Release Notes: Volume 11, 2022

Meghan Bosch
Meghan Bosch
  • Updated

Welcome to the eleventh 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 October 2022.

Addendum: The Zendesk update was added to the Volume 11 release notes on November 11, 2022, but went into affect October 13, 2022.

Notebook

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

Text box names and data modification support

Users must now enter a text box name when inserting a text box. For customers who have enabled data modifications, change reasons are captured when saving changes as a text box.

To enable this feature, please contact a Benchling representative.

Molecular Biology

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

Visible translations on linear and plasmid maps

Users can now visualize translations on linear and plasmid maps. Previously, users could not visualize CDS features on linear and sequence maps.

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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.

Look up results against a specific storable 

Users can now look up the results of a container in both structured tables and workflow task groups.

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Enabled data mods for Registry General Settings 

Benchling now captures data modifications when editing a Registry’s General Settings, like adding or removing a collaborator.

Access Management

Access management is the way customers control who is able to access which resources, and includes things like project permissions, access policies, and admin roles.

Data mods for changes to project permissions

Users are now prompted to add a reason for the change when editing a collaborator’s access permissions and adding or removing collaborators.

To enable this feature, please contact a Benchling representative.

Audit logs include provisioned capabilities for new users, teams, and organizations

Users can now view the capabilities provisioned to new users, teams, and organizations in audit logs.

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.

Schema instructions

Users can now add instructions to task schemas, including:

  • Communicating deadlines and turnaround time
  • Describing the purpose of schema fields and possible relationships between them
  • Entity and container creation requirements. For example, requiring users to fill containers with 100 mL of an entity
  • Web links to more detailed files or systems

To enable this feature, contact a Benchling representative.

Lab Automation

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

Process All option for Lab Automation runs

Users can now process all uploaded files at once by selecting Process All instead of processing each file individually.

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Update and transfer in single automation output processor

Users can now perform both update and transfer options using a single output file processor. Previously, users needed to upload their file twice to perform updates and transfers. 

Output file Config UI action types use checkboxes 

Users can now select Benchling actions in the Output file Config UI using checkboxes. Previously, users selected them from a drop-down menu.

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Edit any transform in Output File Config UI

Users can now edit any transform step in the Output File Config UI. Previously, only the last transform step was editable. 

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.

Consistent capillary registration labeling strategy 

Users can no longer register existing entities using a labeling strategy that is not selected on the entity schema configuration page. For more information, visit the developer platform change log.

Support for POST and PATCH on Users API moved from /v2-alpha to the /v2-beta endpoint

  • Developers can now use the activity object to view a timestamp of the user’s last login. The timestamp can, for example, inform whether or not to suspend user accounts.
  • Developers can now see when users last changed their password using the passwordLastChangedAt property.

Per-app rate limiting

App client credentials have been moved to individual rate limit pools instead of tenant-wide rate limit pools. Each application now has a clear expectation of the number of calls it can make against the API, independent of the other apps. The rate individual limit for apps is automatically set to 300 requests every 30 seconds. 

App configuration

App developers can now make a list of configuration parameters for admins to complete when installing the app, ensuring that developers can re-use an app across multiple tenants without having to rewrite it. Additionally, admins can update app behaviors, like changing the folder where an app stores data in, without needing an Engineering team to make any code changes. The installation flow for apps has also been improved.

To enable this feature, please contact a Benchling representative.

App activation improvements

We have added the lifecycleManagement property to app manifests. It can have either automatic or manual values. If an app has a manually-managed lifecycle, admins can generate the app’s credentials in the developer console. If an app has an automatically-managed lifecycle, admins can’t generate the app’s credentials in the developer console and they must select Activate in the app workspace.

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Zendesk

Updates to help center access and support ticket creation

In the new Benchling help center, users can now create support tickets by completing a form. Users can no longer message Benchling Support from within the help center.

In the Benchling platform, users can continue to create support tickets using the redesigned in-application messenger and can continue to access the help center through the admin console.

To learn more, visit Using Benchling's new help center.

Bug Fixes

Notebook

  • Saving an entry with an attached protocol with no protocol image no longer fails
  • Updating a template’s name now triggers an audit event
  • When pasting text boxes into templates, additional text no longer displays inside the pasted text box
  • @-mentioning a registered entity within a text box no longer results in a dead link
  • Exporting entries with Request Entry tables no longer times out
  • Pipe character no longer displays in emails notifying users of a review change
  • When using snapshot fields, looking up multiple attachments no longer causes errors

Molecular Biology

  • Benchling no longer loses trace data upon realigning a DNA sequence and reindexing the template
  • Large sequences no longer process slower than usual. This bug was caused by updating the annotations and translations panel on sequences
  • Translation links now invalidate appropriately upon changing the genetic code of the translation and when removing translations using an alternate genetic code
  • Translations are no longer imported and exported as the custom fields of a CDS feature

Registry and Inventory

  • Uniqueness constraints no longer prevent surfacing multiple containers with the same name in a snapshot field

Workflows

  • Execute option no longer displays on archived tasks

Insights

  • The ability to hover over a point no longer disappears when there is a maximum set for the Y-axis range

Search

  • The location of a container’s contents are now returned appropriately

Application Core

  • Notebook entry exports now display the correct locale setting on datetimes

Compliance Controls

  • Changing the column name of a structured table now appears in audit trails
  • Exporting audit logs no longer fails when trying to export entries with deleted structured tables
  • Human readable audits now include updates for schema fields, indicating both the before and after values for a schema field

Lab Automation

  • Users can now set up constant variables in the arithmetic form for the Output file Config UI
  • The melt form for the Output file Config UI now allows for an empty Values Columns field
  • The find/replace Output file Config UI feature now allows for an empty find or replace value
  • Lab Automation runs properly parse .xls files
  • Benchling has improved horizontal scrolling on schema configuration pages

Developer Platform

  • Submitting an empty displayIds filter in the API no longer returns a 500 error instead of the appropriate 400 error
  • Archived apps now appear in search
  • Searching for outdated pages in SDK docs now redirects a user back home rather than returning an error

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