Release Notes: Volume 1, 2025

Achala
Achala
  • Updated

Welcome to the 1 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 January 2025.

Notebook

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

Warehouse support for worksheets [2025.1.N.1]
Worksheets are now accessible in the Warehouse.

Updated review team reassignment behavior [2025.1.N.2]
If a review process stage is set as reassignable, reviews will now default to reassignable when sent.

Expanded availability of image annotation [2025.1.N.3]
The image annotation feature is now available to more customers.

2025_Feb17_Image_annoation.gif

 

Cloned templates now linked to source templates [2025.1.N.5]
Duplicated templates now retain a reference to the original template version.

Warehouse support for template publishing [2025.1.N.6]
Publishing record history is now available in the Warehouse.

Molecular Biology

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

Auto-fill translations now support multi-region sequences [2025.1.MB.1]

When using auto-fill translations, Benchling now detects and links amino acid sequences that match existing multi-region translations on the sequence map.

In Vivo

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

=Duplicate cage name warning and filtering [2025.1.IV.1]
If two cages in a study have the same name, an error symbol now appears on the duplicate cages. A new button allows users to filter the view to show only duplicates, making it easier to rename them for uniqueness.

Search bar added to "Add to Group" modal [2025.1.IV.2]
Users can now search within the "Add to Group (Manual)" bulk action to quickly find and assign animals to a group.

Warning for invalid columns when creating a study from a draft [2025.1.IV.3]
If a required group metadata field is missing when creating a study from a draft or cloned study, users will now see a warning prompting them to edit the groups before proceeding.

Filter study samples by metadata [2025.1.IV.4]
Users can now filter the Samples table based on metadata fields.

Bulk sample collection returns users to the Animals table [2025.1.IV.5]
After using the bulk sample collection action, users are now returned to the Animals table with the same animals selected, streamlining follow-up actions such as editing details or marking animals as deceased.

Group capacity displayed in "Add to Group" (Manual) [2025.1.IV.6]
When manually adding animals to a group, users will now see the number of animals currently in the group (x) alongside the group’s capacity (n) in the format x/n, making it easier to track available space.

New option to auto-fill PK dose timestamps [2025.1.IV.7]
A new option for PK Dose timestamp columns in custom data tables allows users to auto-fill timestamps based on a set interval between doses. This can be used to fill missing timestamps or overwrite an entire column.

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.

Export plate to CSV now respects filters and sorting [2025.1.RI.1]

When exporting a plate to CSV, the exported file now maintains the sorting and filtering applied in the well table.

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.

Data modification rationale for workflows [2025.1.W.1]
Users can now provide a rationale when modifying workflow data, improving traceability and compliance.

Enhanced workflow routing with AND/OR conditions [2025.1.W.2]
Workflow routers now support more complex routing rules:

  • AND conditions: All specified conditions must be met to proceed to the next task.
  • OR conditions: If any specified condition is met, the workflow moves to the next task.

Fixed-height tables improve workflow performance [2025.1.W.3]
Workflows now use fixed-height tables, enhancing performance and usability for large datasets.

Benchling Connect

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

Support for .zip files in the file watcher connector [2025.1.BC.1]
The file watcher connector now supports monitoring and processing .zip files.

Allotropy updates [2025.1.BC.2]
Allotropy has been updated to the latest versions, bringing improvements and bug fixes. See the change logs for details:

Liquid Chromatography connector updates [2025.1.BC.3]
Added support for start time settings and peak index.

Plate Reader connector updates [2025.1.BC.4]
Added a custom data cube to the BENCHLING/2023/09 schema.

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.

New permissions UI for project, schema, and registry management [2025.1.AC.1]

A redesigned permissions UI is now available for managing projects, schemas, and registries, improving usability and access control. 

2025_feb17_premissions_UI_update.gif

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 Location History report for empty containers [2025.1.CC.1]

When a container transfer results in zero remaining quantity, it is now recorded as an exit action in the Location History report.

