Notebook

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

Preview Plate Creation Table in Insert modal

Users can now view preview the Plate Creation Table prior to insertion into a Notebook entry. Click on ‘Insert’ in the notebook entry, scroll down to ‘Plate Creation Table’, select a ‘Type’ of Plate Creation Table by specifying the schema and a preview will be generated in the modal to signify what columns need to be included.

Improved messaging on tooltips when a table’s submit button is disabled

Messages on tables will now provide more context to users on why the entities in a table cannot be submitted.

Add to a Worklist from a Plate Creation table

Users can now add items to a Worklist directly from a Plate Creation table. This feature makes it easier to organize entities within the plate creation table in a Notebook entry, as well as access your Worklists.

Icons for structured tables in the Table of Contents

This feature improves the Table of Contents view within a Notebook entry, where each structured table has a corresponding icon representing the type of structured table.

Registration table preview: exclude errors

Previously, when previewing a registration table before inserting it within a notebook entry, columns within the preview showed warnings in required fields. Now, registration table previews are available within the ‘Insert registration table’ modal without red error flags.

View up to 100 Google shared drives when viewing External Data

The External Files listing has expanded to allow users to view up to 100 folders within their Google Drive in ‘External Files’. Previously, users were limited to viewing the first 10 folders in their Google Drive.

Allow filtering by @-mentions

A new filter option has been added to allow users to generate a list filtered by items where a user or item has been @-mentioned.

Updates with No Changes to User Interface

  • Tooltips have been improved for icons within the notebook to improve accessibility.
  • Previously, exports would run the risk of timing out. If an export contained two files with the same name, only one of the files would be included. Now, users will see increased reliability of large exports and exports that have 2 files with the same name.

Molecular Biology

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

Option to download source files from a DNA alignment

Users now have the option to download .ab1 source files for all newly created DNA alignments with .ab1 files. Note that this update will not work with previously created alignments.

Add DNA sequences to a Worklist upon import

Users now have the option to directly add a DNA sequence to their Worklist upon import. This feature makes it easier to organize sequences in easily accessible Worklists.

Search for DNA and AA alignments in Global Search

Users can now search directly for DNA and AA alignments performed in Benchling within the Global Search tool.

Auto-annotate DNA sequences upon import

Users can now import sequences and utilize the option to Auto-Annotate or Auto-Fill Parts. The addition of this option streamlines the workflow to characterize sequences upon import.

Antibody tools can detect multiple variable domains in a sequence

Previously, antibody tools would not look for another chain after successfully finding the first in the sequence. Now, multiple chains within a protein sequence will be recognized and annotated.

Bulk sequence import from Ensembl supports multiple transcript IDs

In addition to importing sequences from bulk search by accession ID, users can search by transcript ID to search for single or multiple sequences from Ensembl.

Edit parameters when attaching primers in bulk

Users can now set preferences to specify constraints for their primers. This feature makes it easy to include parameters when bulk attaching primers. Previously, constraints were not editable and were set to default preferences.

Removed mismatch highlighting in areas of no aligned sequence coverage for DNA alignment PDF exports

Previously, when exporting a DNA alignment to a PDF, gaps at the ends of alignments would be highlighted as a mismatch. Now, red highlighting has been removed for the ends of alignments.

Added a “Genome Request” tool

Users can now fill out a “Genome Request” via a form provided in the UI to collect custom genome import requests for CRISPR. Further instructions for the required information needed to add genomes is provided in the link, shown below.

Set sequence topology in bulk

Expanded listings now provide option to set topology in bulk for multiple sequences simultaneously. This can be found by navigating to the ‘More’ option in the expanded view, then ‘Analyze’, and scrolling down to ‘Set Topology’ as shown here.

Specify total # of mismatches when attaching primers

Users can now specify an accumulative number of mismatches when attaching primers.

Set Schema from the Primer panel

Users can now define a Registry schema for primers, either singularly or in bulk, within the Primer tool on a DNA sequence.

Download .ab1 source files from DNA alignments in bulk

Users will now see the option to export alignment source files in bulk within the expanded Search window. Notice that, in the example below, the “DNA Alignment” search filter has been used to parse files for alignment types.

Note: This option will only be present for alignments created following the release of this feature and does not represent a retroactive change.

Registry and Inventory

Right click to remove item from Worklist

Rather than opening a Worklist to manage items, users can right-click on an item in the collapsed view to remove the item from a Worklist.

