Welcome to the seventh volume of our 2021 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 2021.

Molecular Biology

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

Support for chemically modified nucleotides for RNA and DNA oligo entities

Users can now model DNA and RNA oligo entities with chemical modifications on nucleotides, based on the HELM-monomer system.. Users can define a set of usable monomers in their monomer library, batch import HELM- or IDT-based modified oligos, view modified oligos in a sequence map format, and introduce edits to tweak their oligos.

Contact support@benchling.com to enable this feature. To learn more about Benchling’s integrated functionalities for RNA therapeutics, visit our blog.

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Multi-row monomer editing in the nucleotide tab

When modifying an oligo, users can now select multiple monomer rows in the nucleotide tab to bulk edit nucleotides.

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Computed field for instability index

Users can now pull the Instability index from the Amino Acid Biochemical Properties tab onto their computed fields. To learn more about computed fields, visit Configure Computed Fields.

Copy/pasting chemically modified nucleotides will paste the modified sequence

When copying and pasting chemically modified nucleotide sequences, the modified sequence is now pasted instead of the natural sequence.

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Visual cue on sequence map when editing monomers

When editing monomers, the edited nucleotide is now highlighted in orange on the sequence map and nucleotide list.

HELM notation option added to Copy Special

Users can now copy HELM notation for oligos through the Copy Special modal.

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Support for ‘partially specified’ bulk monomer edits

Users can now bulk edit one selected component monomer in the nucleotide table, leaving the others unchanged. Previously, users had to specify all three component monomers to execute an edit.

Schemas

Computed field for subtracting dates

Users can now use computed fields to find the difference between two events reported in days, hours, minutes and seconds.

Insights

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

Linear regressions

Benchling now offers scatter plots as a chart type, with the option to select a linear regression line for one series at a time. Users can view the regression equation and R2 value on the top-right corner of the chart. Contact support@benchling.com to have this feature enabled.

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Lab Automation

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

New “preserve relationships” option when configuring lookup steps

A checkbox now exists on the lookup config modal for Lab Automation runs called Do not preserve relationship between lookup steps. Leaving this unchecked creates a new column that maintains the per-row relationship of the previous lookup steps. Existing lookup steps will not be changed.

New MELT processing step

Users can now use the MELT processing step to unpivot or flatten data in tables so that all similar values are in two columns (variable and value).

New ARITHMETIC processing step

Users can now perform basic arithmetic (+, -, *, /) between two columns, or one column and a constant. Benchling stores the result in a new column using the ARITHMETIC processing step.

Data Warehouse

The Benchling Warehouse is a database solution where you can track and view assay data, registry entities, and sample data using SQL queries.

Tablefunc extension

The tablefunc extension has been added to the data warehouse to enable easier pivoting data transformations.

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Developer Platform

The Benchling 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.

New GET endpoint to list DNA alignments

Benchling now offers a GET endpoint to list DNA alignments. The endpoint includes the Benchling web UI, URL, and datetimes for when the alignment was modified and created.

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SchemaId filter is supported for the DNA search-bases beta endpoint

Users can now narrow a search that uses the search-bases endpoint by specifying a single schema ID. Previously, this would return all the DNA sequences that contain the provided bases. This feature is currently in beta testing.

Filter API results by creatorIDs for listing endpoints

Filter by users when returning API results from a listing endpoint. Specify the user IDs in the creatorIds parameter by entering either a single user ID or a list that is comma separated.

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Bug Fixes

The following bugs were fixed in this release:

Notebook

  • Row heights are now rendered appropriately after certain user actions, such as deleting rows

  • Entities can no longer be registered with only spaces as names

  • Entries no longer crash when users click on improperly formatted URLs

  • @-mentioning users in a structured table now notifies them

  • In transfer tables, selecting Add from worklist no longer allows users to put a non-bioentity worklist into a bioentity cell

  • Table row heights no longer resize incorrectly after deleting rows or entering long LOOKUPFIELD formulas

  • When adding unregistered entities to a registration table via Add from worklist, the entity ID, entity name, and all other fields now populate without a refresh

  • @-Mentioning someone in a structured table now notifies them

Lab Automation

  • Datetime fields are now editable during runs

  • If a run has duplicated DIRECT fields (i.e. two fields that reference the same column in entitySchemaInfo and destinationInfo), we now raise a user-facing error

Application Platform

  • Public profiles for non-academic tenants were automatically enabled

Developer Platform

  • Creating and registering entities via API required a folderId

  • RNA oligos are no longer returned by the DNA oligos endpoint

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