Release Notes: Volume 11, 2024

Welcome to the 11th 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 November 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.

Table mapping across tables in Bioprocess Worksheets [2024.11.N.1]

Users can now map data across tables within the same step of a Bioprocess Worksheet.

Updated Feature Settings for Review Processes [2024.11.N.2]

The section title in Feature Settings has been updated from "Lab Notebook Settings" to "Review Settings." Similarly, "Entry review processes" has been replaced with "Review processes”.

Improved Entry Template and Sub-template selection tree [2024.11.N.3]

Users can now select entry templates or sub-templates using a hierarchical tree view, better reflecting the organization of template collections. The interface also displays the creator and most recent modification date of each template.

To enable this feature, contact a Benchling representative.

Frozen Chips are generally available [2024.11.N.4]

Previously, if an Entry containing Entity chips was sent into Review and/or Approved, Entity chips in that Entry would continue to live update if the referenced Entity was changed somewhere else in Benchling. Now, Entity chips are frozen after an Entry is submitted for review.

Molecular Biology

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

More layers exposed on transfer step of plate map [2024.11.MB.1]

When a user is in the "define transfer" step of the plate map modal, or viewing the details of a plate map modal, they can use the dropdown to toggle between all layers of the plate map. Before, we only showed the well role and contents layers in the dropdown.

Changed ordering of colors in contents layer of plate maps [2024.11.MB.2]

Updated the color palette for the contents layer of the plate map to be more color-blind accessible (e.g. reducing the chance that red/green colors are next to one another).

Updated defaults for adding sources to wells in plate maps [2024.11.MB.3]

Default setting on contents layer is "add sources to well by pattern" (not "add all sources to each well")

More interactive summary view on plate map [2024.11.MB.4]

When user selects wells on the plate map, values in the summary view table reflect and apply to only the well selection. Previously, the summary view would summarize all wells on the plate map, regardless of the wells that were selected

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.

Unit Types in Inventory Tables [2024.11.SM.1]

Unit types can now be designated for use in inventory Quantity or Concentration fields. Each unit type can only be assigned to one option. This allows users to include unit types, such as length, as needed.

Units Displayed in Results Schema Fields [2024.11.SM.2]

Results schema fields now display the configured unit in the field description during schema configuration. Previously, this information was not visible.

Complex Polymer Support for Oligo Conjugates and Duplexes [2024.11.SM.3]

Oligonucleotide bioconjugates (single and double-stranded) are now Generally Available and can be configured using Complex Polymer features.

New entity sub-types allow users to capture discrete chemical attachments between oligonucleotide monomers and molecules.

Enhanced support for drawing chemical bonds between molecule entities and the nucleotide backbone, or between molecule entities, allows users to model complex attachments accurately.

Archiving and Unarchiving Unit Types [2024.11.SM.4]

Unit types can now be archived or unarchived. Archiving a unit type will also archive all units within that group. Previously, only individual units could be archived.

Staleness Indicator for Out-of-Sync Units [2024.11.SM.5]

When a unit is first assigned to a numeric schema field, any existing structured table columns will display a staleness indicator as a purple bar at the top of the column. To resolve this, users must re-sync the table using the refresh icon.

In Vivo

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

Study Samples Table Enhanced [2024.11.IV.1]

Users can now view up to 500 rows in the animals table and perform bulk actions to edit or delete entries.

Clustered Randomization Optimization[2024.11.IV.2]

The randomization algorithm using K-means clustering has been enhanced. Attributes like date of birth (DoB) are now proportionally distributed across groups of uneven sizes, and randomization outcomes with the highest total p-value for metrics are prioritized upon clicking "Randomize”.

Filtered Device Dropdown [2024.11.IV.3]

When connecting to a device, the dropdown now displays only devices registered with the same Product and Vendor ID. These selections are remembered for future use.

Admin Access to Study Settings [2024.11.IV.4]

Administrators can now access the study settings for all studies. This includes managing study teams, marking studies as complete, and resuming studies without being explicitly added. Admins can also add themselves to study teams, modify treatment groups, and access actions such as data collection and import.

To enable this feature, contact a Benchling representative.

Updates to survival analysis [2024.11.IV.5]

Survival calculations in Data analysis summary tables have been updated to take into account animals that have not yet been marked as deceased or that have been marked as survivors across survival calculations. A new column called “Survived to study end” has been added to the survival summary table which shows how many animals are still alive or marked as survivors using a check box when marking animals as deceased for each group.

Task status and number of animals added to tasks in team calendar [2024.11.IV.6]

Task Status is now displayed on the task in the daily view in calendar and the number of animals that the task applied to is included in the task display in the daily view.

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.

"Tasks Assigned to Me" Quick Filter [2024.11.W.1]

A new quick filter has been added to the Workflows dashboard, enabling users to efficiently view tasks assigned specifically to them.

