Welcome to the 9th 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 September 2024.
Watch our Feature Release Highlights to more deeply explore this month's updates.
In Vivo
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Async validation in the workflow measurement form and error sound [2024.9.IV.1]
When using connected devices an error sound will be heard when a value is invalid, sounds will only be heard when using the workflow measurement form. Users will not hear these sounds when Editing IDs or measurements once saved.
To enable this feature, contact a Benchling representative.
Delete empty cages option after recaging [2024.9.IV.2]
On completion of recaging any cages that will be empty on the study as a result of this recaging process will be automatically deleted.
Proceed directly to recaging after randomization [2024.9.IV.3]
After randomization any animals that have now been allocated to study groups can proceed directly to recaging in a single step.
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.
Mapping in progress indicator [2024.9.W.1]
When tasks are being mapped between nodes in a flowchart we now can display a mapping in progress indicator
Benchling Connect
Benchling Connect, formerly Lab Automation, enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Allotropy: Plate Reader • Add Mapper to REC 2024/06 schema [2024.9.BC.1]
Allotropy: Plate Reader - Add Mapper to REC 2024/06 schema
Update SoftMax Pro Adapter to REC/2024/06 Plate Reader schema [2024.9.BC.2]
Update SoftMax Pro Adapter to REC/2024/06 Plate Reader schema
Support the "empty well" lookup and allow the filter the empty value during the output file processing [2024.9.BC.3]
Previously, in the 'Add column' transform in a Run schema, the lookup would return an error if empty wells were found and the 'Ignore empty wells' option was not checked. With this update, empty wells in the lookup will now result in an empty cell value in the new column. This is useful for handling rows with non-useful data (e.g. data with no associated sample) linked to empty wells, which can be filtered out using the 'is not empty' transform if needed.
Update Agilent Gen5 Adapter for kinetic measurements [2024.9.BC.4]
With addition of kinetic measurement support (profile data cube) to the Plate Reader ASM, the existing Agilent Gen5 adapter is updated to support instrument files that contain this data.
Update SoftMax Pro Adapter for kinetic measurements [2024.9.BC.5]
With addition of kinetic measurement support (profile data cube) to the Plate Reader ASM, the existing Softmax adapter is updated to support instrument files that contain this data.
Release ThermoFisher Genesys30 Connector [2024.9.BC.6]
Genesys30 Connector Release: https://help.benchling.com/hc/en-us/articles/29765849112973-ThermoFisher-Scientific-Genesys30-Configuration-Guide
Release ChemoMetec NucleoView Connector [2024.9.BC.7]
ChemoMetec NucleoView Release: https://help.benchling.com/hc/en-us/articles/25912328518797-ChemoMetec-NucleoView-Configuration-Guide
Updates to Unchained Labs Lunatic Connector • Add fields from XLSX instrument file [2024.9.BC.8]
Additional support of XSLX file extension revealed fields that were not previously included in CSV exports. Incorporate recording of fields when XSLX files are parsed by the Lunatic connector:
Fields to add from XSLX file:
- Software version - > software version
- Test performed by -> analyst
- Client version -> firmware version
- Experiment name -> experimental data identifier
Update Allotropy to 0.1.55 & Update ASM-to-CSV Parser library to 1.0.56 [2024.9.BC.9]
In this release, we've introduced the following updates and improvements:
What's new:
We've added additional metadata fields to the AppBio QuantStudio and introduced support for the Chemometec NC View Connector.
Fixes:
Issues with missing labels in Unchained Labs Lunatic, incorrect numeric casting in Agilent Gen5, optional PCR Detection Chemistry fields, and leading zeros in Perkin Elmer Envision well identifiers have all been resolved.
Changes:
We simplified experiment type inference in the AppBio QuantStudio and allowed software name and version fields to be set as "None" for more flexibility.
Release ThermoFisher Scientific, NanoDrop One Connector [2024.9.BC.10]
ThermoFisher Scientific, NanoDrop One Connector Release: https://help.benchling.com/hc/en-us/articles/29403832789773-ThermoFisher-Scientific-NanoDrop-One-Configuration-Guide
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.
Updated TOS and Privacy Policy on sign up page for Academic tenant [2024.9.AM.1]
The Legal team released new language for our TOS and Privacy Policy for Academic tenant users. As part of the rollout for that change, we updated the string on the Sign Up page for Academic to change "EULA" to "Privacy Policy" and changed where the links pointed.
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.
User link fields can be filtered by current user [2024.9.AC.1]
User link fields can be filtered by current user
Config migration history [2024.9.AC.2]
A redesigned landing page for Config migration which includes records for historical migrations ran on a tenant. Now, migrations can be given names & descriptions and changelogs associated with migrations live natively in Benchling.
More specific error messaging for Config migrations with archived dependencies in Notebook templates [2024.9.AC.3]
Before, Config migration only informed the user when an object was archived and causing export to fail, but gave no indication of where to find this reference embedded in a Notebook template. Now, error messages also include table name and column name, where relevant, to help with locating archived references in Notebook templates.
Critical security updates [2024.9.AC.4]
The Benchling Desktop Sync release 1.3.5 now will prompt the user whenever signing into a different Benchling tenant than was the last to avoid signing into an untrusted tenant. This release also contains a number of bug fixes and security updates for third party dependencies including some critical/high security issues. If your tenant does not enable automatic updates, then it is strongly recommended that you update your installations immediately.
To enable this feature, contact a Benchling representative.
Plate maps: Tools for annotating, filling, and visualizing plates in Inventory and Notebook [2024.9.AC.5]
This release enables us to better support plate-based workflows in Benchling, focusing on the design of assay plates.
