Welcome to the December edition of our product release notes! We have been working hard to bring you some much requested features. Read along to learn about our new product features and enhancements released mid-October through mid-November.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
Bulk unlink and unfill parts in DNA sequences
In the past, severing part links was challenging as it not only required that the parts be unlinked, but the parts must be deleted from the metadata. Furthermore, this could only be done on sequences individually. A new option has been added to the toolbar in the expanded view to both unlink and unfill part links in bulk.
To access this option, select the desired entities, and click “More”. Hover over “Analyze” to select the option “Unlink Parts”. Once selected, choose the fields that you would like to unlink, then select “Remove”.
Auto-fill parts surfaces up to 100 parts on a sequence
A single sequence will return up to 100 parts when using the auto-fill parts feature. Previously, this was limited to 50 parts per sequence.
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.
Allow recording entities or containers used in mixture preparation
Ingredient lots are captured as a text field by default; however, some clients store these lots in the form of entities and containers in Benchling. To support the traceability of these items across entities and containers, users now have the option to configure “Ingredient Component Lot Format” as text, storage (entities and containers), or both in the entity schema settings. In doing so, any of the three columns will appear in the mixture prep table as “Component Lot Container”, “Component Lot Entity”, or “Component Lot Text”. To enable this feature, contact support@benchling.com.
Parent field now optional when creating mixture preps in the notebook
To support the creation of experimental preps that do not have a recipe, parent links are now optional when creating a mixture prep in the Notebook. Such preps will pass validation when non-required parent links are left empty in the mixture prep table.
Insights
Insights is one of our newest applications to the platform. This feature is seamlessly integrated with all Benchling applications, and enables users to query, visualize, and share high quality, structured data that resides on the platform.
Insights embedded in the registry (limited availability)
Insights dashboard is now embedded in the Registry application. Users can easily examine and analyze experimental query data within the metadata of an entity. Please contact support@benchling.com to enable this feature.
Insights table headers are now frozen
When scrolling down an Insights table, the header will stay frozen so that it is visible when scrolling down the output list.
Empty dashboard message visible in insight’s dashboard
When a dashboard does not contain any blocks, users will see the following message visible right above the “Add Block” button.
Search for keywords Insights editor using the “find” shortcut
In the past, searching for keywords using Cmd + F highlighted keywords in the current view of the code editor, but did not search the rest of the code. For this reason, code that was only visible by scrolling up or down in the query editor was not highlighted with keywords. The new “find” shortcut allows extensive search of a keyword throughout the code editor. Clicking into the editor and typing Cmd + F will bring up the search bar. To replace keywords, select the “+” icon below the search bar.
Application Platform
Benchling application platform helps provide an unified experience for our users and makes it easy to work across the Benchling applications seamlessly.
Improved audit trail capabilities
Users can now export the audit trail of a single project, single or multiple users, a team, and/or an organization. To export the audit log of a project, navigate to the project, click on the gear icon by the project’s name and select “Export Audit Logs”.
To export the audit log of a single user, navigate to the Tenant Admin console, click the overflow icon and select “Export audit logs.” For multiple users, select all the users, click the “More options” button on the top right, and select “Export audit logs.”
To export the audit log for a team, navigate to the tenant admin console, click on the “Teams” tab, then click the overflow icon in the team’s row select “Export audit logs.” This button is disabled if you are not a member of the team.
To export the audit log for an organization, navigate to the tenant admin console, click on the “Organizations” tab, then click the overflow icon in the organization’s row and select “Export audit logs.”
Access custom help docs through our new help action button
Industry users can access an additional help action icon that allows them to access their own support systems. Navigate to the bottom right corner and click on the “?” icon to access the custom links to external documents. Please contact support@benchling.com to enable this feature.
Save searches and filters in global search
Searches and filters can now be saved through Global Search to quickly repeat a past search and easily populate data. Save a search by clicking on the “Save” option next to filters or access previously saved searches by clicking on the triangle next to the search heading. The search can be altered, reset or saved as a new search.
Exporting multiple items at once
Previously users could only export an entire project or folder at once, or export a single item individually. Now users can select multiple items to export at once in the expanded view.
Developer Platform
Our developer platform is fundamental to centralizing and standardizing all your R&D data. Benchling’s APIs are built to match the flexibility and speed of modern life science R&D.
Benchling’s event system is now available in beta
Benchling’s Event system allows external services to subscribe to specific events that are triggered in Benchling (ex. Request submission or plasmid registration). Event’s system offers a powerful interface for developers on Benchling. Please contact support@benchling.com if you would like this to be enabled for you.
apiURL now available in API resources
Benchling developers can now leverage apiURL to directly call the API for the full object if they want additional context or resource sub-references.
Create and register entities in a single API call
The endpoints to create entities (individually and in bulk for all schema types) now support optionally registering the entities as well. If the simultaneous registration fails, the entities are not created to prevent the creation of invalid entities. Read more about these API endpoints here.
Set Registry IDs via API
Previously, the option for users to define the Registry ID of entities upon registration was only available in the UI. This option has been extended to the API as an added parameter in the bulk register endpoint. Read more about this functionality here.
Bug Fixes
The following bugs were fixed in this release.
Notebook
-
Narrow columns would display the first portion of long values followed by ellipses. If the number was in scientific notation, the exponent was included, resulting in a potentially misleading representation of the value. Impacted cells will now wrap in the cell to display the full value.
-
Long lists of tables in the “Add from Structured Tables” modal are scrollable when attempting to add a plate with this method.
-
Users no longer need to refresh their browsers to see newly created Notebook templates in the modal.
-
In the “Add from Structured Tables” menu, the selected “Source Table” was sometimes cleared, requiring users to repeatedly reselect the “Source Table”.
-
Entries that contain Lab Automation runs without results can be sent for review without error.
-
Moving the location of a box will display a purple dog ear in the “Location” column of the source box creation table, prompting users to refresh the table.
-
Moving the location of a box will update the “Location” column accordingly in the source box creation table after refreshing the table.
-
Moving the location of a plate will display a purple dog ear in the “Location” column of the source plate creation table, prompting users to refresh the table.
-
Computed fields remain locked in read-only columns in structured tables.
-
Entity link metadata fields that were re-named reflect the updated name in the “Add from Structured Table” modal on registration tables, rather than the old name.
-
In the “Add from Structured Table” modal, long sample names are wrapped to allow the “# of samples” column to remain visible.
Application Platform
-
For a search with multiple features, deleting a single filter would remove the wrong filter. The fix now reflects the right filter to be removed.