Welcome to the 5th volume of our 2024 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 May 2024.
Watch our Feature Release Highlights to more deeply explore this month's updates.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Double click cell dragger to fill down columns [2024.5.N.1]
Users can now double-click the fill handle to fill down empty rows.
Added Inventory tables to the GET/entries/{entry_id} endpoint [2024.5.N.2]
Inventory tables are now included in the GET/entries/{entry_id} endpoint response.
@mention Worklists [2024.5.N.3]
Users can now @mention a worklist to reference worklists in entries and templates.
Template count and type in Collections list view [2024.5.N.4]
Users can now find the number of templates and types of templates in a collection using a new column in the Template Collections list view.
Add notebook authors from teams [2024.5.N.5]
Users can now add authors to an entry by selecting teams. Only authors listed as team members at the time of selection are added as authors.
Insert content to an entry using key strokes [2024.5.N.6]
Users can now add content to an entry using slash inserts. Entering a forward slash ( / ) now displays the menu of insertable options.
Molecular Biology
Benchling’s Molecular Biology s a cutting-edge in silico design tool that supports the latest scientific workflows.
Notes field on AA sequence annotations [2024.5.MB.1]
Users can now add notes to annotations on AA sequences.
Translations hidden at small zoom [2024.5.MB.2]
Residues now stay aligned to translations when zoomed out, until the residues and bases are so small they’re hidden. Previously, translations rendered incorrectly on alignments in some cases.
Improved find primers performance and support searching by schemas [2024.5.MB.3]
Find and attach primers now support filtering by schema and runs more quickly.
Use of registered protein name when autofilling translations [2024.5.MB.4]
Autofill translations names new translations after the matching protein, instead of by the sequence map coordinates.
Responsive sequence map navigation bar [2024.5.MB.5]
The buttons on the sequence map navigation bar now cleanly collapse when window size decreases.
Expanded CRISPR guide design genome matching [2024.5.MB.6]
Users can now automatically find matching genome regions in CRISPR guide design for even more genomes, improving the efficiency and accuracy of CRISPR guide design.
Antibody CDR annotations use canonical abbreviation for framework regions [2024.5.MB.7]
Framework regions are now labeled FW instead of FR.
Option to unlink sequence from others when archiving [2024.5.MB.8]
When archiving a sequence, users can unlink it from other sequences where it’s used as a part by checking the option at the bottom of the pop-up window that launches.
Create a new entity option when using “find and replace” tool [2024.5.MB.9]
When using the Find and Replace tool to create modified nucleotide sequences, users can select Create new entity with modifications to create new entities with the applied modifications, instead of overwriting those in the originating sequence.
Exact molecular weight computed field for modified sequences [2024.5.MB.10]
Users can calculate the exact molecular weight of a modified nucleotide sequence using a computed field (Modification-aware sequence exact molecular weight).
To enable this feature, contact a Benchling representative.
User-facing export of custom notation tokens [2024.5.MB.11]
Users can now export the custom syntax in the monomer library configured for their tenant.
In Vivo
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Unique Tag ID validation [2024.5.IV.1]
Users are now only able to enter unique tag IDs. If a tag ID is already in use, a message displays and the information won’t be saved until a unique tag ID is entered. This validation displays when assigning IDs in workflow and editing animal IDs in the animal profile.
The Tag field was removed from the assign IDs table as this feature is for bulk assign IDs across all or many animals.
To enable this feature, contact a Benchling representative.
Allow connected devices to write data to unmapped fields [2024.5.IV.2]
Users can now allow connected devices to write to any mapped field where the cursor is placed using the new option follow focus.
Re-evaluate alerts on measurement edit [2024.5.IV.3]
When a user edits a measurement that previously triggered an alert, the alert is automatically re-evaluated. If the alert condition no longer applies, the alert is removed.
Remove empty tabs from raw data export [2024.5.IV.4]
When no data is recorded under a specific metric, the corresponding tab in exports and data tables in the Prism report don’t display.
Connected devices can be used when editing measurements [2024.5.IV.5]
Users can now use connected devices linked to the fields in the Edit Measurement form in workflow and animal profile.
Filter out canceled studies from calendar [2024.5.IV.6]
All tasks associated with canceled studies are automatically removed from the team calendar.
Data point exclusion to the graphs and export [2024.5.IV.7]
Users can now exclude outliers from graphs and analysis by selecting values in the measurements table under graphs and submitting changes. This data point is excluded from group summaries and graphs and is formatted to display exclusion status in exports.