With our new tools, users can:
- visually annotate wells in an interactive wizard
- fill a new or existing plate with multiple entities
- visualize metadata on the plate entity
- do all of the above on plate entities in Inventory and in Notebook entries
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.
Audit logs public API promoted to V2•beta GA [2024.9.CC.1]
Audit Log API makes it possible for customers to automate the retrieval of an Audit Log of any Benchling object in supported formats (PDF, CSV). Users inject a single API to pull the object audit trail and can run up to 500 requests within 1 hour.
To enable this feature, contact a Benchling representative.
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.
Removed organization and team membership APIs from /v2•alpha to ensure customers only use /v2 version [2024.9.DP.1]
The organization and team management APIs were added to the /v2 endpoint several weeks ago, now that customers have all moved to use the /v2 endpoint we're removing the /v2-alpha version of the API to make it clear that customers should use the /v2 version of it.
Quartzy's Shareable App (built by Quartzy) is now GA [2024.9.DP.2]
Quartzy made significant updates to their Benchling integration. This new version of the app is now available to all customers.
Many async task methods in the API have been configured to process substantially faster on average. [2024.9.DP.3]
Async tasks in the API are assigned a priority when they are created, and several different task types had their priority increased. This will result in these tasks starting to process faster, which will especially impact tasks with low numbers of items, reducing their completion time by as much as 90%.
Bug Fixes
In Vivo
- Fixed an issue where the user could not open a study after form used to create this study had been deleted by an administrator.
- Fixed a display issue where Prism survival table was not ordering groups correctly.
- Fixed a bug in Treatments where an Error was seen on update when using a non-default display unit.
- Fixed a bug with connected devices where edited an invalid form did not automatically save after when corrected.
Modified Biologics / Chemistry
- Fixed bug where autofill-translations cleared transcriptions from sequences.
- Fixed permission bug where tenant admins were not able to configure custom notation.
- Fixed bug where changing the offset of a duplex disconnected conjugates.
- Fixed typo in molecule creation API spec.
Registry and Inventory
- Fixed a bug where users were unable to find a location in inventory tables due to the menu collapsing during scrolling.
- Entities were incorrectly bypassing registry validation tasks, causing them to remain in a 'validating' state. We forced validation on these entities and fixed the underlying problem.
- Validation errors for duplicate sequence bases was only displaying on one entity and not the duplicate entity. Fixed during asynchronous validation.
- Fixed edit barcodes permissions in policy statements, which were not granting permissions even when granted.
Molecular Biology
- Fixed another bug stemming from a Chrome accessibility update where users couldn't scroll to select bases.
App Ecosystem
- Fixed a bug where the installed Benchling App version did not update if the version was already installed.
- Fixed a bug where the app config API would return incorrect items because permissions were not enforced correctly.
Data Input
- Fixed a bug with how the entity-name field was displayed in CSV exports depending on the user access.
- Fixed a bug where submitting Registration tables with out-of-date DNA Sequences would submit the value in the table rather than resyncing with the current, up-to-date value.
- Fixed a bug with the filldown operation in tables that caused different values to be displayed in the formula bar vs. the cell of tables in rare cases.
- Fixed a bug where empty values in lookup tables appeared as an unchecked checkbox. Lookups will no longer display a checkbox input and will show TRUE/FALSE similar to how users submit data elsewhere.
Compliance Controls
- Fixed bug to allow project level data modifications to function in worksheets.
- Fixed issue with data modification populating when users create new objects and make folder changes.
- Fixed bug where inventory objects with no folder association triggered error upon folder movement with project level data modifications.
Search
- Fixed a count of selected rows in expanded search view.
Connect
- Fixed "Invalid integer string: '1.0'." ASM error from QuantStudio RT-PCR connector.
- Fixed issues with field discrepancies in MabTech Apex adapter (both Single-Plex and Multi-Plex).
- Added additional data exported from QuantStudio adapter.
- Updated SoftMax Pro Adapter to disregard compartment temperature when set to 0.
- Fixed issues with the Spectrophotometry ASM-to-CSV parser errors if location/batch identifier not found in the ASM JSON. These should be optional fields as per the schema.
- Fixed an issue with the Spectrophotometry - ASM-to-CSV missing mass concentration field.
- Fixed an issue with Spectrophotometry - ASM-to-CSV generating duplicate calculated results columns.
- Added logic to catch a case "zero plate reader documents" and raise an AllotropeConversionError.
- Updated QuantStudio RT-PCR: Update Quantity CalculatedDataDocument data sources.
- Fixed a bug where default permissions set on schema access policies were not propagated to newly created connection schemas.
- Fixed a bug where PharmSpec Connection shows 'Unavailable' without error message.
- Fixed a bug where Lunatic connector generated incorrect concentration column header.
- Fixed a bug related to missing columns in QuantStudio output.
- Fixed a bug related to missing 'Well ID' in Gen5 connector CSV output.
Application Core
- Fixed bug where CTRL+F on settings pages brought up the Sequence search bar instead of the system Find control.
Access Management
- Fixed a bug where the Search page would crash when a user selected a project and another object at the same time.
- Fixed a bug where the Users page could not be sorted by Joined On.
- Fixed a bug where the default policy set for org members in internal admin was not being respected when adding orgs to Projects.
Workflows
- Fixed a bug where we allowed setting the owner of a Worklist through the API.
Tenant Lifecycle
- Fixed a bug where dropdown options in templates caused Config migration failure.
- Fixed a bug where Config migration attempted to create archived objects.
Insights
- Fixed how the presence of an archived dropdown that linked to an archived entity schema field would crash the analysis dataset creation tool.