Release Notes: Volume 6, 2024

Welcome to the sixth 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 June 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.

Added icons to Entry, Template and Sub-template title headers [2024.6.N.1]

Icons have been added to Entry, Template, and Sub-template title headers.

Enable Split View Tables for all tenants [2024.6.N.2]

Users can now open a table in Split View to work on it while navigating to different parts of their entry independently.

Added explanation for org handle change impact in the Warehouse [2024.6.N.3]

The language in the org handle rename option has been updated to inform users that changing the org handle will resync the Warehouse, which can take several days.

Molecular Biology

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

Exact molecular weight for monomers [2024.6.MB.1]

The Monomer Library now displays the exact molecular weight of individual monomers.

Alternative start codons [2024.6.MB.2]

Users can specify translations using alternative start codons and:

• View the methionine amino acid at the start of the translation on a sequence map.
• Record translations using an alternative start codon when importing sequence files like GenBank.
• View ORFs on the sequence map using any provided start codon and biochemical properties for a translation using an alternative start codon.

Support for reverse complements in DNA uniqueness checks [2024.6.MB.3]

Users can enable a feature to scan both the forward and reverse directions of registered DNA sequences when a bases uniqueness constraint is configured, identifying sequences as identical if the forward strand of one is identical to the reverse complement of another.

To enable this feature, contact a Benchling representative.

In Vivo

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

Automatic animal exclusion before randomization [2024.6.IV.1]

Deceased animals or animals without recorded measurements are automatically excluded before randomization.

Specify date for randomization [2024.6.IV.2]

Users can choose between using the latest measurements or defining a specific date for randomization. This automatically excludes animals without data recorded on the specified date and proceeds with randomization using only measurement data from that date.

Added ability to name conditions and provide a condition description [2024.6.IV.3]

Users can now name conditions and provide descriptions when defining conditions in a PD study.

Added a results tab to a PD study [2024.6.IV4]

Users can now see all results and related context from a new results tab in PD studies.

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.

Separate access policy for editing inventory names and barcodes  [2024.6.RI.1]

Users now have separate policy statements for editing names and editing barcodes for inventory.

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.

Jump to next task group from outputs table [2024.6.WF.1]

A new shortcut in the output table allows users to quickly navigate to downstream task groups.

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.

Total Number of Options for a Dropdown are now listed [2024.6.SCH.1]

Each dropdown on the main Dropdowns page now shows the number of options it has.

Open an entity, dropdown, or inventory schema after creation [2024.6.SCH.1]

Admins can reopen an entity, dropdown, or inventory schema via a button in the notification after creation.

Keep search query on schema listings page when navigating back [2024.6.SCH.1]

The search query is retained when navigating back to the schema listings page from a schema editor page.

Allow filtering of archived templates in Relevant Templates tab [2024.6.SCH.1]

Filtering now includes archived templates.

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.

Enabled the new IP allowlist management UI for all* tenants [2024.6.AM.1]

The new IP allowlist management UI is now available for all tenants, except for those who opted out ahead of time. Tenant admins can view and update the IP allowlist for both the web app and the warehouse from a new page in the Tenant Admin Console.

Insights

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

Insights Analysis transformations & charting [2024.6.IN.1]

Users can apply data transforms and configure charts within Insights Analysis. Available transforms include joins, pivot tables, and new column formulas. Charting types include bar charts, line charts, scatterplots, pie charts, and heatmaps. 

To enable this feature, contact a Benchling representative.

Benchling Connect

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

Hover Over Output Table to Show Snapshot Data with Timestamp  [2024.6.BC.1]

When hovering over the output table in a run, users will see a pop-up message indicating that the data represents a specific point in time and is immutable. Note: This feature applies only when a field is out-of-date due to a data change and does not appear for all results.

Allow the .pdf extension for the file watcher connector [2024.6.BC.2]

The .pdf extension is now allowed for the file watcher connector.

