Welcome to Volume 2 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 February 2025.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Increased reliability for single item Entry Exports and Snapshots [2025.2.N.1]
Single-item Entry exports and snapshots have been enhanced to achieve a significantly higher success rate for larger Entries.
To enable this feature, contact a Benchling representative.
V2 Export API is now rate limited [2025.2.N.2]
The Export API now includes rate limiting to improve performance and stability.
Audit event for template collection descriptions [2025.2.N.3]
An audit event is now recorded whenever a template collection description is updated.
Add Pending Results to Table respect Default Table Values [2025.2.N.4]
The "Add Pending Results to Table" feature now honors default values within the table. If a default formula is set and the column would otherwise be empty, the formula is automatically applied to the newly added result row.
Support for Table Formula =RSQ() [2025.2.N.5]
Notebook Tables now support the =RSQ() formula, which calculates the R-squared value—the square of the Pearson product-moment correlation coefficient..
Molecular Biology
Benchling’s Molecular Biology is a cutting-edge in silico design tool that supports the latest scientific workflows.
Amino acid sequence map coloring updates [2025.2.MB.1]
AA sequences are now consistent across Benchling, from sequence maps to BLAST to alignments
This release includes visual updates such as:
- The background of residues is now colored instead of the letters themselves when a coloring scheme is enabled on an amino acid (AA) sequence.
- Default font size and zoom settings for amino acid residues have been adjusted for better readability.
- DNA/RNA sequence translations now align with the coloring schemes used for AA sequences.
Updated visibility options menu on sequence and polymer maps [2025.2.MB.2]
The visibility options menu for sequences, oligos, and complex polymers has been redesigned with a modern interface.
Autofill translations supports multi-region translations [2025.2.MB.3]
When autofilling translations, Benchling now automatically fills AA sequences that match an existing multi-region translation on the DNA sequence. Previously, these links had to be set manually.
Modernized annotation panel on AA sequences [2025.2.MB.4]
AA sequence annotation has been redesigned to match annotation for DNA and RNA sequences.
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.
Custom notation v2 endpoints [2025.2.SM.1]
Benchling has introduced two new v2 API endpoints:
- One for creating new custom notations.
- One for bulk-creating custom notation aliases.
Previously, users had to add custom notations individually. Now, developers can streamline workflows by adding multiple custom notations in bulk.
Oligo conjugate and duplex drag and drop [2025.2.SM.2]
Build and interact with oligo conjugate and oligo duplex structures directly in the sequence
The drag and drop interface allows you to more easily view the structure of your conjugate and provides a more streamlined experience for editing connections. You can now create, edit, and delete one or more connections in a single session. The drag and drop interface also allows you to delete individual connections in leaving-group style connections.
Note: This feature requires the Chemistry SKU and complex polymers to be enabled. It is automatically available for customers who meet these requirements.
Deprecated ChemDraw in Notebook feature [2025.2.SM.3]
ChemDraw support in Benchling Notebook has been deprecated. For more details, visit: ChemDraw Feature Deprecation Notice
In Vivo
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Add observation grading information and scoring scale to observation details modal [2025.2.IV.1]
Users can now access grading details in a new collapsible section when reviewing observation information. Additionally, hovering over a score displays the scale it was applied from. In the workflow observation history, the observation name is now a clickable link that opens a modal with detailed grading information.
Registry ID displayed treatment name dropdown [2025.2.IV.2]
When selecting an entity from the registry to associate with a treatment in In Vivo, the dropdown now includes both the registry ID and the entity name for improved clarity.
Data tables templates [2025.2.IV.3]
Create reusable tables that can be used across studies to standardize data collection and reduce setup time
Data Table Templates allow you to create, save, and reuse structured data tables across multiple studies. When applying templates, you can ensure that you are capturing the right measurements, reference dates, and autofilling the right timestamps for dosing or PK schedules. Individual users can create personal templates, while team administrators can create public templates that can be used by anyone on the tenant.
To enable this feature, contact a Benchling representative.
% body weight change tabs added to reports [2025.2.IV.4]
A new tab has been added to the Study Group report and a new data table to the Prism report for % body weight change tracking.
Survived to study end ratio has been added to every summary table [2025.2.IV.5]
A new column in the survival summary table under Analysis now displays the number of animals marked as disease survivors within a group (x/n). This column has been added to all summary tables, including oncology-specific summaries. An animal is marked as a disease survivor when the "survived to study end" checkbox is selected upon marking the animal as deceased.
To enable this feature, contact a Benchling representative.
