Notebook

Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples. As part of this release, we made working with structured data even easier by expanding transfer table functionality, improving access to your favorite templates, and adding more options to registration tables in the Benchling Notebook.

New transfer tables have a streamlined UI and more intuitive functionality

New transfer tables have a tabbed interface to either create new containers or use existing containers. The columns of the transfer table have also been updated to be more descriptive. Finally, users can easily add rows by dragging and dropping the bottom of the table. All of these updates are designed to improve the ease of use while working with transfer tables. Read more about the new transfer tables in this updated help article.

Star entry templates

Star entry templates from the “Create Entry from Template” dropdown menu to favorite frequently used templates. This pins the starred templates to the top of the templates drop down list making it easy to access these templates quickly.

Add 'Entity Name' column to registration table where name template is configured

Applicable for entity schemas that use the Registry ID as a display label and have naming options configured to “Replace name with Reg ID” or “Replace name according to template”: users have the option to add a read-only entity name column. Add this column for registration table exports, as needed.

Molecular Biology

Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows. As part of this release, we added significant new features to our codon optimization tool which enables you to use the tool for bulk actions and also easily track all changes made to the sequences.

Bulk codon optimization

[Academic] This new feature allows users to bulk codon optimize sequences from the expanded toolbar view. When coupled with bulk back translation, this option allows users to take an amino acid sequence and create the corresponding DNA sequences from within Benchling in bulk. Please contact support@benchling.com to enable.

Codon optimization parameters save to the sequence description tab

[Academic] Refer to the description tab of a sequence to view the codon optimization parameters and history. This makes it easy to trace all changes made by the codon optimization tool.

“Copy to” button feature for AA sequences

[Academic] Amino acid sequences now have the option to “Copy to” a user’s clipboard, similar to the existing feature for DNA sequences. This makes it easy to copy and paste AA sequences for use in other applications such as Word or PowerPoint.

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. As part of the updates, we expanded API functionality while working with boxes and added new units to mixtures and containers.

Surface capacity of boxes via the API

Users are now able to surface the number of positions of a box that do not contain existing containers within Benchling via the API. This will allow users to better understand their lab’s inventory from an API perspective. Please see our API documentation for more information: https://docs.benchling.com/reference#list-boxes.

“QS” now a supported value for solvents in mixtures

Users can specify QS (“quantum satis” meaning “enough” or “quantum sufficit” meaning “a sufficient quantity” in Latin) as a valid value for target amount in mixtures tables. This indicates that enough solvent should be added to reach the total desired quantity. This option enables a variety of media and formulation use cases, where QS is used often while preparing samples.

New concentration units for containers

CFU/g, CFU/kg, and (x10^6) cells/mL are now supported concentration units for containers. Select CFU/g and CFU/kg as concentration units for containers with solid media. For cell culture applications, select (x10^6) cells/mL. These units enable microbiology use cases to estimate the number of viable bacteria or fungal cells in a sample.

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 in the platform. With the latest releases, users now have more options to sort through their data and map an even larger set of entity relationships with dynamic warehouse diagrams.

Insights tables support sorting by column

Users can now sort their Insights tables by column. This can be achieved by selecting a column header and sorting the table by that column.

Parameter added to sort by storage type

Within Insights, users can now add additional storage-type parameters. Users have the option to specify storage-type parameters based on schema, such as containers, boxes, plates, and locations.

Dynamic warehouse diagrams support additional relationships

Dynamic warehouse diagrams now support the relationships as listed below:

  1. container_content
  2. container_transfer
  3. request_assignee
  4. request_fulfillment
  5. request_sample
  6. entity
  7. workflow
  8. stage_run_sample
  9. stage_run
  10. workflow
  11. field

Lab Automation

Benchling for Lab Automation enables seamless integration of Benchling with liquid handlers, plate readers, imaging instruments, and more. We released several new features which make Lab Automation even more user friendly and intuitive to use.

Sort by columns now supports alphanumeric order of well positions (i.e. A10 after A9)

Sorting by well position using sortColumns now leads to:

A1

A2

A9

A10

Previously, sorting by well position led to:

A1

A10

A11

A12

A2

A2

New plate layout workflow supports interleaving 96-well plate to 384-well plate

Users can now configure Lab Automation runs to interleave four source plates onto one destination plate. This update will maintain empty source wells.

Results can now be uploaded with blank primary sample via Lab Automation

Results with blank primary sample values can now be uploaded through a Lab Automation run. This can be configured when the result schema does not require a primary sample.

REGISTRY_ID lookup step to return an entity’s registry ID

A new lookup step has been added to allow users to be able to return an entity’s registry ID in a Lab Automation run.

BOX_CONTAINERS lookup step to return containers within a box

A new lookup step has been added to allow users to be able to return containers that exist within a box.

Run output table supports “create request” shortcut for entities and containers

Create a Request on entities or containers directly from a run output table using the “create request” shortcut.

“SPLIT” processing step to separate a combined value from a single cell into two columns by a delimiter

Use a processing step with the new “SPLIT” function when processing output files. This allows users to specify leading and trailing whitespaces as well as the delimiter/space index. This is useful for processing output files from instruments that append index/well position to the Sample ID column.

Ignore rows and columns in Wells LookupSteps

For use cases where edge columns/rows on plates are ignored due to edge effects or control conditions, users can use two new arguments in the Wells LookupSteps: “rowsToIgnore” and “columnsToIgnore”. Read more about these arguments in the [External] Lab Automation: configuration how-to guide.

Application Platform

Benchling application platform helps provide an unified experience for our users and makes it easy to work across the Benchling applications seamlessly. We made a couple of enhancements to the application platform by improving search performance and adding the ability to view full folder names.

DNA sequence search performance significantly improved

Increased performance of DNA string and reverse complement base searches. This performance improvement allows for a more seamless use of searches with DNA indexes.

Hover over folder selector to view long names

When creating a new entry or viewing the information of an existing entry, hover over the folder selector to view long names.

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. As part of this release, we added several filters across our Listing endpoints and added a new API to enable the bulk creation of Request tasks.

SchemaId filter added to experimental /search-bases endpoint

An update to an existing API endpoint has been added to allow users to filter by SchemaId for the experimental /search-bases endpoint. Please see our API documentation for more information: https://docs.benchling.com/reference#sequences

New API ids filters for List endpoints

Use ‘ids’ filters to return a comma separated list of ids from all List endpoints. This allows users to migrate away from Bulk-Get endpoints towards List endpoints, which are more in line with traditional RestAPI conventions. Read more about this feature at docs.benchling.com.

New API barcodes filters for storage List endpoints

Use ‘barcodes’ filters to return a comma-separated list of storage barcodes from all List endpoints. Similar to the ‘ids’ filter, this allows API users to utilize List endpoints instead of Bulk-Get endpoints. Read more about this feature at docs.benchling.com.

Create Request tasks in bulk via the API

Use the new Bulk create Request Tasks endpoint to create Request tasks in bulk via the API. Read more on this endpoint at: https://docs.benchling.com/reference#bulk-create-requests

Bug Fixes

The following bugs were fixed in this release:

Insights

  • Set a limit of 500 chips per a table, to prevent slow loading of tables

Lab Automation

  • Request templates no longer enforce values for required request schema fields

Application Platform

  • “Full Screen” button now allows you to click on the icon directly

Requests

  • Exporting requests to a CSV will now include both the “Requestor” and “Creator” columns

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