To enable this feature, contact a Benchling representative.
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.
Map column names in spreadsheet import [2024.5.RI.1]
The Additional alias column is now mapped automatically when importing entities. Previously, when importing entities with the Additional alias column, it mapped to the Custom field column by default and the user had to manually select the correct column from the drop-down menu.
Better handling of inaccessible contents and containers in a box [2024.5.RI.2]
Users can now click into a box they have access to and view which positions in that box contain inaccessible content or containers. Previously, users couldn’t access a box at all if they didn’t have permission to access all contents or containers in a box.
Default to current user when checking in/out a container [2024.5.RI.3]
When checking a container in or out, the Assignee field is now pre-populated with the user’s name who is checking in/out the container. Previously, users had to manually specify the assignee.
Allow selecting any folder when registering via notebook [2024.5.RI.4]
Users can now select any project folder to transfer entities into when registering from a Registration table in a notebook entry. Previously, users could choose between registering items in the entry's project folder or None which would give the entity registry permissions.
Allow selecting project when creating containers via notebook [2024.5.RI.5]
Users can now select any project to transfer containers into when creating containers from a notebook entry. Previously, when inserting a Create Inventory table, users could choose between creating items in the entry's project or None which would give the container registry permissions.
Sample lot numbers in the warehouse [2024.5.RI.6]
Users can now lookup an entity's sample lot number from the warehouse.
Configuring well schema field lookup from plate + position [2024.5.RI.7]
Users can now lookup schema fields on a well using plate + position. Previously, there were errors when trying to find schema fields using plate + position.
Containable type "None" can no longer be selected in an Inventory table [2024.5.RI.8]
Non-containable entities can no longer be searched for in Inventory tables. Previously, users could select entities of containable type "None" in an Inventory table, but when inserting an entity of this type, a red dog ear with the error message displayed that the entity is not configured for the inventory.
Skip rows with errors in spreadsheet import [2024.5.RI.9]
Previously, when importing inventory data, users had to respond to all validation errors in the spreadsheet before importing. Users can now import successful rows and choose to skip unsuccessful rows. The user will receive an email with the rows with errors.
Searchable label printing template selection [2024.5.RI.10]
Users can now narrow down the label templates they want to use by using a new search bar in the label template picker.
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.
Hide the flowchart tab during task creation [2024.5.W.1]
Users can now hide the flowchart during task creation to allow more space in the model to fill out task details.
Hide irrelevant nodes in flowchart visualization [2024.5.W.2]
Users can now hide nodes in the flowchart that don’t have tasks.
Task schemas with long names can be migrated [2024.5.W.3]
Users can now migrate Task schemas with long names via config migrations.
Task schema properties are now included in config migration updates [2024.5.W.4]
The following properties are now config migrated:
- Can set assignee on task creation
- Can only be part of flowchart
- Is propagate watchers enabled
- Task group instructions
View assigned tasks in home pane [2024.5.W.5]
Users can now view tasks assigned to them in the side panel of the home page.
Benchling Connect
Benchling Connect, formerly Lab Automation, enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Update selected Benchling Connectors to use Allotropy 0.1.30 [2024.5.BC.1]
This version contains no-new adapters, only patches to the QuantStudio RT-PCR, QuantStudio Design & Analysis, and Bio-Plex Manager adapters.
Fixed Inconsistent Status error toast and connection Status [2024.5.BC.2]
The red toast error message from Connection now matches the Connection status.
Tooltips for Run fields [2024.5.BC.3]
Users can now define field tooltip text in a Run schema, which will be displayed on a Run field.
Resizing Run Input Generation button [2024.5.BC.4]
The "Generate and send to connection" button on the run now auto-resizes when changing the window size.
Prevent edit of the automated creation of Connection schema [2024.5.BC.5]
Users are now prevented from editing the fields on the Connection schema after automatically creating the instrument-specific required fields as part of the Connector enablement process. This is to prevent any Connector validation failure when users make accidental modifications.
Update Benchling to use Allotropy 0.1.29 [2024.5.BC.6]
Update dependent changes to deploy Allotropy 0.1.29 within Benchling to all existing connectors.
QuantStudio Design & Analysis connector [2024.5.BC.7]
Users can use this connector for importing data generated from Applied BioSystems QuantStudio qPCR instruments using the QuantStudio Design & Analysis software.
To enable this feature, contact a Benchling representative.
