Welcome to the seventh 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 June 2022.

Notebook

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

New quick link for templates in entry headers

Users can now click Notebook entry headers to open the template the entry is using.

Entry Timestamps when printing

Users can now include entry timestamps when printing.

Copy bulleted items into documents

Bulleted list items can now be copied from Benchling and pasted into Word or other programs with correct formatting.

Get-entry and create-entry API endpoints

The Get Template Entry API endpoint is now available.

Molecular Biology

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

Bulk modify nucleotides within an oligo

Users can now find existing nucleotides that are similar to ribose monomers, base monomers, or phosphate monomers and replace them with different monomers. This enables users to easily bulk modify an entire oligo by specifying a series of these rules.

Search using monomers symbol

Users can now use monomer symbols to search and edit nucleotides and monomers.

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View monomer chemical structures in the monomer library

Users can now render and view chemical structures of monomers in the monomer library.

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Pull Ensembl IDs in real time when importing sequences

Importing sequences from Ensembl now pulls sequences live from Ensembl’s APIs instead of pulling from a limited list of uploaded Ensembl genomes.

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Linked parts and primers displays on previous versions

When viewing a previous version of a sequence, the latest information of linked parts and primers now displays. For users using the legacy parts system, Benchling creates new versions of linked sequences when bases of a part are edited.

Visually identify that a linked part is archived

Users can now visually identify if a linked part is archived within the sequence map. Archived parts will be highlighted in light gray whereas unarchived parts will be highlighted in dark gray.

Multisequence alignments, new MAFFT algorithms, and updated DNA realignment flow

The following updates enhance DNA alignment usability:

  • Users can now upload multiple DNA sequences or .ab1 files and align them in groups, setting up pairwise alignments against one or multiple templates, multi-sequence alignments against multiple templates, or multiple consensus alignments.

  • Benchling also supports two new MAFFT algorithms to provide more flexibility for different alignment use cases. Users can choose between three MAFFT algorithms and one Clustal Omega algorithm then customize the parameters for each.

  • DNA realignment flow, used to modify or rerun an alignment, now matches the new experience and supports the new algorithms.

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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.

Bulk update Inventory quantity

Using the expanded inventory search, users can select multiple wells and containers to bulk update the quantity, even if selected containers don’t share the same schema.

Quantity Lookup Attributes supports units of measurement

Users can perform unit conversions on compatible units of measurements, like grams to kilograms. If a quantity lookup uses incompatible units of measurement, it produces an error. For example, grams to liters.

Insights

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

Y-axis range configuration

Users can now configure the y-axis range on scatter plots.

Outlier detection for logistic regression

For Insights scatter plot charts with a logistic regression, users can now apply outlier detection to detect and/or exclude outlier data points from the regression calculation.

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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.

New hoverbox displays on Workflows task chips

Users can hover over task chips to view important information about each task, such as the status and assignee.

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View watchers on the Task Group page

Task group watchers now display on the task group tab as well as the metadata tab.

Application Platform

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

Human-readable audits

The audit system now generates audit trail exports that are easier to understand and don’t require JSON interpretation.

Export audits as .pdf files

Users can now export audits as a .pdf everywhere Benchling supports exporting audit logs.

Benchling Support activity in audit logs

For additional transparency and improved security, audit logs now include Benchling Support activity. These events are indicated by the user benchlingsupport.

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Columns no longer included in audit exports

Audit trails no longer include columns for Reason Code and Comment.

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Export Users feature no longer exports service accounts

Service accounts can no longer be exported from the Export Users feature in the Tenant Admin Console.

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.

Workflow tasks supported in App Config

Users can now add Workflow tasks to app manifests and configure them on the app config page.

To request this feature, contact a Benchling representative.

Manifest order is now preserved in the App Config UI

The order of config options presented in the manifest now match the order in the App Configuration UI.

To request this feature, contact a Benchling representative.

Bug Fixes

The following bugs were fixed in this release:

Notebook:

  • Entries with templated tables created via API had an extra row when an excel formula was present

  • When creating notebook entries from a template, the root project folder was set as default. Now the folder defaults to the folder the user navigated to.

  • Audit log for an entry now includes when an entry was exported and if the export was successful or if it failed

  • Resolved bug that prevented use of external previewers when the IP_ALLOWLIST flag was set

  • Users couldn’t edit Results schemas that reference an archived drop-down menu.

  • Large result tables on the entity page were loading when they should have stayed collapsed

  • Registration tables weren’t allowing subsequent submissions after the table was initially submitted

  • Relevant items tab now displays entries that reference entities in a registration table

Molecular Biology

  • Users couldn’t delete bases in the template sequence of an alignment

Workflows

  • Task group watchers were not notified on task creation

  • Fix released for workflow creation column mapping logic to allow a custom entity from a workflow task to be mapped to a custom entity

  • Output table rows were not resolving chips and now evaluate formulas correctly

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