Save Worklist order based on column sort

A column in the expanded view now can display the order in which entities are displayed in a Worklist. This allows users to set a Worklist order by a column.

Render label preview alongside ZPL

Users can now generate a live preview of a label alongside the ZPL directly in the Benchling platform. If you’re interested, contact your Customer Success Representative to enable this option for you.

When moving containers, use current box by default

Moving items within a box now is more convenient as the current box is the default option for users to rearrange containers within the same box. This reduces friction in moving items within a box.

Scan entities and plates into a Worklist

Benchling now supports scanning of both entities and plates into their own respective worklists. Find the Scan options by navigating to Worklists, under the Home page, and selecting the Scan icon, as illustrated below.


Display check out status and comments on box view

Users can now view a container’s check out status, along with the checked-out date, time, and comment inputted by user when hovering over a container within a box.

Save Worklist order based on column sort

A column in the expanded view now can display the order in which entities are displayed in a Worklist. This allows users to set a Worklist order by a column.

Schemas

Use the search bar to filter the field type menu

Field type options in schema configuration are now searchable. Users can search for specific field types instead of scrolling through potentially long schema or dropdown options.

URLs in text fields rendered as hyperlinks

URLs in text fields are now automatically rendered as hyperlinks to be displayed in the ‘metadata’ tab of a schema; previously users manually hyperlinked these text fields individually.


Navigate directly to the schema page of an entity link

When viewing linked schema fields in the schema information in ‘Registry Settings’, users can directly navigate to that schema page from the display text of the schema field.

Mouse icon for custom entities

‘Entity Settings’ in the schema configuration of the Registry now has the option to select a mouse icon to visually represent custom entities.

Open schema pages and schema sections into new tabs

Users can now open schema pages and sections in new tabs by right clicking and selecting ‘Open Link in New Tab’. Using CMD+click or SHFT+click would also allow these options.


Trim leading/trailing whitespace in dropdown options

Dropdown options in Registry settings cannot have two options with the same name with leading or trailing whitespaces. This eliminates the chances of a duplicate dropdown option.

Insights

Insights is one of our newest applications to the platform. This feature is seamlessly integrated with all Benchling applications, and enables users to query, visualize, and share high quality, structured data that resides on the platform.

Run subquery

Users can now run selected queries or subqueries within their block query. This allows users to highlight a section of the query, run that selected portion, and view results of that specific portion.

Drag and drop Insights dashboard blocks

Insights blocks can be dragged to other positions within a dashboard by selecting the 6-dot icon located in the top righthand corner of the dashboard block and moving to the position of interest, noted by the blue bar that appears once the block has been positioned correctly.

Export 50K rows in Insights

Users can now export up to 50,000 rows from a query result, allowing the export of bigger datasets.

Unified dashboard level and query level actions

The action icons on the right of the edit block view presents options to delete or edit blocks. Users can now take similar actions to editing dashboards when editing specific blocks within a dashboard. Previously, these actions could only be taken from the dashboard view level.

Highlighted parameters for improved syntax

Parameters are now displayed in a different color from the rest of the query so that users can easily find all places where the parameter is referenced within the query.

Map warehouse table names into the warehouse

A new warehouse name column ‘system_name’ in the schema enables easy visibility into what names schemas are referred to within the warehouse.

Metadata added to dashboard details modal

Dashboard settings modal now displays dashboard creator, when it was last modified, and date/time dashboard was created.

Name CSV file directly from block filename

Downloaded CSV files now are named after the block name in the dashboard. Previously, each block would download as ‘sql_query_results.csv’.

Toggle scale settings for an axis to begin 0

Users can now enable or disable the chart configuration option for the y-axis to begin at 0 for charts by navigating to the gear icon in the top right of the chart view.

Freeze dashboard header

Freeze dashboard headers allows users to view various parameters and actions when scrolling through an extensive query results list.

Item IDs in charts display as item name

Chip item IDs in the query results now show the entity’s actual item name.

Lab Automation

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

Lab Automation Runs in Metadata

Users can now create relevant items for entities in Lab Automation Runs. Navigate to the bottom of the ‘Metadata’ tab to view the ‘Relevant Items’ section for the entity in the Lab Automation Run.

Allow for additional quick actions within Benchling for schema-less fields in Runs

"Insert from worklist" and "Add from structured table" are now available when adding storage items to a Run field that is not schema-specific.

Specify a folder to create entities from lab automation

Users can now set folders for entities to be placed into when created using lab automation.

