Release Notes: Volume I, 2021

Welcome to the first volume of our product release notes in 2021! We have been working hard to bring you some much requested features. Read along to learn about our new product features and enhancements released December - January 2021.

Molecular Biology

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

Searching oligo entities by DNA bases

Previously, when searching for registered oligos, searching for a known DNA sequence using the ‘DNA String’ filter was not possible. Registered oligos can now be searched by first selecting “Oligo” as the type, setting the filter to “Nucleotide String”, toggling on the “includes text” field, and searching for the specified oligo.

Homology detection limit increase for bulk assembly

There is now an increased homology detection limit for “Bulk Assembly”, allowing users to perform Bulk Assembly on much larger sequences with longer homology regions. If homology regions already exist between fragments being assembled, Benchling is able to increase the detection limit up from 50bp up to 600 bp. Users can now input an expected upper range X, and Benchling will scan within a window of 10% of X for existing homology regions.

Note: there is still an upper bound requirement.

CSV-based creation workflow

The bulk oligo creation workflow has been replaced with the standard CSV-based creation workflow, allowing for more flexibility in oligo import, as well as the ability to import directly from a spreadsheet. One important change is that users will need to provide a column header when copy pasting in csv formatted data. Alternatively, users can manually specify which column maps to which base sequences.

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.

Mixture instructions

Users can now include preparation instructions for their mixtures and insert them into Notebook entries. The instructions can be set when creating a mixture from a mixture schema in the “Media Recipe Instructions” section on the creation page. A prep of that recipe can then be made by clicking the “insert” button to add the instructions to the Notebook entry. Contact support@benchling.com to enable this feature for your team.

Admin access to import spreadsheet templates

Customer admins can now download spreadsheet templates to import legacy data from the Registry.

Schemas

Blob links on Registry entities

Users can now configure Registry entity schemas to include “Blob link” types. This enables users to add in images to the metadata of their Registry entities.

Blob links preview

Blob links for entities will now render a file preview in the Registry.

Change Warehouse names for Registry schemas

Admins can now edit the warehouse names for Registry schemas in the Registry settings. Contact support@benchling.com to enable this feature for your team.

Computed field min/max values

Minimum and maximum values can now be hoisted in a computed field over results. Contact support@benchling.com to enable this feature for your team.

Insights

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

Registry embedded dashboards

Benchling now enables users to configure Registry schemas to include Insights dashboards. A new tab “Dashboard” will appear in the Registry entity view so that users can directly see related dashboards in the context of the Registry entity. Contact support@benchling.com to enable this feature for your team.

Block templates

Insights dashboards are now embedded into Registry which allows users to configure Registry schemas linked with specific dashboards. The user can directly run a SQL query in the query editor, or they can use potential templates to “quickstart” their query. When a user clicks on one of the templates, they will be asked to fill out a form indicating what data they need. Contact support@benchling.com to enable this feature for your team.

Download CSV with chips

Users can now use the “Download as CSV” option to download their query results as a CSV file.

Single entity filter

Within the “Block template” feature, there is now the subfeature “filters” which allows users to filter the template by entity type. If you are interested in learning more about Benchling's Insights tool and SQL, please review our SQL Training Series. Contact support@benchling.com to enable this feature for your team.

Lab Automation

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

ADD_COLUMN supports multi-value lookups

Users can now use the ADD_COLUMN to lookup more than one value, which originally supported only returning a single value in a given column. A multi-entity link can now generate a new column in the output file with each value of the field in a separate row (Ex: If the field contains Entity A and Entity B, the new column will contain rows “Entity A” and “Entity B”).

Input file lookup FILTER supports various filter types

In addition to the previous filter types of entity, container or plate, the FILTER lookup now has an additional parameter which can identify a range of values using these filter types: <, <=, >, >=, “is null”, and “not null”.

REPLICATES lookup step applied outside of the source

Previously, when configuring the JSON for Lab Automation, a list of CONSTANTS was required. The REPLICATES lookup step now returns the number of replicates for the previous object. This step repeats a value in the list a specific number of times based on what is configured in the JSON. In the table below, the Destination Plate value is repeated 4 times based on the set configuration.

