Welcome to the fifth 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 April 2022.

Molecular Biology

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

DNA sequence bases available in the warehouse

When querying sequences in the Warehouse, users can now return bases for DNA oligos and DNA sequences alongside Registry metadata, enabling more powerful analysis.

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.

Inventory tables

Users can now use the new Inventory table in notebooks for performing common inventory actions on pre-existing containers and plates, like archiving containers or plates and changing the quantity of existing containers and plate wells.

To request this feature, please contact a Benchling representative.

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Support project selection in the “Set from matrix plate” flow

Users can now choose a project location for containers created in the Set from matrix scanner creation flow.

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Viewing box names and coordinates when printing, instead of the box name and index label

A new variable keyword for label templates called benchling.container.location_with_coordinates is available. When a container is in a box or matrix plate, benchling.container.location_with_coordinates prints <Box Name><XY Coordinate> (e.g., My box: B2) instead of <Box Name><Numeric index> (e.g., My box: 12).

Worm and human icons added to registry entity icons

Users will now see the worm (🐛) and human (🚶) icons in the registry entity icons list.

Error messages for uncontainable entities

If a registry schema is not marked as containable, entities in that schema can not be put into containers. An error now displays when placing an uncontainable entity in a container.

Schemas

Schemas are the structural foundation for how your information is categorized in Benchling. They are categories created specifically for your tenant that can represent materials, data, storage methods, and tasks.

Set precision for floats and computed fields

Users can now select precision for float fields and computed fields.

Context displays when drop-down menu cannot be archived

Users can now view which schema fields are preventing a drop-down menu from being archived, instead of “Cannot archive a dropdown that is in use in non-archived fields”.

Multiply with exponents can now return empty rather than failing

The Multiply with exponents computed field formula can now optionally return an empty value when one of the inputs is missing instead of failing to compute.

Aggregate text computed field formulas support additional arguments

The aggregate text computed field formulas now support up to 15 arguments.

Insights

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

Pie chart visualization

Users can now configure a new pie chart visualization type in Insights to display relative ratios of numerical data.

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Renamed Point aggregation to Aggregation

Point aggregation section in the scatter plot settings has been renamed to Aggregation.

Legend item bar and line charts limit

Bar charts and line charts are now limited to rendering no more than 100 different series or legend items.

Scatter plots

Users can now disable legends on scatter plots.

Lab Automation

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

Smart column mapping for file upload

The column configurator will attempt to infer column types based on column names when defining column names through the Output File Config UI from an external file.

To request this feature, please contact a Benchling representative.

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.

API registration errors identify the original/canonical entity

Error messages that display when registering a newly created or existing duplicate entity will include the name and registry ID of the duplicate entity. The error message also displays in the UI.

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SDK Release v1.3

New release of our SDK includes:

  • Re-raise exceptions thrown by a transaction_manger, such as assay_results.transaction_manager()

  • Relax pinning on typing-extensions

  • Relax pinning on httpx

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 Create workflow tasks shortcut button in lookup tables

Users can now create workflow tasks in lookup tables using the new Create workflow tasks shortcut button.

Per-schema output table name in the warehouse changed from <taskSchemaName>_2 to <taskSchemaName>_output

To improve discoverability, newly created per-schema output table name in the warehouse has been changed from <taskSchemaName>_2 to <taskSchemaName>_output.

Tasks and output schemas now required to have at least one field

Users must now include at least one field to all tasks and output schemas.

Bug Fixes

The following bugs were fixed in this release:

Notebook:

  • Modifying entry schema fields are now updating entry.modified_at in the warehouse

Molecular Biology

  • Benchling now automatically reloads when a sequence is edited by multiple users or in multiple browser tabs to prevent edits on older versions of a sequence

Insights

  • API IDs on pie charts were not displaying the object’s name correctly

  • Tick labels were rotating by 90 degrees in a single column heatmap

Schemas

  • Computed field values now correctly compute and appear via Search within a few minutes. Failure errors no longer display when search indexing fails.

Lab Automation

  • Fixed bug for transform steps for large Lab Auto output files

  • When a user clicks the "Processing" button for an output file that's still processing and the file isn't being processed with chunks, a progress bar doesn’t display

  • Couldn’t expand run output tables more than 500 rows

  • Lab automation input files were generating timing out

Workflows

  • The output table Open in dashboard shortcut now populates the schema type to enable the use of search filters

  • Incorrect schema prefixes were displaying in the warehouse

  • Outputs tables more comprehensively prevent attempted submission with errors

  • Removed the Edit button from the flowchart output table

  • Fixed issue with “snaking” flowcharts

  • Final node in flowcharts without outputs displayed as an oval

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