Welcome to the fifth 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 May 2023.
Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.
Fixed header on notebook tables [2023.5.N.1]
Notebook tables now have fixed headers when scrolling beyond the first row, providing a better editing experience.
Notebook table formula formats [2023.5.N.2]
Users can now easily view table formula details when editing table cells, similar to Excel.
Keyboard insert for cell ranges [2023.5.N.3]
Users can now use the keyboard for cell ranges in tables to make quick changes when entering formulas.
Add entry content by clicking into empty space [2023.5.N.4]
Users can now add new content at the end of an entry by clicking into the empty space at the bottom of the document or dragging and dropping a file into the empty space. Previously, users had to click explicitly into a new line at the end of the entry to add new content.
Updated table of contents location [2023.5.N.5]
To ensure it remains visible, the table of contents now displays to the left of the scrollbar.
Redo keyboard commands [2023.5.N.6]
Users can now redo undone actions in notebook entries by pressing Ctrl + Y (⌘ + Y on Mac).
Allow paste special > transpose [2023.5.N.7]
Users can now use the Paste transpose feature to transpose a column to a row when copy-pasting in Benchling.
Add auto-complete for functions [2023.5.N.8]
Notebook formulas in Benchling now have auto-complete for functions, providing users with a faster way to determine supported functions and offering previews to understand their functionality.
Support for formulas =LEFT() and =RIGHT() [2023.5.N.9]
Users can now extract specific characters from a text string in notebook tables using the =LEFT() and =RIGHT() formulas.
Support for formula =PRODUCT() [2023.5.N.10]
Users can now multiply numbers and calculate the product of multiple values in notebook tables using the =PRODUCT() formula.
Syntax highlighting for literal values [2023.5.N.11]
Literal values in notebook formulas now have syntax highlighting, providing visual feedback and interpretation of the formula as intended by the user.
Schema Table Rename [2023.5.N.12]
When a Results table or Registration table is renamed, Benchling now shows the schema name that is being encoded, making it easier to identify the associated schema.
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
Oligo map and annotations [2023.5.MB.1]
Users can now use the oligo sequence map instead of the oligo tab, which allows for the inclusion of annotations, preservation of oligo properties, and retention of linked sequences without requiring any modifications.
To enable this feature, contact a Benchling representative.
Visualize overlapping parts [2023.5.MB.2]
Users can now view overlapping parts on the plasmid map as annotations with names.
Pop-up window for registry data on sequence maps [2023.2.MB.3]
On sequence maps, users can quickly view important registry data when hovering over parts, primers, and transcription links.
Return DNA and RNA parts [2023.5.MB.4]
Developers can now use the API to retrieve DNA and RNA parts on sequences.
Registry ID on sequence maps [2023.5.MB.5]
Users can now view the registry ID of registered sequences on sequence maps. To enable this feature, enable these options in Registry Settings:
- Use Registry ID as display label
- Include Registry ID in chips
Bulk export AA sequences in FASTA format [2023.5.MB.6]
In the expanded view, users can now select and export amino acid sequences in bulk as a multi-FASTA file.
Assign schema for raw DNA, RNA, or AA sequence [2023.5.MB.7]
Users can now assign a schema when creating a raw DNA, RNA, or AA sequence entity.
Feature library duplicate feature prevention [2023.5.MB.8]
Users will now encounter an error message when attempting to add base match duplicate features to feature libraries. This ensures only unique features are added to the libraries.
Minimum height for alignment rows [2023.5.MB.9]
Alignment row now have a minimum height to enhance visualization of sequence names.
Additional organisms for codon optimization [2023.5.MB.10]
Users can now use additional organisms for codon optimization, including:
- Bos indicus
- Bos taurus
- Capra hircus
- Ovis aries
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.
Custom syntax for oligo API endpoints [2023.5.SM.1]
Oligo Create/Edit/Listing API endpoints now accept custom syntax, enhancing flexibility and compatibility.
New API endpoints for monomers [2023.5.SM.2]
Admins can now manage monomer libraries via the API with new API endpoints:
More monomer filter options [2023.5.SM.3]
Users can now filter monomers in the Monomer Library based on various criteria such as sugar or base monomers.
Filter label descriptions [2023.5.SM.4]
Users can now view descriptive labels in monomer library filters, providing information about each degenerate base natural analog.
Monomer library filters scroll bar [2023.5.SM.5]
Users can now scroll lengthy filter lists in the monomer library using the new scrollbar.
Custom colors for use as monomer visual [2023.5.SM.6]
Users can now choose between more symbols for phosphate monomer visuals and more custom color options for sugar/base monomer visuals.
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Promote team members to admin [2023.5.ST.1]
Admins can now promote team members to admin directly from the users table, eliminating the need for external requests.
Filter Tables by Metadata [2023.5.ST.2]
Users can now filter tables in Studies based on custom metadata fields, enabling easier search and navigation.
