Welcome to the ninth volume of our 2022 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 August 2022.

Notebook

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

Archive results during entry archival

Benchling offers a tenant-wide option to automatically archive all results in an entry when that entry itself is archived. A modal populates the results that will be archived when the entry is archived, preventing potential mismatches in Result statuses (archived or not archived) between the archived entry and the Registry and Warehouse data. This opt-in feature affects all users within a tenant.

To enable this feature, contact a Benchling representative.

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.

Display nucleotide structure in hover-over tooltip

When hovering over a nucleotide, the nucleotide’s full chemical structure now displays, which encompasses the sugar, base, and phosphate groups. Previously, users could only view the names of the monomers used.

To enable this feature, contact a Benchling representative.

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.

Well coordinates available in lookup columns

Users can now look up well coordinates using well_coordinates. Previously, users could only perform this action through snapshot fields.

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.

Remove whitespace on schema names

Benchling no longer displays the trailing and leading whitespace for entity schemas. For example, “ name ” is shortened to “name”.

Application Platform

Application Platform provides users a way to manage permissions, leverage administrator capabilities, and organize teams, organizations, projects, and folders.

Added E-Signature audit events to human-readable audits

E-signature events are now tracked in human-readable audits as their own events. Previously, these events were included under the event “Updated review status.”

Lab Automation

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

Results schema creation from Lab Auto Run schema config

Users can now create Results schemas through the Run schema creation modal using sample data.

Entity schema configuration from Lab Auto Run schema output file config

Users can now create Entity schemas with sample data using the output file config UI.

Transfer and record results through Lab Auto output files

Users can now transfer entities and record their results when configuring the Lab Auto output file.

Insights

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

Multi-value parameters

With parameters, users can now filter results on a dashboard by specific conditions, and can insert an array of values by using multi-value parameters. At this time, Benchling doesn’t support multi-value parameters for date, folder, number, project, and text parameters.

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.

Reformatted createdAt filters for /assay-results endpoint

Users can now filter the /assay-results endpoint with new createdAt filters formatted in the RFC3339 time format. Filter modifiers include .lt, .gt, .lte, and .gte. Previously, these filters were in a non-standard format.

Discontinued field$raw table

The field$raw table is discontinued on all new tenants due to its large and unwieldy nature. Existing tenants will continue to have access but can request to disable the table by contacting a Benchling representative.

Queries against this table are generally very slow, and syncing data to this table from Benchling’s internal database has become resource intensive. Most customers do not use this table, as it is confusing and tedious compared to per-schema tables.

Discontinuing the table allows for lower sync latency and more performant warehouse queries across all Benchling customers. The table data is still generally available across other schema and per-schema tables. View the changelog for more information.

RNA endpoints available in the API

Users can now access RNA API endpoints using /rna-sequences. Users can now also access both DNA and RNA alignments using /nucleotide/alignments, as the /dna-alignments endpoint has been discontinued.

Support for POST/PATCH operations on Users v2-alpha endpoint

The Users API endpoint now supports POST and PATCH operations, enabling developers to create and update user properties such as name, email, and suspended status. Benchling users can leverage these features in scenarios such as automating user on- and offboarding or updating user properties.

Bug Fixes

Notebook

  • When users upload an attachment with an unsupported file format to Benchling, a chip will now indicate that the image file cannot be previewed

  • When submitting a structured table, Benchling no longer jumps to different portions of the entry

  • When importing spreadsheets with formula errors (displays in spreadsheet as #VALUE), Benchling no longer returns a numerical value of 15 in that cell and correctly imports #VALUE

  • If the configuration flag RESULTS_FILTER_TO_REVIEWED_DATA_OUTSIDE_ENTRY is true, Benchling no longer pulls Results from unreviewed entries into Lookup Columns

  • Printed entries no longer include the printer settings modal

  • Benchling now responds better to removing tool tips when navigating away from an entry

  • Benchling no longer misinterprets Boolean values in lookup columns as 1/0, but correctly as true/false

  • Reliably jump to search results within an entry

  • Result tables in runs no longer flicker when loading new Results pages

  • Tooltips that display when hovering over entities now appropriately disappear upon moving the mouse

  • Result tables now recognize dates formatted as DD-MON-YYYY

  • Lookup columns returning multiple URLs no longer concatenate the links

  • Users can now scroll through the structured table selector menu

Molecular Biology

  • To prevent potential performance issues, users can no longer bulk align more than 100 DNA alignments at once

  • Users no longer lose selected translations on sequence maps upon double- or shift-click

  • Users will now receive a warning when attempting to run AlphaFold on an empty amino acid sequence

Registry and Inventory

  • Benchling now correctly calculates volumes after transferring contents from one container to another

  • Lookup tables no longer introduce errors in concentration units

  • µL no longer displays as mL in the Inventory

Schemas

  • Audits no longer report a dropdown-menu name change after reordering the dropdown’s options

Lab Automation

  • The Creator field is now visible when importing a Lab Automation run in the inbox

  • Output file processors no longer strip the lead zeros from a file’s numerical values

Insights

  • Y-axis label for aggregated bar charts and labels on pie charts no longer lose the original column name

  • The tick labels on the axes of heatmaps are now numerically sorted

  • Multi-value parameters no longer error when a parameter name contains a space

  • Fixed a typo in the multi-value parameters help message

Access Management

  • Long-text access policies no longer overflow past the given text box on the Project Settings modal

Developer Platform

  • Workflow schema IDs now correctly populate in the v2.workflowOutput.updated.fields rather than the Workflow output task schema ID.

  • The /transfer endpoint no longer crashes when destination container contents concentration is null

  • docs.benchling.com now returns a 429 error if /warehouse-credentials cannot obtain the database connection

  • Users can now filter schema fields by datetime in the API

  • The Benchling SDK no longer errors after creating an assay_run using from_dict whose input did not have its validationStatus filled out and subsequently running to_dict

  • The docs page originally showed a return type of CustomEntity, whereas the actual return type was a list of models

  • check_for_csv_bugfix function now supports Python iterables as well as lists

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