Welcome to the eighth volume of our 2023 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 August and September 2023.
Addendum: The update for merging cells in structured tables [2023.8.N.2] was added to the Volume 8 release notes on October 9, 2023, but went into affect September 8, 2023.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Updated forms drop-down menu [2023.8.N.1]
Users can now access drop-down options in form fields by clicking the arrow at the end of the input box.
Merge cells in structured tables [2023.8.N.2]
Users can now merge cells of the same data type in structured tables, replicating the same value across the range.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
DNA and RNA concatenation [2023.8.MB.1]
Users can now visually and comprehensively join RNA or DNA oligos and sequences end to end, facilitating modular sequence design at scale.
Visual assembly history [2023.8.MB.2]
Users can now view visual representations of assembly histories, enabling quick insights into how a sequence was designed in-silico when constructing via the Assembly Wizard, the combinatorial concatenation, or the combinatorial cloning tool (currently in limited availability).
Additional BLAST algorithms [2023.8.MB.3]
Users can now use three more BLAST algorithms (blastx, tblastx, and tblastn) and configure parameters for all supported algorithms.
Small Molecule
The molecule entity in Registry helps users model and interact with chemical compounds throughout the platform, enabling users to draw, visualize, store, and search chemical structures.
Bulk modify oligos with modification patterns [2023.8.SM.1]
Users can now apply modifications from any existing oligo onto a new set of oligos.
In Vivo
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Skip dosing in a workflow [2023.8.ST.1]
During dosing setup, users now have the option to skip dosing for animals that don’t require treatment during the current session. During their workflow, users are seamlessly directed to the next step, without interruptions on an empty dosing page.
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.
New concentration units available in the inventory [2023.8.RI.1]
Users can now apply these units of measurement in the inventory: GC/mL, umol/g, and cells/vial.
View a grid preview in a pop-up window [2023.8.RI.2]
Users can now hover over a grid object within a structured table and view its available and full positions in a pop-up window.
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.
Flowchart task name displays in root node [2023.8.WF.1]
Users can now view the task schema name in the root node of a flowchart, instead of “Tasks”. Previously, a flowchart task name was only displayed during the configuration of a flowchart template.
Insights
Insights enables users to query, visualize, and share high quality, structured data that resides in Benchling.
Create dataset from Registration, Result, or Lookup tables [2023.8.IN.1]
Users can effortlessly add a dataset to a new or existing analysis from a structured table within a Notebook entry (Registration, Result, Lookup tables).
Lab Automation
Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Allow optional field when configuring column mapping in a Run schema [2023.8.LA.1]
In the column mapping window of a Run schema, users can now choose to select a "Required?" checkbox to define which column(s) in the file can be ignored during output file processing if the column(s) is not present in the file. Previously, the lab automatically assumed that all column(s) in the column mapping window were required field(s) during output file processing.
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.
Updated default settings for idle timeout and session timeout [2023.8.AM.1]
When new tenants are created, the idle timeout is now set to 720 minutes (12 hours) and the session timeout is set to 144 hours (6 days). These values were chosen to balance the need for better security around authentication and the usability of requiring users to sign in more frequently. Existing tenants are not affected. Tenant admins can change these values in the Tenant Admin Console.
Remove space usage meter on Academic tenant [2023.8.AM.2]
The space usage meter has been removed from Academic tenants, so users can no longer view their space usage.
Create users in bulk with a tab-delineated spreadsheet [2023.8.AM.3]
Users can now use tab-separated values in a spreadsheet to create users in bulk in the Tenant Admin Console. Previously, the input for bulk creating users needed to be comma-separated.
Updated capabilities settings [2023.8.AM.4]
When making changes to capabilities, only the updated capabilities are applied to org or team members. Unchanged capabilities are ignored and remain unchanged. Previously, if capabilities were changed on an org or team in capability management then all of the capability settings for that org or team were applied to all members, even if their capabilities weren't changed.
Compliance Controls
With Compliance Controls, gathering required information for compliance is simple, intuitive, and performant. The team’s primary focus is on our auditing platform but we also own exporting and archiving.
Audit log .pdf header improvements [2023.8.CC.1]
Users can now view the following header information in audit log .pdf exports: Object Type of the Audit Log, Exported By User, Exported Date, and Exported Time.
Bug Fixes
The following issues were fixed this month:
Notebook
- Attempting to add an additional attachment to a Registration table resulted in the new attachment replacing the existing attachment
- Inserting a sub-template containing cross table formulas multiple times broke the formulas
- Retracted reviews still displayed in users' To Review inbox.
- Internal links and @-mentions did not display when using Cmd/Ctrl+F to search
Molecular Biology
- Partial translations weren't copied when one sequence was created from another, even when users had declared they wanted to preserve those partial translations
- An unclear error was provided if a circular sequence was imported as RNA. Users are now blocked from importing circular sequences as RNA
- Links to enzyme product pages in the Digests panel were outdated
Registry and Inventory
- Users couldn't assign a sample owner to a container in an Inventory table without also indicating a restriction status unless they deleted the Restriction Status column or explicitly marked it as N/A. Users can now leave this field blank, and it will be treated as if it were deleted in the table
Workflows
- The template flowchart visualization in Task schema configuration was unscrollable
- Users could use the mouse wheel to scroll an unscrollable view
- Users couldn't edit Output schema fields in the Workflows dashboard
- The flowchart view was not scrollable/pannable in the task creation window
- Workflows schemas didn't show a loading indicator
- The Flowchart tab was missing from the Task Details page
- Buttons didn't display in the flowchart editor when mouse-clicked
- Changing the warehouse name on a task or output field didn't trigger a Warehouse resync
Lab Automation
- Lab Auto run displayed the message "Output file too large to process without ‘Skip Rows with Errors’ enabled" despite the checkbox toggled
In Vivo
- Editing optional treatment fields triggered validation, implying the field was required
- Admins were unable to remove inactive users from Request forms
- Cages were getting deleted when they weren’t assigned to a study from Colony
Access Management
- Members of an org were allowed to remove the org's avatar via the remove-avatar endpoint. Now only org admins can remove the org avatar.
- Benchling Support was listed as an admin on a project, and was emailed for access requests even though they should not be changing permissions. Now, Benchling Support is included on access request emails
- A footer on the email verification page had low contrast and illegible text
- There was a missing audit when a user signed up and got added to a project/folder from an invite
Application Core
- If a spreadsheet had a number with a leading 0, and it was being uploaded into a text field, the spreadsheet importer would remove it
Compliance Controls
- Mixture prep table names didn't appear in audit logs
- Lengthier rows on .pdf audit log exports overlapped on multiple pages