Release Notes: Volume 12, 2024

Achala
Achala
  • Updated

Welcome to the 12th volume of our 2024 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 December 2024.

Watch our Feature Release Highlights to more deeply explore this month's updates.

Notebook

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

Convert Column to Single Input [2024.12.N.1]

New option to convert a column into a form field that appears on the top of the table. The value entered into this field will be used for all rows in the table.

Molecular Biology

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

High-Throughput Assembly [2024.12.MB.1]

Our assembly tools previously supported the design of up to 100 constructs at once (roughly the capacity of a 96-well plate). However, modern sequence design often requires much higher throughput. This release expands the scale of assembly 50-fold, allowing users to assemble up to 5,000 constructs from hundreds or thousands of fragments. High-throughput assembly now supports cloning methods such as Golden Gate, Gibson, and homology-based approaches, as well as concatenation for AA, RNA, or DNA sequences.

Export Transcription Links as Features [2024.12.MB.2]

When exporting a sequence as a GenBank file, transcription links are now exported as features with the type misc_RNA.

Ability to Lock Oligos [2024.12.MB.3]

Previously, users could "lock" sequences of all types except oligos. With this update, oligo sequences can now also be locked. Note that locking can be enabled or disabled by any user with edit access to a sequence. For stricter control, permissions and access policies should be used.

Improved Visibility of Contents in Source Containers During Plate Filling [2024.12.MB.4]

In the plate filling workflows, users can now view the contents of source containers directly without hovering, simplifying the process of adding items from a worklist or structured table.

In Vivo

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

Prism Report Column Title Updated to Include the Reference for Days Plotted [2024.12.IV.1]

The Prism column title now aligns with the Summary export, displaying either the Tracking Date or Disease Induction as the reference for days plotted.

Randomization Optimization of Attribute Distribution [2024.12.IV.2]

The randomization algorithm for clustered randomization, which uses attributes like sex and date of birth, has been improved. It now applies a proportional distribution ratio to ensure balance across uneven groups.

nmol/kg Unit Added to Dose Volume Method [2024.12.IV.3]

The Dose Volume method for calculating treatment doses now includes an option to use the nmol/kg unit.

Link Task Setup to Workflow for Task Execution [2024.12.IV.4]

Task execution has been streamlined with workflow setup. Users can now define task types—such as Samples, Observations, Doses, and Measurements—when creating tasks. Selecting a task from the schedule guides users to a pre-populated workflow setup, filtering out animals not included in the selected tasks.

To enable this feature, contact a Benchling representative

Study Schedule Shows Tasks from Today and Highlights Overdue Tasks [2024.12.IV.5]

The schedule page has been updated to display tasks for the current day by default, removing the page title. The date picker defaults to today but can be cleared to show all study tasks. Clicking the warning message for overdue tasks shows all tasks starting from the first overdue date.

Confirmation Step Added for Moving Animals [2024.12.IV.6]

When moving animals between studies, a final confirmation step now explains the implications, such as the removal of the animal and its associated data (e.g., dosing and alert history). This ensures users proceed with full understanding.

Update Partial and Complete Regression Calculation to Extend Across the Entire Study [2024.12.IV.7]

The partial and complete regression columns in oncology-related analysis summary tables now include the number of animals meeting the criteria at any point from the tracking date to the end of the study, rather than focusing solely on a defined study day.

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.

Increased Default Maximum Allowed Tasks Per Entry to 500 [2024.12.W.1]

The default limit for tasks that can be executed into a single entry has been increased from 100 to 500, allowing for greater flexibility and scalability in workflows.

Mapping Completed Event [2024.12.W.2]

A v2.workflowTaskGroup.mappingCompleted event is now triggered for a Task Group when all mappings initiated by a user action—such as completing tasks or creating outputs—are successfully completed.

Benchling Connect

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

Releases: Connectors [2024.12.BC.1]

The Meso Scale Discovery Workbench Connector is now available.
Connector Guide: Configuration Guide

The AKTA UNICORN Connector is now available.
Connector Guide: Configuration Guide

The Magellan Connector is now available.
Connector Guide: Configuration Guide

The Beckman Coulter Connector is now available.
Connector Guide: Configuration Guide

The Genesys On-Board Software Connector is now available.
Connector Guide: Configuration Guide

Updates: Allotropy Versions [2024.12.BC.2]

Allotropy has been updated to version 0.1.66.
Change Log: View Details

Allotropy has been updated to version 0.1.67.
Change Log: View Details

Allotropy has been updated to version 0.1.68.
Change Log: View Details

UI Enhancement: Timezone Picker in Run UI [2024.12.BC.3]

An info icon has been added to the Timezone picker in the Run UI, along with an updated display name to clarify its function for datetime conversion.

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.

Read-Only Computed Field Description [2024.12.SCH.1]

Customers with computed fields can now view detailed descriptions of these fields on the schema detail page. Each description includes two key properties:

  1. Formula Description – Explains the logic behind the computed field.
  2. Formula Dependencies – Lists the inputs required for the formula to compute the field's value.

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.

Dropdown Option Name Updates Are Now the Only High-Impact Change in Config Migration [2024.12.AC.1]

Previously, both option name updates and position updates were considered high-impact changes. Now, only option name updates are marked as high impact during config migration.