Animal number used as column headers in Prism Report [2025.2.IV.6]
In GraphPad Prism Reports, the Study Animal No. is now used as subcolumn headers, ensuring users can match individual animals with their corresponding data. The identifier is shown under the "No." column in the study animals table for each In Vivo study.
Add up to 365 days when scheduling conditional tasks [2025.2.IV.7]
Users can now enter or paste a comma-separated list of study or tracking days when scheduling conditional tasks, supporting up to 365 days.
Disease induction and Pre-treatments [2025.2.IV.8]
Track disease induction and pre-treatments in bulk before assigning animals to study groups
Disease induction and pre-treatment dosing allows you to administer disease induction treatments to animals in bulk for efficiency and accuracy. Updates to reporting capabilities allow you to track pre-treatment dosing across all animals in a study and automatically assign a disease induction date which enhances protocol flexibility and data capture.
To enable this feature, contact a Benchling representative.
Analysis
Benchling Analysis enables users to query, visualize, and share high-quality, structured data that resides in Benchling.
Data flagging [2025.2.IN.1]
Flag and add comments to data to help you track outliers or other issues directly in your data for better data management
Data flagging allows you to manually flag and insert comments about specific rows of data to help you quickly and clearly react to samples that might need to be removed from a completed analysis through filtering. All comment creation and modifications are recorded to ensure complete traceability.
Embedding Charts in the Notebook [2025.2.IN.2]
Send charts from analyzed data back to the Notebook to re-contextualize your analysis
Sending charts to the Notebook allows you to embed an interactive chart from Analysis into a new section of an existing Notebook entry so that it is able to be viewed alongside the experimental steps and other notes that led up to data capture. Click Create Outputs, then select As Chart to begin embedding visualizations seamlessly.
Plate Schema in Analysis [2025.2.IN.3]
Directly ingest data into Analysis from plate schemas for a more streamlined Analysis experience
You can now bring the metadata collected from plate records into an Analysis directly from the “Add table” screen. In the From plate schema modal, you’ll be able to choose which plate schema and which plate object you’d like to import. For each plate you bring into Analysis, you’ll choose what metadata appears as columns in your Analysis tables.
VLOOKUP [2025.2.IN.4]
Computed columns in Analysis now support VLOOKUP, enabling easy access to values from a different column based on a searched value. This enhancement makes computed columns function more like traditional spreadsheets, improving efficiency and saving time.
Benchling Connect
Benchling Connect, formerly Lab Automation, enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Allotropy Updates [2025.2.BC.1]
Benchling has updated Allotropy to the latest versions, improving stability and functionality. Key updates include:
- Version 0.1.73: Performance improvements and bug fixes. Change Log
- Version 0.1.74: Enhancements for data processing. Change Log
- Version 0.1.75: Further optimizations. Change Log
- Version 0.1.76: Refinements to improve compatibility. Change Log
- Version 0.1.77 & 0.1.78: Additional stability improvements. Change Log
Release CFX Maestro Software Connector [2025.2.BC.2]
A new Benchling connector is now available for the Bio-Rad CFX Maestro Software. Connector Guide
Updates to connectors for the Liquid Chromatography instrument class [2025.2.BC.3]
Enhancements include:
- Incorporating peaks data to capture details about identified chromatogram peaks.
- Supporting Void Volume and Flow Rate measurements.
- Adding fraction documents to record details about collected fractions.
- Enabling device document support for better traceability.
Automated Connect & Analysis workflow [2025.2.BC.4]
Allows data in Benchling to go from a raw data file to fully analyzed in three clicks
The automated Connect and Analysis workflow allows you to leverage Run schemas and Analysis Templates to process instrument information and perform an analysis directly in a Notebook or Worksheet entry. Allowing you to automate analysis execution, standardize data capture, and reduce manual processing of repetitive data handling. In a Run, click to retrieve the data and process data and the resulting analysis will be inserted as new sections in the Entry.
Note: This feature requires the Connect and Advanced Analysis SKUs.
Specify a tab when processing multi-tab files [2025.2.BC.5]
Define exactly what subset of data you bring into Benchling from multi-tab files
We now support the ingestion of multi-tab files to streamline your workflow and eliminate manual data manipulation, which saves time and ensures accuracy. Specify which tabs of a multi-tab output file are processed during a run by entering the tab name in the Output File Configuration section. If no tab name is specified, the first tab will be selected by default.
Make the extension field check case-insensitive on Connection [2025.2.BC.6]
.csv and .CSV are now both acceptable formats.
Select all checkboxes when uploading files for lab auto-run processing [2025.2.BC.7]
Users can now bulk-select all checkboxes when choosing files to upload to a lab auto run output file processing
Update extension fields and attach files during run output processing [2025.2.BC.8]
Users can modify an extension field and attach files directly within the output processing workflow.
