Welcome to the seventh 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 July 2023.
Notebook
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Expanded Export Footer Length [2023.7.N.1]
Users can now include up to 200 characters in the footers of exported files.
To enable this feature, contact a Benchling representative.
Close Formula Help drop-down menu [2023.7.N.2]
Users can now close the Function Help drop-down menu that automatically populates in tables when entering formulas. To re-open the menu, click the question mark icon.
Enhanced copy function for structured tables [2023.7.N.3]
Users can now copy structured tables from notebook entries into notebook entry templates and vice versa.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
Enhanced error messaging for duplicate annotations in Feature Libraries [2023.7.MB.1]
Users can now view the names of duplicate features in the error message that displays when duplicating annotations in feature libraries.
Search for sequence similarities using BLAST [2023.7.MB.2]
Users can now conduct DNA, AA, and RNA sequence searches using the blastn and blastp algorithms directly within Benchling.
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.
Lookup steps displaying chemical structure for molecule entities [2023.7.SM.1]
Users can now view the chemical structure associated with any linked molecule entity in lookup steps, giving additional visual context to support their research and analysis.
Studies
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Edit and delete samples in bulk [2023.7.ST.1]
Users can now edit or delete multiple samples using bulk actions for the Study Samples table. This feature streamlines data management and ensures uniqueness validation for sample IDs.
Select integration folders [2023.7.ST.2]
Users can now browse and select folders when creating in vivo studies to ensure accurate syncing of studies using the Studies data sync feature.
Support for negative measurements [2023.7.ST.3]
Users can now enter negative values as study measurements using the workflow for manual data capture and import.
Workflow sample and observation preselction [2023.7.ST.4]
When setting up workflows for the day's tasks, users can now select the samples and observations to be recorded and define the order of collection. The preselected configuration applies to all animals but can be amended for individual animals as required.
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.
Container Name templates [2023.7.RI.1]
Users can now use name templates for container names. This feature allows users to align on standard nomenclature for containers and makes them easily searchable in the lab and across the platform.
Label printing time zone awareness [2023.7.RI.2]
Users can now select their preferred time zone for label printing, improving accuracy and convenience. Previously, all labels were printed in UTC without timezone indication.
Enhanced list of supported date formats for spreadsheet import [2023.7.RI.3]
Users can down use the YYYYMMMDD (e.g., 2023Feb28) and YYMMDD (e.g., 230328) date formats when importing from a spreadsheet into a Benchling table.
Entity Search using SG3 [2023.7.RI.4]
When performing @ mentions, the corresponding entities will surface based on a combination of name and relevance.
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.
Searchable drop-down menus for router config [2023.7.WF.1]
Customer admins can now search drop-down menus in the Routers configuration pop-up window.
Live refreshing of Workflows UI [2023.7.WF.2]
Users can now view real-time changes to task and output data made by integrations or other users without refreshing the page.
Saving users' last viewed form to local storage [2023.7.WF.3]
When creating a task, Benchling now remembers the user's last viewed form, eliminating the need to default to the generic form upon loading.
Insights
Insights enables users to query, visualize, and share high quality, structured data that resides in Benchling.
Result audit logs export for analyses [2023.7.IN.1]
Users can now export the audit log for results created from a dataset in an analysis.
Lab Automation
Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Validating transfers defined within Input File [2023.7.LA.1]
Runs can now validate transfers to ensure sufficient transfer volume before performing the transfer.
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.
Removal of Google OAuth contact linking feature [2023.7.AM.1]
The Google OAuth contact linking feature (available only Academic tenants) has been removed.
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 audit log file names [2023.7.CC.1]
Users can now view the object name and/or type of in the file name of the exported .df or .csv audit log. This enhancement allows users to easily identify the source of data in the file.
Before: apiId_userHandle_currentDate_audit_logs.csv or .pdf
After: workflow_task_group_audit_logs_prs_66VXWiAS_L.Pasteur_28Jul2023.csv
Exportable audit logs by user time zone [2023.7.CC.2]
Tenant admins can now configure audit logs to display audit log exports in individual user time zones based on their locations. Configure this feature in the Tenant Admin Console Settings under Configurations.
User Name column in audit logs [2023.7.CC.3]
Tenant admins can now add a Name column to audit logs across the tenant, displaying the first and last names of users.
Enforced fields in customizable audit logs [2023.7.CC.4]
The following audit log columns are now always visible in customizable audit logs and can’t be disabled:
- Timestamp
- User
- Event Description
- Action
- Old Value
- New Value
- Item
- Electronically Signed
- Reason Code (only if data mods turned on)
- Reason Comment (only if data mods turned on)
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.
App status exports [2023.7.DP.1]
Exporting app status messages is now more comprehensive. Users can now access the full history (up to 100k rows) in the Activity tab of a Benchling app. Additionally, users can easily filter their results and exportable data.
Enhanced API security with bearer auth [2023.7.DP.2]
API security has been enhanced by replacing basic auth on the Swagger page with bearer auth. Users will now experience short-lived bearer tokens that expire within minutes, reducing the risk of unauthorized access and misuse.
Canvas APIs [2023.7.DP.3]
All Canvas and app status API endpoints are now generally available in our V2 stable API. The /app-sessions endpoints allow developers to create and display status messages about their app's activity in Benchling.
User API removed from /v2-beta endpoint [2023.7.DP.4]
The read/write capabilities of the Users API have been in /v2 for 6 months now, so it has been removed from the /v2-beta endpoint since it is now fully supported.
Bug Fixes
The following issues were fixed in the last month:
Notebook
- The Entry position would jump upon Lab Auto Run creation
- Notebook search displayed outdated column names
- The fill-in specification upon creation of a template was not propagated to the template editor
- No text wrapping occurred when copying over large sequence files into Notebook
Molecular Biology
- Ctrl+F within a sequence didn't find translations
- Sequence maps were not reliably being updated while in use, even though the data was saved
- Bulk auto-annotate and auto-fill transcriptions could error when editing both a sequence and its part that each have an annotation
Registry and Inventory
- Inefficient relevant entity queries. Relevant Items tabs now load faster
Workflows
- Updating a flowchart configuration with a router required deleting and re-creating the router when updating transitions
- Users could not add an edge to an already configured router when updating a flowchart configuration
- When a Task Creation window was open while editing the task's schema, the creation modal crashed
- The Copy Request button was not copying schema field values from the source request as expected
- Flowchart task status did not update to complete for flowchart tasks that went directly to outputs, primarily affecting router use cases
- The Import From Spreadsheet window could not be closed using the X button
- Changing a schema field type could produce a routing error, leading to unintended behavior in routers. Now, type-checking is enforced, raising a mapping error instead
- Users were prevented from creating Task schema descriptions longer than 10k characters, as descriptions beyond this point caused issues with automatic hyperlinking of URLs
- Addressed a bug where workflow tasks do not support multiple assignees, but some tasks could accidentally have multiple assignees set. Now, only the most recently added assignee is listed
Insights
- Minor UI inconsistency in column sort arrows on dataset tables was resolved.
- A bug was fixed where files containing forward slashes previously caused errors. Users will be automatically prompted to update to the latest version of the JMP add-in for smoother integration with Benchling.
Studies
- The Set button wasn't applying custom exclusion criteria in Randomization
Access Management
- Service accounts were unable to create feature libraries using the public API