create/edit project dialogs.
- Fixed incorrect checks in _join2 API endpoint.
- Fixed alignment tree availability for some documents.
- Fixed issue preventing removal of annotations from entities using serial IDs as table names.
- Fixed inability to set deactivated users as members or owners.
- Fixed broken entity links in job history sidebar.
- Fixed errors in comparison matrix for differential enrichment jobs.
Registry and Inventory
- Fixed inconsistencies in barcode behavior.
- Corrected unexpected merge behavior across test/prod environments.
- Improved scrollbar usability when selecting locations.
- Fixed missing attribute population when creating snapshot fields in result schemas.
- Fixed error when creating containers via entity inventory tab in restricted projects.
- Fixed incorrect permission intent checks preventing project folder moves for archived/registered entities.
Schemas
- Fixed results snapshot field display issues.
- Corrected UI issue when bulk updating date fields.
- Fixed dropdown option matching for schema fields with commas.
- Improved error messages for invalid schema prefixes.
- Fixed missing audits for changes to min, max, and legalTextDropdownId.
- Fixed computed field errors on fieldsets.
- Fixed error when adding snapshot fields to result schemas linked to “Latest Result.”
Small Molecule & Other Modalities
- Fixed auto-archival of schema fields when units are archived.
- Fixed CSV import to monomer library.
- Corrected molecule rendering in complex polymer connection modal and components tab.
- Fixed wrong monomers shown on reverse strand in oligo duplex creation.
- Fixed Marvin clean running on non-SMILES input.
Workflows
- Fixed issue where create workflow dropdown extended off screen.