Revvity Kaleido connector [2024.5.BC.8]
Users can use this connector for importing data generated from Revvity plate reader instruments using the Kaleido software.
To enable this feature, contact a Benchling representative.
Agilent Gen5 connector update [2024.5.BC.9]
Updated to Agilent Gen5 connector to align format of data output with other plate reader connectors.
To enable this feature, contact a Benchling representative.
Bio-Rad Bio-Plex Manager connector [2024.5.BC.10]
Users can use this connector for importing data generated from Bio-Rad multi-analyte profiling instruments using the Bio-Plex Manager software.
To enable this feature, contact a Benchling representative.
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.
Disabled Save button in Manage Collaborators pop-up window when users were selected but not added [2024.5.AM.1]
Users must now add or remove collaborators pending in the search box before they can save their changes.
Users often forget to finish adding collaborators in the Manage Collaborators dialog, then click Save without finalizing their changes. The Save button is now disabled if there are pending collaborators in the search box.
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.
Maintain collapsed state for Feature Settings side panel [2024.5.AC.1]
The Features Settings side panel now stays collapsed during navigation. Previously, the side panel did not stay closed.
Added a Study schemas pane to Configuration Migration [2024.5.AC.2]
Users can now move Study schemas with linked templates between tenants with Configuration Migration.
Unarchive template, subtemplates, and template collections in config migration [2024.5.AC.3]
Users can now unarchive templates, subtemplates, and template collections via config migration.
Config migration files expiration warning [2024.5.AC.4]
Migration files that include a template expire after 6 hours. Now, a warning displays before the files expire, where previously, the files expired without warning.
Updated helper text in full org export of config migration [2024.5.AC.5]
Previously, if an admin exported a full organization, helper text informed the user about how dependencies were being gathered. Dependencies are not gathered when a full organization is exported, so this language was removed.
Updated placeholder logic for config migration of templates [2024.5.AC.6]
Previously, if a template referenced the same object several times, duplicate warnings displayed. Now, each unique placeholder warning is only displayed once.
Updated config migration warning language when entry schema values are found [2024.5.AC.7]
When Entry schema field values are found in config migration, the warning that now displays explains that the value can’t be imported but it will still be migrated. Previously, the language didn’t explain that the value would be migrated, which caused confusion.
Updated config migration language [2024.5.AC.8]
Users can now find more consistent UI text between Feature Settings and the import and export pages for certain config objects.
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.
Updated customizable timestamp language in TAC [2024.5.CC.1]
The customizable timestamp setting help text was updated to indicate that it also applies to the Chain of Custody reports.
Audit log header improvements [2024.5.CC.2]
If one item is exported in an audit log:
- Audit Log displays in the .pdf header and in the file name for .pdf and .csv exports
- The item's name is appended to the title in the header
Notebook entry context in Sample Container History report [2024.5.CC.3]
Users can now find a Document Context column in Container Chain of Custody (Sample Container History) reports. If the container creation or update event occurred in an entry, like a structured table submission, this column displays the document type, name, and ID.
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.
Updated Apps overview page [2024.5.DP.1]
Users can now find the following information in the Apps overview page (Feature Settings > Developer Console > Apps):
- Distribution setting
- Publish state
- Version
Include `featureId` in all Canvas webhooks [2024.5.DP.2]
Because the featureId is now included in the Canvas webhook payload, users can make fewer API calls, making Canvas interactions snappier.
Updated design and copy on Create App window [2024.5.DP.3]
The instructions in the Create App window are clearer and the text easier to read.
App API keys discontinued [2024.5.DP.4]
Users can no longer generate new API keys for their apps. This was fully replaced with app credentials in 2022.
API Keys are no longer retrievable in the UI [2024.5.DP.5]
To improve Benchling security for customers, users can now only copy API keys when they’re first generated and are no longer accessible after generation. Previously, users could copy existing API keys from the user settings page.
Several sequence endpoints in alpha/beta/experimental promoted to stable [2024.5.DP.6]
A range of v2-experimental, v2-alpha, and v2-beta endpoints for DNA, RNA, and amino acid sequences, along with enzymes and codon usage tables, have been promoted to stable v2 equivalents. The deprecated endpoints, including specific functionalities like back-translation, matching regions, and bulk upsert, will be fully sunset on June 3, 2024. Users should transition to the stable v2 endpoints to ensure continued functionality.
For more details, visit the Benchling Changelog.