To enable this feature, contact a Benchling representative.
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.
Fieldsets GA [2025.2.SCH.1]
Establish more precise relationships between entities across multiple schemas to improve data integrity and governance
Fieldsets allow you to more efficiently model complex scientific data relationships in the Registry by creating structural constraints that apply across multiple schemas. Downstream entities can be connected to entities registered under separate schemas with these shared structural constraints using Category links. Together Fieldsets and Category links allow you to improve governance and reduce data input errors.
Fieldset support in Add From Structured Table [2025.2.SCH.2]
The Add from Structured Table action on Lookup tables now supports Fieldsets, allowing for more streamlined and structured data entry.
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.
Config migrations placeholder support for legacy table types [2025.2.AC.1]
When migrating templates with unsupported table types, config migration now inserts a placeholder for the table, ensuring the migration can proceed without errors.
System Name [2025.2.AC.2]
The Warehouse Name label has been replaced with System Name to better reflect its use across both the V3 API and the Warehouse. This change does not alter functionality:
- The Warehouse continues using this value without modification.
- In the V3 API, System Name serves as the resource identifier for schema and field API requests.
Improved config migration warnings [2025.2.AC.3]
Config migration warnings now specify the type of unsupported object, improving clarity during the migration process.
Available beta Tenant Comparison Report added [2025.2.AC.4]
With feature settings, there is a placeholder for Tenant Comparison, providing admins the ability to request access to this beta.
For more details read the beta guide on Zendesk
Schema Detail Page update – Warehouse Name is now System Name [2025.2.AC.5]
To improve clarity, the Warehouse Name label on the Schema Detail page has been updated to System Name. This change reflects its use in both the Warehouse and the V3 API, ensuring consistency in naming conventions.
New search operators for schema tag filters [2025.2.AC.6]
Enhancements to schema tag filters introduce new search capabilities:
-
String filters now support:
- “Starts with”
- “Is one of”
- “Is none of”
-
Numeric and date filters now support:
- “Between”
- “Relative range”
These additions improve flexibility in search queries.
Revoked permissions for creating temporary Warehouse tables [2025.2.AC.7]
Previously, all users could create temporary objects in the Warehouse using pg_temp. Now, this ability is restricted to existing pg_temp users, enhancing fine-grained permission control.
Hide archived study schemas from search filters [2025.2.AC.8]
Archived study schemas are now excluded from type filters in search interfaces, aligning with how entity schemas are handled.
Deprecation of legacy warehouse metadata queries from Insight Access
[2025.2.AC.9]
In the coming months, certain legacy metadata fields will be removed from access within Insight queries. If any of these changes impact your current workflows, additional details will be sent to your account via email. For additional support or clarification, contact your Benchling representative.
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.
Parameter min/max values in auto-generated analysis for Recipe and Assay execution [2025.2.BP.1]
Auto-generated analysis datasets now include minimum and maximum parameter values for Recipe and Assay execution. This applies when generating an analysis from:
- The Overview page of a PD Study.
- An individual Worksheet for Assay and Recipe execution.
This enhancement allows for easy comparison between the measured parameter value and its defined min/max range in the Recipe or Assay.
Configurable entity links on study schemas [2025.2.BP.2]
Study schemas now support entity links to specific schemas, aligning them with other schema types. Previously, study schemas were limited to broad categories such as "Any Entity" or "Custom Entity." Now, fields on study schemas can be configured to point to specific entity schemas for improved data structure.
Naming templates for Studies [2025.2.BP.3]
Naming templates are now available for all study types. These templates:
- Are configured on Study schemas.
- Follow the same framework as naming templates in the Registry, ensuring a familiar experience for users.
API READ endpoint for Study schemas [2025.2.BP.4]
A new API READ endpoint allows users to access information about specific Study schemas. This feature is part of the V3 API.
Studies as parameter types for insights dashboards [2025.2.BP.5]
Insights dashboards can now use Studies as a structured parameter. This enables:
- More reliable dashboard filtering by selecting one or more Studies.
- Elimination of fragile, text-based filtering methods previously required for study-based queries.
Removal of "Provide Feedback" link on Study overview pages [2025.2.BP.6]
The "Provide Feedback" link, originally added during the Studies beta, has been removed as Studies approach General Availability (GA). Feedback is now collected through other channels.
Study Display ID added to Study warehouse tables [2025.2.BP.7]
The Study Display ID is now included in Study warehouse tables. This refers to the UI "ID" field, not the API ID, which was already present in warehouse tables. The column name for this field is "display_id."
