Welcome to the tenth 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 October 2021.

Notebook

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

Page numbers for entry exports

When using enhanced exports, users can now see comprehensive page numbers on every page in the .pdf. Previously, page numbers were only added for the entry contents and not for appended data, such as attached files or metadata.

Clarified timestamps on entry exports

Users can now view the following timestamps at the beginning of entry exports:

  • Entry Created On

  • Entry Last Modified

  • Export Generated On

Review comments are now viewable in an exported PDF’s review history

Any comments made during a Notebook entry review now populate in a new comments column in the Review History table of exported PDFs.

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Molecular Biology

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

Modified oligos can be updated via CSV using HELM or IDT syntax

Users can now update modified oligo entities using a CSV with HELM or IDT syntax. Previously, modified oligo entities could only be updated using natural bases.

Annotation metadata from Geneious files populates in annotation notes

When importing a Geneious file, users can now view any additional annotation metadata in the annotation notes field. Previously, users could only import an annotation’s name and type into Benchling.

Custom monomer colors

In the monomer library, Registry admins can now customize the colors of non-natural monomers. Visual customizations apply to the entire tenant and its members.

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Registry and Inventory

Registry and Inventory combine to form an extremely powerful solution for life sciences R&D samples. Registry can be used to model and log any biological entities while Inventory provides an interactive digital window into the physical storage system of your lab.

Open images in tabs

Users can now click on images in Registry schema fields, Result fields, and Insights to expand and view them in separate tabs. Previously, users could only view image previews.

Support for mol, μg, and kg units of measure for mixture ingredients

Users can now use moles per quantity (e.g., mol/L), micrograms per quantity, and kilograms per quantity as units for mixture ingredients. Additionally, users can specify mixture ingredient amounts as per microgram (e.g., 0.1 μL/μg).

Improved drop-down menu for all schema field editors

Users can now define schema fields through drop-down menus for different schema types. For example, hover over Number to view the options Integer and Decimal in a sub-menu. Additionally, “Floating point” is now Decimal, and “Blob link” is now Attachment.

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Relevant items redesign

Users can now view an entity’s relevant Items in a separate tab, and search and sort relevant items.

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Lab Automation

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

Audit log changes for processing output files

The audit log field “Error files” has now been renamed to “Additional files”.

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.

Python SDK for the Developer Platform

Developers can now interact with Benchling APIs and develop on the Benchling platform using Benchling’s Python Software Development Kit (SDK). The Benchling Python SDK streamlines API calls to Benchling to accelerate development timelines. Using the SDK package and API key, developers can initiate API calls and integrate other systems. Benchling handles the details of connecting, error handling, pagination, and re-entries. Previously, developers using Python had to write these complex interactions using standard libraries.

Get started with the Python SDK.

A modified_at filter available on new endpoints

With the addition of the modified_at filter to the listing APIs of entity schemas, automation output processors, and registries, users can now find recently updated items to enable integration use cases.

Handle filter added for ‘Users’ API endpoint

Developers can now filter users by an array of handles on the “Users” API endpoint.

Policy statements added to Permissions API

Users can now view policy statements in the access policy and schema access policy APIs. These statements describe the access provided by a given access policy.

Entry templates available in the API

Users can now use the API to retrieve entry templates' metadata. Note that it does not retrieve template contents.

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Box contents in the API

Users can now use the API to retrieve a specific box’s contents, including concentration and volume. Box contents were previously retrieved by searching for entities with that box as the parentStorageId.

Request fulfillments modified_at filter

Users can now filter request fulfillments by the time they were last modified. Previously, users were unable to retrieve recently modified request fulfillments.

Entry schemas modified_at filter

Users can now filter entry schemas by the time they were last modified. Previously, users were unable to retrieve recently modified entry schemas.

Worklist APIs added

Worklists have all CRUD (create, read, update, delete) API operations available, allowing developer platform users to manage worklists through the API.

This API is currently under development and accepting customer feedback.

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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

Task groups added

With Workflows, users can define a task schema representing a job to do, such as an assay, a sample management request, or a lab automation queue. The task schema configures tasks, execution formats, and outputs.

Users can now add one or more tasks of the same schema to a task group directly from the global create menu, the Workflows dashboard, or a structured table. Each task is directly assigned and scheduled, has a unique status, and can be executed independently. Users can also create outputs for each task — via a Notebook entry or the API — that represent the outcome or transformation of the task.

Bug Fixes

The following bugs were fixed in this release:

Notebook

  • Re-enabled column locking for legacy Result tables

Users can no longer:

  • Rename locked columns

  • Add or delete columns in structured tables of fill-in entries

  • Delete plain tables in fill-in entries

Molecular Biology

  • Detaching all primers on an unfinalized Gibson assembly no longer causes crashing

  • Attempting to trim an alignment in quick succession no longer generates an error message

Registry & Inventory

  • Weekly Registry validation script no longer fails for large registries

  • Modified_at date is no longer affected by changes to validation status

Developer Platform

  • Plates endpoints now enforce container permissions

  • EntityType is no longer incorrectly included in some endpoints

  • Updating schemas with many fields no longer causes API errors

  • Entries no longer return #name! in parts of the notes field when there is a valid name present. This occurred when using the GET/entries endpoint.

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