Create PDF Reports for Chromatogram Parsing in Chromeleon Connector [2024.6.BC.3]

In COPY_OBJECT, if the report_template argument is set, the SDK will generate a report for the sequence.

Make the connection file extension check case insensitive [2024.6.BC.4]

Allow the connection file extension check to be case incentive. i.e. both .csv and .CSV should be allowed for the file parsing.

Update Instrument Service to Allotropy 0.1.35 [2024.6.BC.5]

Update the currently published connectors to use Allotropy 0.1.35

Revert Benchling Gateway to LocalSystem [2024.6.BC.5]

When the Benchling Gateway service user is changed to another user and then back to LocalSystem, the configuration will be restored to benchgw_user.

Release Gen5 Imaging connector [2024.6.BC.5]

We have released the Agilent Gen5 Imaging Connector. This new connector allows seamless integration with Agilent's Gen5 Imaging software, enabling automated image acquisition, analysis, and data transfer between Gen5 and Benchling. For more details on configuring the Gen5 Imaging Connector, refer to the Agilent Gen5 Image Configuration Guide.

Release CTL ImmunoSpot connector [2024.6.BC.6]

We have released the CTL ImmunoSpot Connector. This new connector facilitates the integration with Cellular Technology Limited's ImmunoSpot software, enabling automated data transfer and analysis of ELISPOT assay results between ImmunoSpot and Benchling. For detailed instructions on configuring the CTL ImmunoSpot Connector, refer to the CTL ImmunoSpot Configuration Guide.

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.

Indicate Many Search Results in Registration Dropdowns [2024.6.APP.1]

A new banner notification will inform users to refine their search when the registration table search exceeds the dropdown display limit.

Refined notification opt-out language [2024.6.APP.2]

Opt-out language for promotional emails has been refined and now includes an opt-out link.

Added support for config migrating entry schema field values [2024.6.APP.3]

Entry schemas can be applied to Templates. Now, entry schema fields values specified for Templates can be moved with config migration. The following types are now supported: Text, Long text, Decimal, Float, Date, Datetime.

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.

Canvas interaction webhooks now include user ID [2024.6.DP.1]

When a user interacts with an App Canvas, that user's ID now gets captured when clicking a button in Canvas. The user_id is automatically included in the payload for the webhooks that are sent for these interactions. 

Webhook subscriptions are now explicit [2024.6.DP.2]

Developers can now specify subscriptions to any type of event in the app manifest. Previously, these subscriptions were implicit. 

All events delivered over webhooks are now available in the v2 shape [2024.6.DP.3]

The new v2 payload shape excludes redundant properties and all events and app signals are soft-promoted to v2. v0 will be deprecated on July 11. 

Workflows APIs and events updated from beta to stable  [2024.6.DP.4]

Flowchart APIs and flowchart-related properties have been added to stable capillary endpoints and events.

Clustal and MAAFT Parameters in Alignment API  [2024.6.DP.5]

Parameters used with Clustal and MAFFT alignments are now exposed in the API in addition to the UI.

Alpha endpoints for assembly [2024.6.DP.6]

New v2-alpha endpoints allow customers to model assemblies in the API. Developers can:

• Validate an assembly by providing a method, bins, fragments, primers, and constructs.
• Finalize an assembly creating new sequences and an Assembly object.
• Get an Assembly object to leverage the record of all fragments assembled into particular constructs.

Bug Fixes

Notebook

• Fixed bug that prevented Worklists from being sorted on anything other than Position.

• Fixed bug that caused "TRUE/FALSE" values imported from Excel to appear as "0/1" in Structured Tables.

• Fixed issue where Spreadsheet Import didn't replace rows containing default values in Tables.

• New Results Bulk Create API allows Results to be added to an Entry's table even if the Entry is out for review.

• Resolved issue where 'Ctrl + F' search in Notebook constantly reloaded, rendering the search non-performant.

• Fixed issue where review processes did not maintain the user-selected order in project settings.

