Welcome to the eleventh volume of our 2021 product release notes! We have 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 November 2021.

Notebook

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

Lookup columns and tables

Using new lookup columns and tables, teams can input live data from Registry schemas, Inventory containers, and results tables into the Notebook in a read-only format. Previously, customers used a variety of workarounds that involved legacy result tables with Lookup Fields, Registration tables, or Insights.

To enable this feature, contact your Benchling representative or Benchling customer support.

New Results table

Use new results tables to manage, submit, and archive results in the Notebook. With these tables, users can now:

  • Add rows from other structured tables, worklists, or spreadsheets

  • Archive results

  • Reference the sample ID column using formulas

  • Use the drag function to add rows in both Notebook entries and templates

  • Utilize the DisplayName in the result schema JSON to rename SampleID

  • View cell validation status when submitting results tables

These new results tables functionally resemble registration and transfer tables for a consistent user experience across Benchling’s structured tables. Additionally, users can utilize new features, such as lookup columns, in these structured tables.

To enable this feature, contact your Benchling representative or Benchling customer support.

Upload from spreadsheet for plate creation tables

Users can now upload previously formatted plates via spreadsheet into plate creation tables.

Molecular Biology

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

Protein data bank files (.pdb) attached in Notebook entries can be viewed using MolStar (Mol*)

Users can now upload and preview .pdb files in notebook entries. Opening a .pdb file in a new tab will run MolStar, rendering the protein structure and allowing users to orient the protein in various ways.

To enable this feature, contact your Benchling representative or Benchling customer support.

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Support for populating modified bases of an existing oligo

Users can now update the modified bases of a registered oligonucleotide using HELM or IDT notation via CSV. Previously, updates to sequences and oligos were made using natural bases.

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 log biological entities while the Inventory provides an interactive digital window into your lab’s storage system.

Box and plate page improvements

Users can now expand the table view on box and plate pages, displaying the contained entity’s field values.

To enable this feature, contact your Benchling representative or Benchling customer support.

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Multi-key sort for worklists

To further tailor data organization to unique analysis needs, users can now sort multiple worklist columns at once via Sorting.

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Schema-level permissions for entities

With schema access policies, users with appropriate permissions can now control:

  • Which entity schemas display in filters and dropdown menus in the product

  • Who can create objects under specific schemas

  • Who can edit the schema definition and manage collaborators on the schema

These access policies work in conjunction with registry and project permissions to provide specific control over the information users have access to.

To enable this feature, contact your Benchling representative or Benchling customer support.

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View results for child entities on the parent entity’s Results tab

Users can now view any results recorded against a child entity in the Results tab of its parent entity.

To enable this feature, contact your Benchling representative or Benchling customer support.

Schemas

Schemas are the structural foundation for how your information is categorized in Benchling. They provide the framework to track and manage relationships between entities, how they are used, where they are stored, and results collected against them.

Computed fields for results

With computed fields for results, admins can configure Benchling to capture results and sample metadata at that point in time, enabling scientists to view and query information in context with the experiments, workflows, and samples used.

To enable this feature, contact your Benchling representative or Benchling customer support.

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New “Any entity” type option for entity link fields

When configuring a schema, users can now define entity links by Any entity so fields will no longer be restricted to a specific entity schema.

To enable this feature, contact your Benchling representative or Benchling customer support.

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.

Benchling apps

Using Benchling apps, developers and admins can develop, define, identify, manage, and permit application integrations independent of an individual developer’s credentials. Benchling apps improve how teams experience long-term data sharing between Benchling and other essential applications or instruments.

PUT endpoint for custom entities

Developers can now use the PUT endpoint to directly look up an individual entity. Previously, users had to call the list endpoint, then call “create” (POST) or “update” (PATCH) to search for an existing entity.

Stage entries from legacy workflows can be exported via the API

Developers can now use the /api/v2/exports endpoint to export stage entries.

Ownership added to worklist collaborations

Developers can now use the /worklists/{worklist_id}/collaborations endpoint to return information regarding collaborations on specified worklists.

SDK supports ids and names filters for Projects Service

Developers can now filter by IDs and names in Benchling’s Python Software Development Kit (SDK).

SDK support for mixtures

Benchling’s Python SDK now has a mixtures service to support API operations with mixtures.

Bulk Upsert on custom entities

Developers can now use the Bulk Upsert (PUT) endpoint to bulk create and update multiple entities at once. Previously, users had to call the list endpoint, then call “create” (POST) or “update” (PATCH) to find and create/update entities.

Role filtering for Users API

Developers can now apply the /users API endpoint to filter users by organizations in which they have an admin or user role.

Workflows

Workflows is a process management tool for standardizing request fulfillment, managing assay and task requests between teams, and connecting processes in your R&D pipeline. Please note that these updates only pertain to new Workflows; Legacy Workflows will not be updated unless specifically noted.

Configure default creation and execution project folders on the task schema

Users can now configure default project folders when creating task groups and execution entries.

Warehouse tables created and populated

Users can now access Workflows data through the warehouse.

Outputs creation is limited to when the task is in progress

Users are now limited to creating outputs for tasks in progress to prevent the appendage of outputs to completed tasks.

Preview snapshot fields in the tasks and outputs tables before submission

Users can now view snapshot fields before submitting a task and/or output table.

@mention tasks and outputs by ID and create relevant items on the task group

Users can now @mention tasks and outputs by ID in a Notebook entry. These references populate in the relevant items section of a task group.

Relevant items now created for entities and entries used in task and output schema

When a user associates an entry or entity with either a task or output, the tasks and outputs now populate in the relevant items section of entries and entities.

New confirmation message displays when transitioning a task to a terminal status

A confirmation message now displays in a pop-up window when updating a task’s status to Cancelled, Completed, or Failed.

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Lookup step filter limits lookup results to those created on the task’s execution entry

Lookup step filters now limit users to exclusively lookup results relevant to a task’s execution entry rather than all results.

Workflow task and output schemas can be migrated using config migration

Users can now migrate workflow tasks and output schemas using config migration.

Task group status summary now listed in lifecycle order instead of alphabetical

Task group status is now displayed in order of lifecycle. Previously, task group status was displayed in alphabetical order.

Updates in EventBridge events

The following updates have been made to EventBridge events:

  • Entries created in EventBridge events now include legacy workflow stage entries.

  • Users can now view updated output schema fields.

  • The updated task and output schema fields now include snapshot fields.

  • When an entry’s review status is changed, an update displays as a legacy workflow stage entry.

Bug Fixes

The following bugs were fixed in this release:

Notebook

  • In modifiable entries, users can no longer rename a locked column in a plain table

  • Cell formatting (color, highlight, scientific notation, etc.) is no longer lost after submitting a structured table

  • In PDF exports, wide tables were scaling incorrectly, sometimes causing overlapping text

Registry & Inventory

  • Location picker no longer lags for tenants with many locations

Workflows

  • Data is no longer propagating from the task table to the legacy result table using Add samples

  • Archived schemas are no longer included in the Create workflow task shortcut from structured tables

  • Snapshot fields that return multiple primitive values no longer crash

Application Platform

  • Previous admins can no longer leave an organization

Developer Platform

  • Preservation of Results order for Results uploaded in the API

  • Decimal values previously displayed as 12 digits in the UI, but stored as 15 digits. They now display the full 15 digits

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