Other Lab Automation Updates

  • Remove quotes from instrument output files
  • Configure lab automation to stamp a plate in quadrants
  • Configure output file to process a file based on column name, instead of column position
  • Set container fields when processing instrument output file
  • Output files can be processed if concentration is denoted with a negative value

Developer Platform

Our developer platform is fundamental to centralizing and standardizing all your R&D data. Benchling’s APIs are built to match the flexibility and speed of modern life science R&D. More information on the endpoints below can be found here.

Bulk Create Containers via the API

Users can now use the BULK CREATE CONTAINERS API endpoint to create multiple containers using the API simultaneously. More information on using the endpoint can be found in our API docs here.

Bulk update custom entities endpoint supports updating folders

Users can now use the BULK UPDATE CUSTOM ENTITIES API endpoint to update folders for entities. More information on using the endpoint and its parameters can be found here.

Mentions filter added to listing endpoints

Listing endpoints now include a filter to list items that @-mention another item in the notes section; one example of an endpoint that utilizes this new feature can be found in our API docs here.

MentionedIn filter added to listing endpoints

Listing endpoints also include a filter to list items that were @-mentioned in a notebook entry; one example of an endpoint that utilizes this new feature can be found in our API docs here.

Filter containers by checkout status

List containers endpoints can now be filtered by checkout status; more information on this endpoint and parameters can be found in our API docs here.

Endpoint to list all dropdowns

Users can now list all dropdowns using the API via the listing endpoint v2/dropdowns nested under the registry, ensure that registry-based permissions are checked prior to using this endpoint.

Endpoint to list schemas without requiring a registry ID

Users can now list all types of schemas via listing endpoints using the API, without the need for the registry ID. Examples include: /v2/batch-schemas, /v2/box-schemas, /v2/container-schemas, /v2/entity-schemas, /v2/location-schemas, /v2/plate-schemas. Several endpoints were added to this list. More information on one example can be found here.

Endpoints to retrieve schemas by ID

Users can now list all types of schemas via listing endpoints using the API, without the need for the schema ID. Several endpoints were added, information for one example can be found in our API docs here.

Endpoint to create a folder

Users can now use the API to create a folder. More information on this endpoint can be found in our API docs here.

Endpoints to archive and unarchive oligos

Users can use a POST endpoint to archive or unarchive an oligo. More information on this endpoint can be found in our API docs here.

Filter by empty DNA sequence

DNA listing now supports filtering by an empty sequence. More information on using the endpoint and its parameters can be found here.

Add filters for Request listing fields

Filters can now be added for fields in Request listing. More information on using the endpoint and its parameters can be found here.

Requests and Workflows

Benchling Requests is used to seamlessly manage almost any type of assay or task request between teams or users. Workflows are a sequence of research processes that are performed to answer a research question or synthesize new material. This helps users understand the information flow through all the connected steps.

Set default project on request template

The request template now allows the user to specify a default project folder within the template settings, this is useful when Requests are mapped to a specific project, so that the Request process is simplified.

Bug Fixes

The following bugs were fixed in this release, ordered by product area:

Notebook

  • Corrected behavior around the “out-of-date” indicator when using the Registry ID as the display label.
  • Image sizes when creating an entry from template are preserved.
  • When removing an Alias column and adding back an Alias column in the Registration table, existing Aliases will populate accordingly.
  • Previously, in-line text next to an attachment placeholder was erased upon uploading the attachment itself. Now, text beside the attachment will be preserved.

Molecular Biology

  • A common file import error seen from .gb files exported from Vector NTI has been addressed. Previously, a number of .gb files generated VectorNTI contained unexpected characters - causing errors in .gb importer.
  • Previously, setting Registry ID as the display label was being ignored on the sequence map for registered primers, now the sequence map displays the registry IDs for primers. If you do not see the Registry ID as the display label for a sequence map, please contact your Customer Experience representative to enable this for you.
  • Reverse primers are now always reflected when creating PCR products.

Insights

  • Parameter scroll has been fixed. Menus now intelligently determine the view based on menu length so that the menu does not scroll off of the page.

Schema browser now saves state of schema when collapsing row preview.

Requests and Workflows

  • Creation of a request via API with missing required fields is now blocked so users have to set all of the required fields.

Lab Automation

  • Results created through lab automation can now be surfaced through LOOKUP fields.
  • Output files can now be processed if they link to other storage items (plates, containers, etc).
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