Release Notes: Volume 10, 2022

Meghan Bosch
Meghan Bosch
  • Updated

Welcome to the tenth 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 September 2022.

Notebook

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

Audit logs in structured tables

Users can now export the audit logs of structured tables.

More options to add samples in legacy Transfer tables

When users add samples to legacy Transfer Tables, they are now prompted to select between Input sources or Add from structured table. Previously, Benchling defaulted to the Input sources option.

Released Benchling Sync 1.3.2

Users can now choose Benchling Sync’s installation location and includes support for Apple M1 Macs. We have also made several security updates to Benchling Sync.

To enable this feature, contact your Benchling representative.

Molecular Biology

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

Import and export of GenBank feature metadata

Users can now import, store, edit, and export all data associated with GenBank annotations and translations. Additionally, Benchling has a modernized expanded view where users can select and bulk edit translations and annotations. Previously, GenBank data did not properly map to Benchling annotations and translations upon import and did not export in the appropriate format.

Alternative genetic codes on translations

Benchling now supports alternative or non-standard genetic codes for translations and when auto-filling translations on DNA sequences. Users can now preserve genetic codes when importing and exporting CDS features, create translations on sequences, and update the genetic code directly within the sequence.

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.

Drawing and editing chemical structure files in Notebook entries

Users can now design and edit molecules and chemical reactions directly in Notebook entries using chemical structure files. This feature is available to customers who have purchased the Reg+Chem license.

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.

 

Sample search

Users can now group containers by their contents, and aggregate certain values, like total volume, at the entity level. Users can also now select multiple Entities and click on one of their Inventory links to see containers for all selected Entities, grouped by their contents.

This feature allows users to quickly gather all containers they might need to interact with in a single action, and to have them grouped in order to use aggregate measures to determine their next steps.

Container content removal warning

Benchling now warns users when removing contents from containers that have been transferred, instead of blocking removal.

BarTender information banner

A new BarTender informational banner displays in the label printing settings. It explains that BarTender servers run on a local network and contains links to help articles.

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.

Update Results schemas warehouse names

Users can now independently update result warehouse names for Results schemas.

To enable this feature, please contact a Benchling representative.

Schema creation events

Users can now see schema creation events in the schema audit logs.

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.

Flowchart builder

Users can now create non-linear flowcharts using the flowchart builder, enabling greater flexibility in the Workflows application. When creating a task group, users can design a new flowchart from scratch and add or remove steps from a flowchart, given their permissions on the task schema.

To enable this feature, contact a Benchling representative.

Task Details page

Users can use the Task Details page to view additional metadata regarding a task or output, edit task schema fields outside of the table-based format, and view the resulting outputs of the task and the flowchart for the task’s lineage.

To enable this feature, contact a Benchling representative.

Output table expanded view

Users can now expand the Outputs table, making it easier to interact with extensive data.

Remove default folders from Task schema

Users can remove the default creation and execution entry folders from a Task schema, allowing them to save a task group or execution entry to a different folder upon creation.

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.

Relevant Templates tab for schemas

After updating a schema, users can now use the Relevant Templates tab to view the downstream templates and relevant tables affected by the updated schema. Admins can then open and update these templates from the tab as needed to more quickly review and enhance affected templates.

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.

New endpoint to bulk upsert molecules

Developers can now create and update molecule entities through a single call available in v2-beta. Previously, users had to split calls between Create and Update endpoints.

Bug Fixes

Notebook

  • Audit logs for submitted tables now display a dropdown option’s name rather than its API ID

  • When configuring Lookup Columns, archived schemas are no longer available as an option

  • Errors in table cells no longer lead to infinite error loops

  • When different fonts are used, Notebook export files now properly render symbols and bullets

  • Archiving a Results table with Data Mods enabled now prompts users to provide a reason for archival

  • Changing a protocol’s name now triggers an audit event

  • After submitting structured tables with a date schema field, they no longer display as unsubmitted

  • Exports containing locked structured table columns no longer display an Fx icon

  • Entry exports containing excerpts of attachments no longer repeat the attachment

  • .pdf exports of entries with inline attachments turned can now include .rtf and .csv files

  • Users could not properly select and copy text using the right-click keyboard function

  • Plate creation tables with formulas referencing a location column within that same plate creation table no longer blank out the entry

Molecular Biology

  • Improved error messages on imported JBEI sequences when Benchling does not detect associated sequence data

  • When copying and pasting bases into a sequence longer than 300kb, the dialog box previously showed incorrect sequence information regarding the sequence in your clipboard

  • Benchling no longer errors when calculating reindexing position at realignment

  • Feature libraries can now be scrolled through, allowing users to view all available libraries

  • Users can now see melting temperature data for RNA when RNA oligos are disabled

  • Translation links now invalidate appropriately when direction changes

  • The create protein modal was not presenting the selected tag schema ID

  • Users can now press enter to save annotations and translations in the new features panel

  • Folder selector for DNA and RNA sequence imports now defaults to the most recently used folder

  • Registered sequences now lock when they are moved to a locked project

  • Oligos can now be deleted in bulk on academic tenants

Chemistry

  • .sdf imports no longer fails when the file contains empty lines

  • Benchling no longer renders phosphate monomers on 3’ terminal nucleotides without a phosphate

Registry and Inventory

  • When opening Benchling URLs from object pages, these URLs now open in Benchling tabs rather than in a new browser tab

  • Print label is no longer disabled in the grid toolbar of boxes and plates

  • Including archived containers in Transfer tables no longer causes an error upon table submission

  • Benchling now lists “merged” as a valid reason for archiving bioentities

  • Registration tables no longer duplicate the entry registration process

  • Benchling wasn’t properly importing the text values in a spreadsheet when a dropdown field didn’t match the text

  • Lookup columns in update containers inventory tables didn’t appropriately populate entities in the Contents column

Workflows

  • Copying and pasting assignee values from Excel to the Assignee column of a Task table no longer causes validation errors when submitting the Task table

Insights

  • Read-only dashboards no longer display the “isMulti” checkbox

  • Integer axes on heatmaps are now ordered properly

  • Dashboards no longer crash when switching from log scatter plots to bar charts

  • Users can now properly @-mention Insights dashboards in the Notebook

  • Hovering over a point in a scatter plot displaying the X, Y, and category information no longer disappears when a Y-axis range maximum is set

Access Management

  • Audit log events now include access policy name changes

  • Audit log events now track name changes for users, organizations, teams, and folders

  • Users can now see audit events for created

Application Core

  • Improved the error messaging for failed file deletion events

Compliance Controls

  • Reordering schema fields are now recorded in the Updated order column instead of the Updated name column

Developer Platform

  • The Results API now has improved error messaging for invalid strings

  • Submitting empty aliases objects now returns a 400 error code

  • After transferring Inventory items through, subsequent API requests now reflect these transfers immediately

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