• Fixed bug where after submitting results in a table, the content in view jumped to other sections in a notebook entry.

• Recipe Instruction Window was not visible for Mixture Prep Tables (regression due to Split Screen Table View).

• Some 'storable' chips were not resolving correctly after being passed with Table Mapping to another table.

• Green cell background saturation was very high (regression).

• Table borders were doubled on low-res monitors.

• Overlapping tooltips in table header.

Molecular Biology

• Fixed bug where 3' sequence end mod detection was implemented incorrectly, preventing registration of some RNA oligos.

• Cut site dropdowns were shown incorrectly for reverse fragments in GG assembly.

• Issue in linear fragment cloning to select the other side of the enzyme or change orientation.

• Primer wizard generating primers outside the Tm range provided.

• Inconsistent errors in homology cloning.

In Vivo

• Fixed issue where measurements in data tables were not calculating for offscreen cells after copy-and-paste.

• Resolved bug where the manage cages bulk action option timed out in colony.

• Fixed bug when clicking "more" when using the move cage option in colony animals.

• Added missing validation for strain and DOB when adding animals to cages in the study cages page.

• Groups were not displayed in the correct order when cloning a study.

• Resolved formatting issues when editing samples using multi-select metadata fields.

• Fixed issue that resulted in sub-optimal outcomes when using multi-parameter randomization. All randomization outcome metrics were calculated and displayed correctly, including p-values and group summary data.

• Alerts on calculations in data tables were not clearing when the values triggering the alerts were deleted, requiring a page refresh to resolve.

• Fixed issue in the animals table filtering where the filter by observation option was not returning all applicable animals.

• Users could not see graphs page if Summary statistics returned a zero.

• Dosing exports where columns were not correctly aligned with headers for deceased animals.

Registry and Inventory

• Improved performance of Inventory location picker.

• Fixed bug where emails were not sent when rows were intentionally skipped in a data import. Now, users receive emails again when any rows are skipped.

• Grouped containers with multiple unit types now display "Mixed units".

• Fixed issue where containers with different unit types were grouped together.

• Inventory shortcuts can now be used on the output table during direct-execution tasks.

Workflows

• Snapshot fields were not always re-evaluating based on new information.

• Permissions error when migrating a workflow task schema w/ flowchart.

• Fixed issue where Router lookups ran validation on every lookup step when reopening an existing lookup pane.

• Router failed mapping did not send notifications.

• Fixed issue where default field values populated inconsistently in Requests.

• Flowchart tasks were unexpectedly marked completed.

• Worklists could not be sorted on anything other than Position.

• Fixed issue where the "Scheduled on" field did not resolve for FieldType.DATE values.

• Pasting a date into "Scheduled on" would not successfully trigger autosave.

Benchling Connect

• Connections saved in Connect Runs in Worksheet templates do not persist/auto-populate when a study is created.

• Input file post-transform processing step(s) were not sent into the input directory.

Access Management

• Fixed issue where the auditor column was not showing in certain circumstances where it should be there.

• Projects were not displaying the favorites star in the UI.

Application Core

• Fixed bug where unarchiving an entity also unarchived the associated folder.

• Emails were not being delivered to emails with a "mailto:" prefix.

• Fixed rounding error on negative numbers in data tables.

• The "% change" option in the show menu was not working.

• Metadata options were filtered out of the show menu.

• The searchable menu will open on top of the parent menu option.

Developer Platform

• creator.handle was missing for container.contents when created by a Benchling App. The App's API ID is now included.

• Fixed issue where $ was incorrectly dropped in cross table cell references when the referenced table is renamed.

• Column header context menu was not opening on a single click in full screen tables.

• Fixed issue where navigating users to the bottom of the table when double-clicking columns to fill.

• Inventory Update tables for 'Any Inventory' didn't have a tooltip explaining the schema was none.

• Entity Name column data type icon was an entity instead of text.