Bug Fixes
Notebook
- Fixed an issue where a locked column’s value change (e.g., due to a formula update) incorrectly marked the row as out-of-date instead of unsubmitted. The row is now correctly marked as unsubmitted, allowing resubmission.
- Resolved a bug in spreadsheet uploads where fields "auto-populated" via name-matching or saved column mappings could incorrectly select locked columns.
- Fixed an issue where lookup table mapping failed when looking up Plates or Boxes.
- Addressed a problem where highlighting applied to a chip in a Notebook entry disappeared when the entry was sent for review.
- Resolved an issue where an unexpected error message was added to attachment excerpts during a downstream vendor outage. Excerpts have been regenerated.
- Fixed an error message appearing when viewing an entry share link as an authenticated user without proper permissions.
- Corrected a regression that caused an error message and missing columns in template search results.
- Fixed an issue where tables were inadvertently renamed when executing a new recipe in BioProcess.
- Resolved a text overlap issue in tables when using Firefox.
- Fixed a bug where the Subtemplate Selection modal did not allow users to deselect a selected subtemplate. The modal would close and fail to reopen without refreshing.
- Notebook Section titles now wrap correctly when printing.
- Fixed an issue where review criteria warnings were not blocking self-reviews using Review Processes. Now, review criteria must be removed before proceeding.
Molecular Biology
- Fixed a bug where assembly tables only allowed 500 rows instead of the intended 5,000.
- Resolved an issue in homology assembly and "existing overlaps" in Gibson assembly where overlaps on fragments were temporarily not detected when used in the reverse direction.
Small Molecule
- Fixed an issue where registration tables with oligo duplexes and conjugates did not allow or respect the "no project folder" setting.
- Resolved a problem where unit fields for inventory values (such as Quantity and Concentration) did not properly support unit-based searching.
In Vivo
- Doses in the animal profile are now displayed in descending order by the latest administration date. The recorded date is also shown for clarity.
- In exported dosing reports, if some animals lack tracking or disease induction dates, the "Dosing (Study Day)" tab now shows data based on days post-study start date.
- Animal ordering within cages has been updated to sort animals first by cage, then by Study Animal Number instead of Animal Number (A000xxx).
- Fixed an issue where tasks were being duplicated when using the status filter in the calendar after marking them as done.
- Empty cages created from Manage Cages in Colony now appear successfully after creation.
- Resolved an error triggered when exporting the summary table from the study graphs page under Analysis.
- Fixed an issue where studies could not be created if links in drafts had no description set due to a validation requirement.
- Dosing methods can no longer be edited after doses have been administered. The dropdown is now properly disabled.
- Fixed an issue where users experienced multiple tasks being created and errors when attempting to mark closed tasks as "Done." This fix prevents duplicate tasks from being created. If you have duplicate tasks from before this fix, please contact Support for resolution.
Registry and Inventory
- Improved error handling and messaging in the Bulk Capillary Create Containers API when handling invalid well numbers.
- Fixed an issue where editing a registered entity’s name with data mods enabled caused the edited name to persist until a page refresh or tab switch. The name now correctly reverts after canceling the data mod.
- Fixed a disappearing popover issue in plate view.
- Improved spreadsheet import logic by ensuring "Look for linked items in" defaults to the selected registry or destination folder, rather than defaulting to the registry when only one is available.
- Child lot and registry ID are now allowed in naming templates, provided they are single-select fields.
- Fixed an issue where the record chip covered the feature settings submenu.
- Renaming an organization or registry now propagates changes to the entity metadata page.
Workflows
- Users can now archive flowchart and task schemas even if they contain task schemas, ensuring smooth archival processes.
- Archived tasks are no longer included in aggregate task counts across workflows.
- Legacy Request task filters are now visible again.
- Fixed an issue where capillary action incorrectly checked for API IDs in text fields, preventing updates when text resembled an API identifier.
Benchling Connect
- Fixed an issue where importing .XLSX files produced decimal values with extra, unexpected decimal digits by rounding down appropriately..
Access Management
- The IP allowlist now supports individual IP addresses instead of requiring CIDR block notation (e.g., x.x.x.x is now allowed alongside x.x.x.x/32).
Application Core
- Fixed an issue where long strings in schema fields were not properly indexed in search queries.
- Some saved searches failed to load due to schema tag filter changes. The system now converts old filters to the new format for backward compatibility.
- Fixed a bug where attempting to add items from an empty worklist caused the modal to close with an error. The system now provides a clear message that the worklist is empty.
- Resolved an edge case where databases were unintentionally deleted daily, causing Blast to stop working.
- Fixed an issue with the Desktop Sync client, which previously prevented users on benchling.com from accessing the software.
- Starred status for items in Search now displays correctly.