Insights

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

Statistics (Regression & Interpolation) [2024.11.IN.1]

Regressions & Interpolation allow for the fitting of linear, quadratic, and 4PL curves to data in a scatter plot within Analysis. The parameters of those fits can then be extracted and used as needed. Additionally, the regression models can be used to interpolate new inputs to predicted outputs. Customers should contact their account manager for access.

Analysis Templates [2024.11.IN.2]

Analysis Templates can be created from any analysis, allowing all of the steps of that analysis to be replayed on a different set of data with a few clicks. Analysis templates are stored in Template Collections. For access, please contact your account manager.

Benchling Connect

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

VISIONlite Connector Released [2024.11.BC.1]

The VISIONlite Connector is now available. For configuration details, refer to the ThermoFisher Scientific VISIONlite Configuration Guide.

Allotropy Updates Version 0.1.63 [2024.11.BC.2]

Version 0.1.63 introduces updates and improvements. Refer to the Change Log for details.

Allotropy Updates Version 0.1.64 [2024.11.BC.3]

Version 0.1.64 includes additional updates. Refer to the Change Log for details.

Solution Analyzer Updates [2024.11.BC.4]

The Solution Analyzer instrument class now supports the Region format.

Allotropy Updates Version 0.1.65 [2024.11.BC.5]

Version 0.1.65 introduces improvements and fixes. Refer to the Change Log for details.

Solution Analyzer Measurement Transform Support [2024.11.BC.6]

The Solution Analyzer instrument class now supports Measurement transform.

Plate Reader Updates [2024.11.BC.7]

The Plate Reader instrument class has been updated to remove duplicate columns for calculated data in the Plate Reader group file.

Polymerase Chain Reaction Updates [2024.11.BC.8]

The Polymerase Chain Reaction instrument class now supports the DATACUBE transform type.

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 "Related Schemas" Tab [2024.11.SCH.1]

A new tab has been added to the dropdown settings page. When editing a dropdown, users can now access the "Related Schemas" tab to view all schemas linked to that dropdown.

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.

Removed Users Tab from Legacy Admin Pages [2024.11.AM.1]

The "Users" tab has been removed from legacy admin pages at https://<tenantsubdomain>.benchling.com/<org_handle>/admin. The tab contained duplicate information and functionality already available in the Users page in the TAC. Additionally, the legacy page had not been updated for years and no longer aligned with supported product features.

Removed Constraint on Teams for Permissioned Items [2024.11.AM.2]

A previous constraint restricted adding collaborators to objects owned by individual users to teams within the same organization as the owner. This constraint did not apply when the object was owned by an organization and did not provide added value. The restriction has now been removed.

Improved Experience for Unauthenticated Users Accessing Deep Links [2024.11.AM.3]

Unauthenticated users who accessed a deep link (e.g., a specific entry) previously encountered a 404 error. This has been updated to redirect users to the sign-in page and then to the original deep link after authentication, improving usability and reducing confusion.

Updated Error Message on Academic Login Page [2024.11.AM.4]

A new error message has been added to the Academic login page to guide users who might mistakenly try to log in on Benchling.com instead of their enterprise domain (e.g., customer.benchling.com). This update aims to reduce support tickets by helping users identify and correct login issues independently.

Admin Policy for Schemas Created via Config Migration [2024.11.AM.5]

When schemas are created through the UI, the creator is granted the Admin policy in addition to the default schema access policies. This behavior is now extended to schemas created via configuration migration imports.

Added Audit Event for Schema Collaborators on Organization Creation [2024.11.AM.6]

Benchling now audits the creation of the default set of schema collaborators when a new organization is created.

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.

Archived Studies Behavior Updated [2024.11.AC.1]

Archived studies now appear greyed out in the list view and include an Unarchive option. Users with appropriate permissions can unarchive the study directly from this view.

Consistent Error Message for Failed Unarchive Actions [2024.11.AC.2]

When a parent object is archived, child items cannot be unarchived. Previously, multiple error messages were shown based on the conditions of the unarchive attempt. This behavior has been consolidated into a single, consistent error message.

Improved Error Message for Config Migration with Unit Updates [2024.11.AC.3]

Previously, config migration failed when attempting to edit unit assignments, displaying a generic error. Now, the error message clearly warns users that the unit must be updated manually after migration.

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.

Location History Report Enhancements [2024.11.CC.1]

Users can now generate and download a Location History Report from any inventory location. The report can be exported in CSV or PDF format and includes a specified date range. It provides detailed information on all sublocations, entities, and inventory objects within the selected location, including:

Entry and exit times
Actions prompting movements
Associated metadata

The report is queued and sent via email for user convenience.

Username Display in CoC Reports [2024.11.CC.2]

Chain of Custody (CoC) reports now include usernames displayed in parentheses alongside the user's first and last name. This addition serves as a unique identifier for improved clarity.

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.

Audit Logs for Embeddable App Canvas [2024.11.DP.1]

A dropdown has been added to all embeddable App Canvases, allowing users to export audit logs for a specific canvas.

