Welcome to the first 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 during December 2021 and January 2022.

Notebook

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

Exported .pdf entries include timestamp and entry status

In exported entry .pdf headers, timestamps now display when an entry was accepted for review.

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To enable this feature, contact your Benchling representative or Benchling customer support.

Archived result schemas

Archived result schemas are now filtered out when configuring a lookup.

Rename lookup columns

Users can now right-click on column headers to rename lookup columns.

Molecular Biology

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

Indicator to show when aligned sequence is reversed

When using the MAFFT alignment function, users can now view when a sequence has been reversed.

Option to specify schema and translation link when creating AA sequence from DNA sequence

Users can now assign schemas and translation links for AA sequences derived from DNA sequences.

Search bar added to Bulk Assembly sequence selector

A search bar now allows users to easily find input sequences.

Added confirmation prompt when deleting or pasting bases on sequence map

A confirmation prompt now displays when a user deletes or pastes new bases on a sequence map.

Consensus alignments factor in trace quality when making tiebreaking base calls

When generating a consensus alignment, a new voting mechanism chooses the nucleotide that appears most frequently across all aligned sequences and assesses the trace quality at that position.

Autofilling single-link translation links defaults to the longest valid translation

The auto-fill translation link feature now defaults to the longest valid translation when multiple, valid translation links are identified.

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.

Viral particles (vp) and (x10^9) cells/mL unit type added for concentrations

Users can now use viral particles (vp) and (x10^9) cells/mL as a unit for concentrations.

Insights

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

System_name column added to schema_field table in warehouse

A system_name column now displays on the schema_field table for users doing meta queries.

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Fully dynamic pivots

The new Insights dynamic pivot function allows users to group lists into tables by pivoting lists into dynamic columns.

Lab Automation

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

Configure processing steps via custom transform step

Users can now use their own code to transform data files before uploading it into Benchling through the Output File Processor.

Access Management

Benchling’s access management capabilities provide secure data management and tight control over platform permissions and access.

Updated Schemas Permissions checkbox on Teams page in Settings

In Settings, the Schemas Permissions checkbox on the Teams page now includes a description of capabilities that admins can grant user access to.

Workflows

Workflows are a sequence of research 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.

Filter tasks and outputs with new search filter

Users can filter tasks or outputs across all schemas using the Linked items search filter to find those that reference a given entity, container, box, or plate.

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Shortcut to create Workflow tasks from global search

Users can create tasks based on the results of an entity, container, plate, or box search in global search.

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Invalid terminal status added to better capture operational data

Invalid tasks must now be cloned before the task can be retried.

Create task group modal can be expanded

Modals for creating task groups can now be expanded to view task tables with multiple columns.

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.

Permissions APIs have been promoted to v2-beta

The /access-policies APIs have been promoted from v2-alpha to v2-beta so developers can set permissions for users, teams, and organizations.

/apps can be filtered by ids

In the API, the /apps listing endpoint now supports the ids filter.

Improved error message for schema fields

Error messages in the API now include additional details such as which field values are invalid.

Bug Fixes

The following bugs were fixed in this release:

Notebook

  • Users can now create worklists from Lookup tables.

  • Users can now add containers to results by using ‘add from structured table’.

  • Entries that contain sequences with custom fields and live in a registration table no longer time out.

Developer platform

  • Assay run filter on assay results endpoint is no longer broken for specific runs.

  • Specific entries are now able to be retrieved via the API without retrieving an error message.

  • Bulk actions using the API no longer timeout.

Workflows

  • Users are now assigned as values in the “Assignee” column when tasks are uploaded from a spreadsheet.

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