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.

Expanded flexibility for updating study schemas [2025.1.BP.1]
Users can now modify the schema prefix and name for study schemas, even after they have been used to create studies. Changing a schema prefix does not affect the IDs of existing studies—it only applies to newly created studies.

Template flowchart version filter added to procedure_run API [2025.1.BP.2]
A new filter has been added to the procedure_run API, simplifying operations for Bioprocess API users in the V3 API beta.

Replicate limits displayed during Bioprocess experiment planning [2025.1.BP.3]
Total replicate limits are now shown in the experiment planner and Add Conditions modal. Users cannot exceed the allowed number of conditions.

Study schema now displays warehouse table name [2025.1.BP.4]
The warehouse table name is now visible when viewing a study schema.

Task ID column added to procedure_run warehouse table [2025.1.BP.5]
A new Task ID column simplifies warehouse queries by allowing users to link a procedure_run to its corresponding workflow task ID, such as for execution status tracking.

Model column added to Bioprocess and assay experiment design tables [2025.1.BP.6]
The Model column is now displayed in Bioprocess and assay-related experiment design tables, helping users select the correct equipment entity.

Bug Fixes

Notebook

  • Fixed an issue preventing .tif files from being uploaded or previewed.
  • Prevented protocols from being added when an entry is locked.
  • Resolved an issue where the first row was blank when adding from a worklist.
  • Users can now add entries to Analysis with read-only permissions (write access is no longer required).
  • Fixed copy/paste failures when transferring data from Excel.
  • Resolved an issue where multi-select entity links did not pass correctly between tables.
  • Scientific notation can now be toggled for the Concentration column in the Update Container table for biologics.
  • Fill-in-only entries no longer allow column reordering.
  • Protected documents (is_protected) are now filtered out from Analysis Chart outputs.
  • Added a vertical scrollbar to the Template List in Template Collection Management.
  • Worksheet reverts/undos are now locked to the original step.
  • Fixed worksheet step reordering issues.
  • Protocol tabs now maintain a consistent order.
  • Fixed an issue where users were unexpectedly redirected when viewing a protocol.

Molecular Biology

  • Users can now clear the Units field in the Total Well Volume section.
  • Improved handling of pI configuration when using multipliers from schema field values.
  • Fixed an issue where parts were not copied when using RevComp from a sequence map.

Small Molecule

  • The folderId field is now nullable in the response from the molecules list endpoint.
  • Fixed an issue where attachment states were sometimes not saved for drawn attachments upon creation.

In Vivo

  • Fixed incorrect target assignment when animals were added to or removed from a study from the colony.
  • Resolved a bug affecting the Samples Page for In Vivo users.
  • The Clear (X) option in the schedule task search bar now functions correctly.
  • Fixed an issue where workflow measurement order did not match the task for Typed Tasks
  • Resolved an issue where Cage Metadata disappeared upon navigating back from the Cages and Animals Summary Page.
  • Addressed a pagination issue in the Randomization Report.
  • Conditional tasks are no longer duplicated when a task specification is updated.

Registry and Inventory

  • Resolved a character limit issue preventing entity registration.
  • Fixed an issue where the Grid Cell Table did not load for plates with inaccessible well contents.
  • The Name Template section is now properly aligned in the Entity Schemas page.

Benchling Connect

  • Fixed an issue where updates to Connection Fields were not being captured in audit logs.

Application Core

  • Fixed a bug where pasting from Excel resulted in a mix of text and numerical inputs.
  • Migration diffing for schemas no longer shows updates for objects with no changes.
  • Improved the width of immutable dropdowns in the Manage Access modal.

Developer Platform

  • Fixed an issue where get_simple_bnch_typedef did not handle unions correctly.
  • Archived app installations no longer return features in queries.
  • Users can now archive installed global apps without errors.

BioProcess

  • Removed the humanId field from ProcedureTypedValue and ProcedureSearchInput to improve system consistency.

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