The public documentation for result endpoints (read and write) has been updated to clarify that warehouse names, rather than schema field display names, must be used in the "fields" property. Examples of AssayResult.fields now correctly show warehouse names as keys in the fields dictionary.

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.

Warehouse Tables for Bioprocess Execution [2024.11.BP.1]

New warehouse tables are available to capture detailed bioprocess execution data, including:

Parameter setpoints, confirmations, and measurements
Material input planned values, confirmations, and output confirmations
Equipment planned values and confirmations
Recipe execution runs and unit operation instances
Conditions and replicates
Creation context linking entities, containers, and results to specific steps, unit operations, and conditions/replicates

These tables provide a comprehensive view of bioprocess execution for improved data tracking and analysis.

Audit Trail for Study Schema ID Generation Settings [2024.11.BP.2]

The study schema audit trail now includes the ID generation mode setting for improved visibility.

Enforced Limit on Study Items [2024.11.BP.3]

A limit is now enforced on the number of items that can be associated with an individual study.

Improved Error Message for Permission Constraints [2024.11.BP.4]

Users now receive a descriptive error message when an action fails due to permission constraints on items, studies, or both.

Bug Fixes

Notebook

Fixed an issue where users couldn't insert content above tables.
- Pressing the Return/Enter key creates a line break after the selected component.
- Pressing Shift+Return/Enter keys creates a line break before the selected component.
Fixed an issue where sub-template names were cut off in the new sub-template selection modal.
Fixed an issue where a horizontal blue line appeared above attachments uploaded to a Notebook entry.

Molecular Biology

Fixed bugs to increase the success rate of searching for and importing sequences from databases.
Fixed a bug where the selection highlight disappeared after navigating away and back to a protein tab.
Fixed a bug where a missing annotation name in a POST request to the v2 dna-sequences endpoint returned a 500 error. It now correctly returns a 400 error.
Added a clearer warning message in the database import tool when a gene name matches a different organism than specified.
Fixed a bug where CTRL+X acted like CTRL+C on the sequence map. CTRL+X now deletes the bases after confirming the cut.

In Vivo

Fixed the display order of species and strains. It is now alphabetical.
Fixed a bug where large study export files could not be downloaded using the "Send to Email" option. Timeout has been extended.
Fixed an issue where small groups did not display correctly when randomizing by sex with uneven groups.
Fixed a bug where the study timezone was not applied to conditional tasks.
USB vendor and product ID fields are no longer required for device registration.
Added validation for bulk dosing comments (maximum 255 characters).
Fixed an issue where drag-and-drop actions in the preset builder caused errors for calculated measurements.
Fixed an issue where device selection was not applied if users selected a device other than the autodetected one.
Fixed a bug where users could not search for or display alternative IDs (tail, tag, ear) in workflows.
Fixed the Days Plotted option in study settings so survival data now exports correctly to GraphPad Prism.
Fixed an issue where clicking into a data table cell with long text now opens a larger box to display the entire text.
Fixed the Days Plotted option in the Kaplan-Meier survival curve to correctly show days post-disease induction.
Fixed pagination issues in the new doses table; the default view is now set to 100 rows.
Fixed a bug where the final task on a study schedule was not displayed when the study timezone differed from the user’s timezone.
Prevented users from selecting deceased animals when using Assign Identifiers in colony workflows.
Fixed an issue where users could not import JSON files to create presets.
Fixed an issue where Search by ID dropdown settings were not remembered after reopening workflow setup.
Fixed the task target animal list so it updates correctly after randomization changes.
Made the Date field mandatory for one-off tasks.
Fixed an issue where users could not create studies from drafts if no treatment metadata existed in the tenant glossary.
Fixed an issue where some groups were not visible when editing tasks in studies with many groups.
Fixed a validation issue in the dosing page of workflow setup. Treatment selection is no longer required.
Fixed device reconnection issues when switching devices on the same port. A page refresh is no longer needed.

Workflows

Fixed a bug where the Type filter in the Workflows dashboard did not display outputs from intermediate nodes.
Fixed a performance issue where loading a high number of tasks in the Calendar view caused timeouts.
Fixed a crash when creating tasks from tables with fieldset columns.
TaskFinder configuration UI now prevents invalid configurations where a filter step is not the final step.
Fixed a bug where bulk editing schema fields caused errors after selecting from the dropdown.
Fixed a UI bug in the Create Task modal where the schema field type icon did not match the field type.

Benchling Connect

Fixed an issue with NanoDrop 8000 where sample transforms led to missing values.
Fixed duplicated columns for calculated data in PCR CSV files.
Fixed a duplicate absorbance column in measurement CSV files.

Schemas

Fixed a regression that caused text values containing URLs to lose hyperlink formatting. Links are now restored.
Fixed an issue where renaming a dropdown option did not trigger recomputation for computed fields.

Access Management

Fixed audit issues where some user email updates were not logged correctly.
Fixed missing audits for user property changes made from the profile page.
Removed the Copy action for items accessed via share links.