Live body weight percentage change display [2023.5.ST.3]
Users can now view real-time changes in body weight percentage (%) while capturing data, providing valuable insights into animal welfare before saving.
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.
Faster and more reliable registration [2023.5.RI.1]
Users can now benefit from the enabled registry granular locks across all areas. This update allows for concurrent registration with reduced errors and waiting time.
Separator field in registry naming templates [2023.5.RI.2]
Users can now define a separator type when generating names using the new Separator field in registry naming templates.
Consolidated icon for fill, transfer, and remove contents [2023.5.RI.3]
Users can now find Fill, Transfer, and Remove Contents options on containers’ metadata pages in one icon.
Remove ability to archive contents [2023.5.RI.4]
Admins can now remove the Archive contents option to prevent accidental archiving of entities still in use.
Update to Print labels button [2023.5.RI.5]
Users can now view a tooltip on the Print Labels button that provides context and guides users on selecting rows in the Inventory table rows before printing labels.
Allow printing labels from location settings [2023.5.RI.6]
Users can now print labels from the Inventory settings page, along with other Inventory-level actions.
Label template properties for Sample Control Roles [2023.5.RI.7]
Users can now create label templates for Sample Control Roles, which display information such as restriction status, sample owners, and restricted sample users, enabling clear authorization of container usage.
Search bar added to dropdowns registry page [2023.5.RI.8]
To streamline the process of finding specific dropdowns in lengthy lists, users can now search the Dropdowns Registry page.
Result schema entity fields on the overview page [2023.5.RI.9]
Admins can now more easily identify the schema a metadata field is contained in using the Results schema entity fields on the overview page.
Lookup container’s parent location [2023.5.RI.10]
Users can now look up a container's parent location in a Lookup table, simplifying the verification and retrieval of container locations in the lab.
Lookup inventory object’s barcode [2023.5.RI.11]
Users can now look up an inventory object's barcode in Lookup tables, making inventory management more efficient for organizations using barcodes for identification.
Starred inventory items [2023.5.RI.12]
Users can now prioritize and bring starred inventory items to the top of the location transfer modal, facilitating easy access during object transfers.
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.
Lazy Task Group Creation [2023.5.WF.1]
Workflows now creates task groups for nodes only when tasks are routed to them.
Bulk setting responsible parties [2023.5.WF.2]
Users can now set responsible parties for multiple tasks directly from the dashboard view, improving efficiency in task management.
Insights enables users to query, visualize, and share high quality, structured data that resides in Benchling.
Analytics Integrations [2023.5.IN.1]
Users can now curate Benchling data into a dataset and send that dataset to another tool for analysis. From there, users can push analyzed data back to Benchling. Included in this release is a JMP add-in that enables JMP to pull and push data to and from the analysis.
To enable this feature, contact a Benchling representative.
Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Sending input files directly to output file processors [2023.5.LA.1]
Users can now send input files directly to output file processors, eliminating the need for manual downloading and uploading of files.
Duplicating Run schemas [2023.5.LA.2]
Users can now duplicate Run schemas with one click, simplifying the creation of new versions. The new version must still have a unique name to distinguish it from the previous version.
Maintaining collapsed state of runs [2023.5.LA.3]
Benchling now maintains the collapsed state of runs in the notebook when navigating to new tabs, preventing overcrowding and enhancing user experience.
Copying a run within the notebook [2023.5.LA.4]
Users can now copy a run within the notebook, simplifying the process of creating new runs by utilizing copy and paste functionality.
Specifying the registry as destination [2023.5.LA.5]
Users can now specify the registry as the default destination for all entities registered via a Lab Auto run, eliminating the need for repeated specification per run.
Schemas are the structural foundation for how your information is categorized in Benchling. They are categories created specifically for your tenant that can represent materials, data, storage methods, and tasks.
Warning for schema field type change [2023.5.SCH.1]
Users now receive a warning when changing schema field types from dropdown A to dropdown B, preventing potential data loss.
Lookup columns for child entities [2023.5.SCH.2]
Users can now conveniently lookup child entities in lookup columns.
Entity Name lookup step [2023.5.SCH.3]
Users can now use entity names in lookup steps within the Results table.
Faster loading for Registry Settings [2023.5.SCH.4]
Benchling has improved the loading speed of Registry Settings and Schema Settings, providing faster access to menu and schema details.
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.
Essential cookies [2023.5.AM.1]
Zendesk and Gainsight cookies are now categorized as Essential for proper functioning, and users cannot opt out of them.
Session and Idle timeout settings [2023.5.AM.2]
Customer admins can now modify session and Idle timeout settings. This update allows for custom authentication and inactive interaction times.
API now supports filtering by email address [2023.5.AM.3]
The Users API now supports filtering users by email address, simplifying user management tasks by enabling direct identification based on email.