Application Platform

Benchling's Application Platform helps provide a unified experience for our users and makes it easy to work across the Benchling applications seamlessly.

Remove avatar

Users can now remove their avatar in the bottom left corner of the Benchling platform.

“Open in new tab” option

Workspace tabs now support an option to “Open in new tab” in the menu that appears upon right clicking on the entity tab.

Sorting filters

Project listings can now be sorted by ID, name, date modified, and created.

Notebook entries status

The Notebook entries list now has a column called “Status” which depicts the review status of the Notebook entries in the list.

Refresh page maintains last opened side panel

Previously, when a user refreshed the page, the side panel returned to home. Now, upon refreshing the page, Benchling will display the previously opened side panel.

“Starts with” filter added for names

Users can now use the search filter “starts with” in order to narrow down names that begin with a certain character or set of characters.

Last name search function

Users can now be searched by their last name in addition to their first name and username.

“Results per page” option for users tab in tenant admin console

“Results per page” option has been added to the options to sort in the users tab of the tenant admin console.

“Create organization” button in tenant admin console

Users can now use the “Create Organization” button 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.

Added “NameIncludes” filter on storage list endpoints

When searching for a list of containers in the API, the “nameIncludes” filter can be used to parse through any results that contain the substring in the name. For example, for a container named “Cryovial Tube”, inputting “Cryovial” in the search will output any container with “Cryovial” in the name. This expands upon the previous search capabilities associated with the “name” filter that required the exact name of the container to return results. Learn more about this filter here.

Event bus expiration status added to Events UI

Previously, AWS would delete an event bus if it was not added to an AWS account within 2 weeks of having the event subscription in Benchling. The status of events subscriptions is now shown in the Events UI, giving users the option to re-subscribe to events or delete them altogether.

Additional Barcodes filter on searching storage

When searching for containers using the API, the barcodes filter allows you to filter by a list of container barcodes as opposed to a single barcode. In addition, the query returns the containers that match the specified barcodes or gives an error message with a list of the barcodes that are invalid. Read more about this filter here.

New filter operator

There is a new filter operator “anyOf” on the “entityRegistryId” filter for entity LIST endpoints. Previously, when searching for a list of entities by their Registry IDs using “entityRegistryId”, the BulkGet registered entities endpoint would result in an error if not all Registry IDs were found. The “anyOf” filter operator allows users to search for entities using a list of Registry IDs, and returns the entities that match.

Filtering by “assayRunId”

Users can now use the “assayRunId” filter on container endpoints to narrow down runs by their associated API.

Filtering by ID

This allows filtering by id on results and runs listing endpoints.

Bug Fixes

The following bugs were fixed in this release.

Notebook

• Previously, users were able to add incorrect entities to a Result through “Add Samples” with no validation error. Now users are notified to remove an entity from the table once the sample has been added.

• Previously, entries failed to save when copying batches and pasting them into Registration tables from the Request Input table. However, now Batches can be pasted with chips into the Registration tables.

• A fix has been rolled out to prevent entries from crashing when a user tries to access the entry without access to a Result schema used within it.

• Previously, some container schemas were not appearing in the “Transfer Table Insertion” modal. A fix has been released to rectify this error.

Insights

• Insights dashboards with many chips no longer crash the browser.

Lab Automation

• The FILTER LookupStep now validates values for dropdown schema fields.

• Previously, upon using a lab automation run to try and link to an entity whose name is duplicated in another org or Registry within a multi-org tenant, the link would fail silently and need manual correction. Now, duplicated entity names notify the user when processing output files.

• Now, there is improved error messaging when processing invalid CSV output file types to provide more detail on why the output is failing.

• Archived runs can now be unarchived via the UI.

• Bug fixed where plate filtering was not performing expectedly.

• Bug fixed where looking up multiple field values for “entitySchemaInfo” was not performing expectedly.

Application Platform

• The “Re-import AA Sequences” option has been re-added into the “Create” menu options.

Developer Platform

• Missing support has been added for entityRegistryId field to Post endpoint when creating oligos in the Registry.