Welcome to the sixth 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 June 2023.
Addendum: The sub-templates update was added to the Volume 6 release notes on August 16, 2023, but went into affect July 19, 2023.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Archiving collections [2023.6.N.1]
Users can now archive collections from the Template collections list view or the collection page toolbar, providing better organization and management options.
To enable this feature, contact a Benchling representative.
Multiple review processes per project [2023.6.N.2]
Users can now enable multiple review processes for a project. When sending entries for review, authors select the appropriate review process to use.
To enable this feature, contact a Benchling representative.
Sub-templates [2023.6.N.3]
Sub-templates can be created and shared in the Template Collections page alongside entry templates. Authors can insert sub-templates into modifiable entries via the Insert menu, which behaves like a copy and paste - the content added via the sub-template becomes indistinguishable from the rest of the entry.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
Search by translation name within a sequence [2023.6.MB.1]
Users can now search for translations by name within the sequence map, expanding the search capabilities beyond annotations.
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.
API endpoints for HELM RNA sequences [2023.6.SM.1]
Users can now create, list, and edit modified RNA sequences using HELM syntax through the API.
Hide Physicochemical properties tab [2023.6.SM.2]
Users can leverage computed fields to calculate Physiochemical properties in lieu of the Physicochemical properties tab.
To enable this feature, contact a Benchling representative.
API update to allow listing and creating monomers [2023.6.SM.3]
Introduces capillary monomer model and list/create endpoints.
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.
Name part descriptions display on hover [2023.6.RI.1]
Users can now hover over a part type to differentiate between text and separator name part types.
Container names display in Inventory tab [2023.6.RI.2]
Users can now view the container names in the Inventory tab on entities. Previously, the container table in the Inventory tab on an entity did not contain the container’s Name column.
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.
Update search empty state [2023.6.WF.1]
If no results are found when users search the list of available tasks, the system now displays an informational message indicating there are no task schemas with that name.
Expanded routing lookup types [2023.6.WF.2]
Users can now use strings, integers, and decimals for routing in flowcharts. Any tenant with Routers enabled will receive this functionality.
Insights
Insights enables users to query, visualize, and share high quality, structured data that resides in Benchling.
Archive and unarchive an analysis [2023.6.IN.1]
Users now archive analyses and remove them from their tenant.
Analysis API endpoints promoted to GA [2023.6.IN.1]
Analysis API endpoints can now be found under v2-beta (GA) documentation.
Lab Automation
Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Lab Auto runs in global search [2023.6.LA.1]
Users can now find Lab Auto runs via global search, making it easier to locate specific Run schemas and navigate to associated Notebook entries.
Application Core
To create a seamless Benchling experience, our platform must be consistent, compliant and predictable. The Application Core provides the central capabilities platform to create a smoother user experience.
Insert searches in entries and templates [2023.6.APP.1]
Users can now insert saved searches into Notebook entries and templates as chips. Clicking the chip runs a search using the filters stored in the saved search.
Paste as text into table cells [2023.6.APP.2]
After copying a cell, users can now right-click and select Paste as text to paste formatted text into another cell. This enables users to copy linked text, like from a chip, into another cell without copying the link itself.
Bug Fixes
The following bugs were fixed in this release:
Notebook
- Users without access to an entry would receive email snippets
- Users could create entries from templates via the calendar view, even when blank entry creation was blocked in the tenant
- Ctrl + F search in entries constantly reloaded, making search impossible
Molecular Biology
- The axis in AA alignments didn't automatically resize when zooming in or out, but now it adjusts appropriately for a better viewing experience
- Users can now Users couldn’t reliably search by entity name and registry ID in the bulk assembly folder tree search bar
- AlphaFold structures were not returned if permissions on the sequence were adjusted after the structure prediction request was submitted
- CDR annotations were displaying on AA sequences even when the display setting wasn’t selected
- 3' sequence end mod detection was implemented incorrectly, preventing registration of some RNA oligos
Workflows
- Query execution in the web application and data warehouse transactions had slow performance
- The graph builder crashed when partially saving flowcharts between adding and deleting new nodes
- A permissions error occurred when migrating a workflow task schema w/ flowchart
- Router lookups ran validation on every lookup step when reopening an existing lookup panel
- Router failed mapping did not send notifications
- Default field values populated inconsistently in Requests
- Flowchart tasks were unexpectedly marked completed
Data Input
- Tables with un-submitted changes in an archived row were preventing entries from sending for review
- Expanded tables gear icon options overlapped the first row
- TRUE/FALSE values imported from Excel appear as 0/1 in structured tables
- Spreadsheet import didn't replace rows containing default values in Notebook tables
- New Results Bulk Create API that allowed results to be added to an entry's table even if the entry was out for review
Access Management
- Clicking on @-mentioned users went to 404 page
- Project and folder picker control wasn’t properly indenting empty projects and folders
- Re-arranging access policies didn't save
Application Core
- DLocalized parsing wasn’t skipping drop-down options
- The Benchling icon wasn’t properly coloring pagination icons in the Nucleotide tab
- Flag value changes were not audited when updated via script
Compliance Controls
- Schema naming templates audit events didn’t track additional name template updates, including text, separators, dates, and name changes
- Incorrect Service Account Type was recorded in audit events for Benchling App objects, setting the type columns to User instead of App
Studies
- Users were able to to create a study without completing mandatory fields in the study info section
- Rounding error on negative numbers in data tables
- % change option in show menu was not working
- Metadata options were filtered out of the show menu