Tenant admins can manage org membership [2023.5.AM.4]
Tenant admins can now manage organization membership and make themselves admins.
Users list sorted by all columns except [2023.5.AM.5]
Admins can now sort the users list in the Tenant Admin Console by all columns except Organizations and Teams, allowing admins to quickly find users based on various criteria.
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.
Feature Settings side panel collapse [2023.5.APP.1]
Users can optimize screen space by clicking the new Collapse icon, collapsing the Feature Settings side panel.
Consistent Benchling iconography [2023.5.APP.2]
Implemented consistent iconography across Benchling to enhance visual coherence.
Find worklists in global search [2023.5.APP.3]
Users can now find worklists via global search.
Remember the last folder open [2023.5.APP.4]
When navigating back to the Project listing, Benchling now remembers the last folder open, improving the navigation experience between applications and projects.
Split workspace preference [2023.5.APP.5]
The "Split workspace" preference is now saved for all objects except bulk assemblies, enhancing the user's viewing experience across Benchling.
Keyboard shortcuts for switching tabs [2023.5.APP.6]
Users can now use keyboard shortcuts (Cmd + Shift + 9 or Cmd + Shift + 0) to switch tabs in Benchling.
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.
API for direct blob download [2023.5.DP.1]
An API endpoint for direct blob download has been introduced, allowing customers to download blobs without impacting their rate limit and improving integration speed.
Returning parameter rollout [2023.5.DP.2]
The returning parameter, which limits the data retrieved from Benchling's API, is now available in several new endpoints, significantly speeding up integrations and apps.
App Status and App Sessions [2023.5 DP.3]
Users can now log and display the status and status messages for their app using the app status and app sessions endpoints.
Display app version [2023.5 DP.4]
Users can now view the version information alongside other app details on the app homepage.
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.
Customizable columns for audit log exports [2023.5 CC.1]
Tenant admins can now configure the displayed columns in audit logs across their tenant. Admins can choose to display only relevant information.
In the Tenant Admin Console, open the Configurations tab and choose between Export all columns to export all available columns or Select columns for export to customize the columns displayed. Note that certain columns may require specific configuration flags or validation.
- Delete option is added back to the Notebook Template Information panel.
- A bug where a 500 error code was returned instead of a 400 error code with an error message on container bulk-update endpoints has been fixed.
- A bug where Schema Validation status wouldn’t properly sync to the warehouse was fixed.
Registry and Inventory
- Increased contrast of colors for checked-in, checked-out, archived, and empty positions within a box or plate.
- Both the barcodes and names columns are now frozen on the expanded inventory search page for better usability.
- Fixed error when returning RnaOligos from the API.
- Fixed bug where annotation/feature labels were not shown for some features when zoomed in on the linear map.
- Fixed highlighting bug where primer selection did not properly highlight bases on sequence map.
- The appearance of the blue focus box when clicking or selecting a range in the oligo map has been eliminated.
- Fixed bug where alignment success toast did not disappear.
- Fixed issue where the sidebar width did not adjust correctly at different browser sizes.
- Fixed issue where the last node was cut off from the sidebar when scrolling.
- Benchling has updated the error message for logically equivalent paths in the router to provide clearer information.
- The placement of the edit button (pencil icon) for the router title in Benchling has been improved for better accessibility.
- Task Schemas in the flowchart configuration now include links to the relevant schema.
- The flowchart node error message icon has been moved to the left side of the cell, ensuring it is no longer covered by the delete button on hover.
- Benchling now displays the execution type of task schemas on the schema settings page.
- In the graph builder UI, nodes in the right sidebar now display a grab cursor when hovered over.
- On the flowchart, users can now scale node icons (e.g., delete button and error message) with the zoom level.
- In the graph builder UI, when dragging nodes onto the canvas, the node is dropped directly under the cursor for precise placement.
- Flowchart task schemas can now be exported as a subset of config migration.
- Users can now edit warehouse names directly on the task schema page.
- In the graph builder UI, the scrollbar for nodes in the right panel now scrolls all the way to the bottom, ensuring complete visibility of all available nodes.
- The flowchart is now centered on the graph builder canvas, providing a better visual focus and alignment.
- The archived status is now displayed on the task group page, allowing users to quickly identify whether a task group is archived or active.
- When cloning an entry template as a Task schema's execution template, invalid (already cloned) entry templates are filtered out, improving the cloning process.
- The request execution modal now correctly displays "Legacy Workflow" as an execution option instead of just "Workflow".
- A bug related to localized parsing has been fixed to skip formulas for proper data ingestion.
- A bug related to the new Benchling icon has been fixed to properly color pagination icons in the Nucleotide tab
- The Clear button in the collapsed side panel has been moved to a consistent location.
- An "All Archived" option has been added to the Archived filter, allowing users to easily filter and view all archived items.