Updated Default Action for Templates to Create/Update in Config Migration [2024.12.AC.2]

The default action for templates in config migration has been updated from Ignore to Create/Update. This change ensures that duplicative actions are avoided when users select objects to migrate during export.

Audit Trail API Promoted to V2-Stable State [2024.12.AC.3]

The Audit Trail API has reached V2 stable status, enabling all users to programmatically retrieve audit logs in PDF or CSV format using the object’s API ID.

Consolidated Audit Events for Result Table Updates [2024.12.AC.4]

Result table audit logs have been optimized by consolidating all updated values within a single row into one audit event. Previously, each updated cell value generated a separate audit event.

Larger Audit Log PDFs Will Be Emailed to Users [2024.12.AC.5]

For audit logs in PDF format exceeding five minutes of processing time, users will now receive the file via email. A UI toast message will alert users to the delivery.

Added Audit Events for Default Schema Collaborator Updates [2024.12.AC.6]

When default schema collaborators are updated, all changes will now be logged as audit events.

Auditing the Creation of Default Schema Collaborators [2024.12.AC.7]

The creation of default schema collaborators is now audited when new organizations are created. These default collaborators are automatically set on schemas created for the new organization.

Added "createdAt" Field to Teams in the /v3-alpha API [2024.12.AC.8]

A new createdAt field has been added to Team objects in the /v3-alpha API. This field allows sorting and filtering of Teams by their creation date. For teams created before the introduction of audit events, the creation date defaults to the Unix Epoch (January 1, 1970). Newly created teams will have accurate timestamps.

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 Canvas Audit Logs Now Include Submitted Values [2024.12.DP.1]

Audit logs for App Canvas have been enhanced to include the submitted data, in addition to previously logged actions taken by the app. This improvement provides greater transparency and traceability for App Canvas operations.

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.

Recipes and Assay Configuration: "Step Configuration" Tab Renamed to "Steps" [2024.12.BP.1]

The "Step Configuration" tab in Recipe/Assay configuration has been renamed to "Steps" for simplicity and clarity, as it exists within the broader context of Recipe/Assay configuration.

Bug Fixes

Notebook

  • Resolved an issue where reordering rows in tables by dragging with the mouse caused cell references to break if the references were to cells that didn't yet exist.
  • Ensured that timezone settings are respected during spreadsheet imports into tables.
  • Fixed an error that occurred when inserting columns in a mixture prep table.
  • Corrected indentation for the single input section to align with the table.
  • Added a warning that tables do not support monospace formatting (Cmd+Shift+K).
  • Fixed an issue where the preview icon was cut off on image attachments in staging.

Molecular Biology

  • Improved performance for bulk assembly to address slow user experiences.
  • Enhanced inventory performance on the plate entity page ([Spike] Plate entity page performance improvements).
  • Updated final concentration validation to check if it exceeds source concentrations for a specific well rather than the entire plate.
  • Made the "find primers" fields mandatory in the UI.
  • Resolved an issue where the cut site at the origin of a circular fragment was not accepted in bulk assembly.

Small Molecule

  • Fixed an issue where archived units appeared as options in inventory table column configuration.
  • Corrected cell-level display precision for unit-aware cells.
  • Ensured the frontend state refreshes after saving a unit on an entity schema field.

In Vivo

  • Fixed an issue where suspended users were not reflected appropriately in cloned studies (Amgen Dev: In Vivo).
  • Corrected measurements and graphs showing for the wrong animal after marking it as deceased.
  • Fixed incorrect workflow dates when using task execution.
  • Resolved 403 errors when shifting dates/timezones on task specs in completed studies.
  • Addressed "InVivoError" when adding tasks to completed studies.
  • Fixed errors transitioning or executing tasks from completed studies (403 error).
  • Corrected an issue preventing the creation of cages in a colony (Exception: Invalid study ID).
  • Fixed incorrect group ordering during randomization.
  • Addressed shifting dates causing an API error (InVivoError: PATCH /api/v1/studies/{studyId}/task-specs).
  • Ensured that UI updates validate a maximum of 50 characters for cage names.
  • Resolved issues with recurring tasks creating duplicates on rescheduling (IllegalStateException).
  • Fixed an error preventing edits to recurring tasks in cloned studies (Unhandled exception: Cannot read properties of null).
  • Ensured saved mappings are retained if a device is disconnected and the tab is closed.

Workflows

  • Prevented users from submitting the output confirmation modal while queries are still in progress.
  • Resolved an issue where creating an entry task template from a pre-existing template did not de-duplicate table names.
  • Fixed an issue preventing the export of audit logs for sample groups.
  • Addressed failures in bulk task creation in capillary workflows due to empty task specifications.
  • Corrected automated mapping that incorrectly created processes in archived projects.

Application Core

  • Fixed serialization issues for old property values logged during creation.
  • Resolved a problem where config migration incorrectly showed archived fields as requiring archiving.
  • Fixed intermittent failures with the insertable search feature.
  • Addressed missing math glyphs in FPDF documents.

Compliance Controls

  • Fixed query timeouts for retrieving entities in plate CoC workflows.

Developer Platform

  • Resolved issues with allOf not rendering properly for example payloads in v3 REST API documentation.
  • Added validation to reject query parameters in webhook URLs.

Benchling Connect

  • Resolved issues with incorrect timezone conversion when processing a file containing a datetime with a timezone offset via the Lab Auto Run output file processor.

Was this article helpful?

Have more questions? Submit a request