Welcome to the fourth 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.

Notebook

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

Must archive submitted results tables prior to removal

Users must now archive submitted results tables before removing them.

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Lookup tables support containers

Users can now create lookup tables with containers as well as entities.

Option to set a new template to fill-in only now available within the “Create template” modal

The template editor now has an option to create fill-in templates. Users can now check a box to create fill-in only templates.

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Text boxes available for fill-in templates

Users can now insert text boxes into fill-in templates, allowing template users to @-mention and type directly in fill-in templates.

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

Molecular Biology

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

Extended homology detection limits for Bulk Assembly

Users can now detect homology when cloning with our Bulk Assembly tool by searching for particular region lengths from a dropdown list.

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Waitlist for protein structure predictions using AlphaFold

Users can now join the waitlist to gain beta access to protein structure prediction using AlphaFold 2. This beta feature enables users to predict the structure of a given protein sequence and interact with that 3D structure directly in Benchling. This beta feature was released on April 12th. 2022.

To join the waitlist, navigate to any AA Sequence in Benchling and open the 3D Structure tab. Select Join the waitlist, and you’ll be prompted to fill out a short form with your role, field, and expected use case. This form helps us better understand how you want use this feature and the value it might provide to you. To complete signing up for the waitlist, submit the form by selecting Join the waitlist a second time.

Note: if you are using our academic offering, your account must be associated with a verified email address from our current list of academic institutions.

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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.

Hoist fields can now correct hoist attachments

Any result fields that are hoisted now include hoisted attachments.

Insights

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

Regression model parameter settings

For scatter plots that have a 4-parameter logistic regression line, the parameters of the regression model can now be constrained or initialized.

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Lab Automation

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

Create options for run schemas

Lab Auto schemas can now be configured to allow for all runs to default to being created through inbox, through the Notebook, or both options. This allows users to choose how they would like to configure Lab Auto schemas, and limits the chance for error by the end user.

Lab Automation Config UI

Users can now configure Lab Automation with a new user-friendly interface and no longer need to code or use JSON.

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Automatic status refresh and indication

Users can now view current status updates and indications on output files every 60 seconds.

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Access Management

Access Management provides users a way to manage permissions, leverage administrator capabilities, and organize teams, organizations, projects, and folders.

Permissions Clarity

Permissions Clarity is a new user-based permission’s view that includes a centralized and holistic view of a user’s access to Projects and Registries in Benchling. Admins can now navigate to the user view from any of the admin consoles (Tenant, Organization, or Team) and see members’ basic setting information and their permissions on these major data types. Users can view a user’s Project and Registry permissions.

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

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 support for bulk updating AA sequences

The endpoint AaSequencesBulkUpdateRequest has been added for bulk updating AA sequences.

API support for feature libraries

The following new API endpoints allow users to manage their own feature databases into Benchling and allows for more reliable auto-annotating:

  • POST /feature-libraries

  • GET /feature-libraries/{feature_library_id}

  • PATCH /feature-libraries/{feature_library_id}

  • GET /features

  • POST /features

  • POST /features:bulk-create

  • GET /features/{feature_id}

  • PATCH /features/{feature_id}

  • POST​/features:bulk-create

Developer changelog

Developer-related updates are now captured and documented in a dedicated changelog hosted alongside our developer documentation.

Registration conflicts return registry ID of conflicting record

Users experiencing error messages in the API will now see the associated Registry ID. Previously, there was limited data on what entities were associated with the error.

Workflows

Workflows are a sequence of 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.

Tasks appear in the calendar by “scheduled on” date for assignees and for watchers

Tasks can now display on the calendar view by the date the task is scheduled. This viewing option is available for tasks, assignees, and watchers.

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Legacy workflows no longer displays the “batches” option for input samples

The “batches” option no longer displays as an option for input samples for users who have batches disabled on their tenant.

Workflow options configuration

Task, task group, and output prefixes can now be updated on the configuration page, which allows users to manage their tasks.

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Bug Fixes

The following bugs were fixed in this release:

Notebook:

  • When cloning entries, all version history will now display the initial clone date.

  • Password-protected files now prompt a message to indicate they are not included in exported entries

Workflows

  • Using the “open in dashboard” shortcut from the task table is no longer overridden by a previously opened saved search

  • Archiving a project folder containing a task group now correctly archives the task group

  • Tasks can no longer be cloned if their schema is archived

Molecular Biology

  • Resolved issue with Lab Automation runs being stuck in a processing state

  • User can’t set column mapping in new Output Config UI

  • The link to the Primer3 manual on the Primer Wizard tool that previously returned a 404 error has been resolved

  • Users can now view a user’s name on the DNA sequence history tab. Previously, users were only able to view the handle of the user

Access Management

  • Teams must now be enabled for teams to be configured within tenants.

Developer Platform

  • “Modified At” was not receiving updates when an entity was unregistered

  • Error messages in the API now display the associated registry ID. Previously, there was limited data on what entities were associated with the error.

  • When any field in an entry schema associated with an entry is updated, the update is now tracked in the entry or entry schema warehouse field modified_at. Users can now identify updates to an entry and sync updates to the warehouse using modified_at from entry warehouse schema.

Lab Automation

  • Bug fix for new Output File Config UI

  • Bug fix for Lab Auto API stats

  • FIND_REPLACE transform for files with duplicate column names was silently doing a no-op

  • No longer crashes when someone uses the wrong syntax for an ARITHMETIC transform configuration

  • Storage project selector in Output File Config UI now allows users to save their selection

  • Allow going back to no selection after selection in folder/project/location selectors in Output File Config UI

  • No longer crashes when setting the name of a schema field column in the Output File Config UI

  • Properly update the column mapping modal in the Output File Config UI when user goes back and changes the entity/storage/result schemas after setting the columns

  • Design polish for Output File Config UI

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