Bug Fixes
App Ecosystem
- We tried to load all of a user's App Sessions all at once in the UI, causing the UI to crash for users with many Sessions.
In Vivo
- Resolved an issue where animals without alerts were being returned when filtering animals table by alert.
- Fixed a display issue where the device connection dropdown only showed 10 devices.
- Fixed a bug with task target animals list for recurring tasks when animals were added to groups after study creation.
- Fixed a bug where study cloning or duplicate treatment couldn't save when treatment multiselect metadata fields were cleared.
- Resolved an issue where sorting the study animals table by cage removed deceased animals.
- Fixed an issue where pending users were being added to the calendar filter before accounts were created.
- Fixed unwanted behavior where recaging animals in the study cage view appeared to have been moved in error but were in the correct position upon page refresh.
- Fixed an issue where raw data export files were corrupted when truncated Excel tab names ended in a superscript character.
- Inactive metadata was not removed from cloned study.
- Measurements that included a calculation of exponents ending in 0 (e.g., E10, E20) were calculated incorrectly.
- Typing "D1" for the conditional task schedule was erroring, validation has been added to ensure only numbers are input into this field.
- Bug where the admin was unable to open "cage cards" section in manage team.
- Issue resolved where the Task assignees list did not match team users list in study cloning.
- Fixed a bug where sample metadata multi-select options were not being saved in the correct format.
Workflows
- Fixed an issue where users could not create Outputs from the Output table in Task Details or the Task Group page.
- In the highly unlikely case a Task Group is moved into a Registry folder, the Task Group page no longer crashes.
Search
- In type filter searchable menus, the dropdown was set as a static height, if not enough items populated the list, the list would not scroll.
Schema
- Fixed an issue where an error message appears twice when a schema does not satisfy a Benchling system field.
Application Core
- Fixed a bug where Config Migration was not properly displaying warning icons during template export.
- Fixed a bug where bulk field edits violated name constraints in Config Migration.
- Fixed a bug where tenants with several orgs would show Registry settings non-deterministically. Registry settings are now alphabetized in the Feature settings.
Access Management
- Fixed a bug where the folder picker was unresponsive with large results.
- Fixed a bug where the /v2-alpha org/team membership APIs allowed callers to add suspended users to a group.
- Fixed a performance bug in rendering the Project pane for tenants with a very large number of projects or folders.
- Fixed an issue on Worklists where adding a Team from outside the owning user's Organizations threw a 500 (server) error instead of 400 (expected) error code.
- Fixed issue where TLDs on email addresses were limited to 10 or fewer characters (new limit is 50).
Inventory
- Fixed a bug where columns configured to look up wells down columns actually looked across rows.
- When selecting positions in a grid, the grid table would jump to a position that was not the position selected in the grid.
- If there was a lookup column in a structured table, the add from spreadsheet option failed in a Fill Inventory table.
- We no longer pre-select positions in a box/plate when moving containers between one box/plate to another.
- Once a hyperlink was added to a text field, it could not be removed.
- Barcodes are no longer editable in the transfer modal container view.
- Show error if there is a duplicate numeric and alphanumeric destination position in the transfer table.
MolBio
- Fixed bugs where ORF visualizations and translation regions could have each initial AA incorrectly coerced to M.
- Fixed a bug with Cmd-F showing MolBio search on incorrect pages.
- Bulk update DNA sequence endpoint accepts parts, rather than erroring.
- /dna-sequence
endpoint no longer incorrectly returns RNA sequences. - Fixed bug where autofill translations cleared transcriptions from sequences.
Notebook
- Fixed an issue where embedded hyperlink options were not available.
- Fixed an issue where the user was unable to reassign the review process, while having admin access.
- Fixed an issue where text/formatting edits were not audited in Entry Templates.
- Fixed an issue where navigating away from a template while it was saving did not prompt a browser warning.
- Fixed an issue where changes to template metadata did not immediately reflect in the UI.
- Hitting enter when in a cell of some data types re-selected the cell instead of navigating to the next row.
- ISNUMBER formula incorrectly returned TRUE for blank cells.
- Update inventory table isn't readily showing new locations of containers on moving them.
- Could not use a plate snapshot column as a source for "Add From Structured Table."
- Users could not undo "Add from structured table" actions.
- When selecting items in the 'add from structured table modal,' if there was an archived entity, clicking a checkbox toggled the checkbox above it.
- Leading zero dropped when dragging down values in tables.
Connect
- Fixed issues with displaying random characters when retrieving the zip files via Connect.