Welcome to the eighth volume of our 2022 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 2022.

Notebook

Benchling Notebook helps users log their experiments, create protocols, and capture results against their samples.

Notebook virtualization

Users will experience significantly faster load times in entries as Benchling now only loads interface elements that are in the viewing window. The remaining entry components load when users navigate to them. Specific time-performance enhancements include the initial loading of entries, switching between entry tabs, submitting structured tables, and clicking on entry chips.

Archival status of results available in .csv download

Users can view the archive status of results when they download the Results table as a .csv.

Prevent entry reversion

Users can now disable entry reversion for an entire tenant. Customers can opt-in to this feature.

To request this feature, contact your Benchling representative.

Molecular Biology

Benchling’s Molecular Biology is a cutting-edge in silico design tool that supports the latest scientific workflows.

RNA sequence entities

Users can now create and import RNA sequence entities. They behave similarly to DNA sequence entities, with a similar set of sequence-specific features, such as annotations, translations, and primers. Further, users can visualize an RNA sequence's chemical modifications.

To request this feature, please contact your Benchling representative.

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Small Molecule

Small molecule entity in Registry helps users model and interact with chemical compounds throughout the platform, allowing users to draw, visualize, store, and search chemical structures

Molecule entities and chemical structure search

Users can now model and interact with molecules in Benchling using molecule entities.They can use SMILES strings in Registration tables and enforce basic chemical structure uniqueness constraints based on canonical SMILES.

Users can also:

  • Design and draw chemical structures with MarvinJS

  • Import molecules using SMILES, .mol, and .sdf file formats, and bulk import using SMILES strings via .csv files

  • Calculate common physicochemical properties, such as log P and molecular weight, and display them alongside the registered molecule

  • Search for molecules by substructure or similarity

  • Manage chemical inventories, collect molecule data from liquid handlers, create and edit molecules via API, and standardize data capture in warehouse tables

To request this feature, contact a Benchling representative.

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Monomer chemical structures display when editing nucleotides

Users can now view the chemical structures of monomers when editing in the Edit Nucleotide modal. This release includes the modified nucleotide functionality.

Chemical structure displays in modified nucleotide legend

Users can now view chemical structures when hovering over the modified nucleotide legend in a sequence map.

Relaxed formatting requirements for HELM imports

Users no longer need fully formed HELM strings to create an oligo or sequence via HELM. This change is reflected on single oligo creation modals, .csv import flows, and Registration tables.

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Computed field for modification-aware molecular weight

Users can now calculate modification-aware molecular weight based on the chemical structures associated with each monomer using the Modification-aware sequence molecular weight computed field. Previously, molecular weight computed fields only calculated natural-sequence molecular weights, even if users incorporated chemical modifications via monomers.

To request 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.

Bulk update plate and box locations via spreadsheet

Users can now bulk update the parent storage location for plates, boxes, and containers via spreadsheet.

Bulk update concentration and units

Using the Inventory expanded view, users can now bulk update the concentration or quantities of containers and wells even if the inventory items do not share the same schema type.

Insights

Insights enables users to query, visualize, and share high quality, structured data that resides in Benchling.

Clear parameters from dashboards

Users can now select Clear All Parameters in the Edit Parameters modal.

Lab Automation

Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.

Assign aliases to registered entities

Users can now map a column to type Alias to assign registered entities aliases.

Application Platform

Application Platform provides users a way to manage permissions, leverage administrator capabilities, and organize teams, organizations, projects, and folders.

Unambiguous date format

Users can now set date and time formats to International (12 hour) and International (24 hour). This update provides clearer date formats for global teams.

Access Management

Idle timeouts

Use idle timeouts to automatically log users out of Benchling when users are idle for a predetermined period of time. This feature provides additional security and privacy for users who store sensitive data on Benchling.

To request this feature, please contact your Benchling representative.

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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.

View app display names

Users can now view app display names in fields like Authors and in @-mentions instead of app IDs.

App management

You can enable App Workspace so users can view when particular Benchling applications were last in use, what teams use the application, and what projects have access to the application.

SDK 1.4.0 Release

Version 1.4.0 is a re-release of version 1.3.0, which was rolled back due to unanticipated breaking changes; version 1.4.0 has fixed the missing dependency issue present in 1.3.0, including:

  • Selective support for alpha and beta APIs

  • App configuration support

  • Custom httpx client support

  • Python version 3.10 compatible

For more information on the new functionality originally introduced in version 1.3.0, visit the change log post.

Bug Fixes

The following bugs were fixed in this release:

Notebook

  • Users couldn’t drag and drop sequences from the Registry into Notebook entries

  • Applications crashed when users tried to create, move, or open folders in projects

  • Users using the Firefox browser experienced unresponsive copy and paste menu options

  • Uploading a spreadsheet to a Results table matched outdated schema field names to a spreadsheet’s column name

  • Extra scrollbars appeared on tables

  • Users were experiencing error messages when filling out cells in a table with values ending in .0

  • Newly added rows and archived rows couldn’t be deleted before submitting

Molecular Biology

  • Linear maps of sequences were not rendering when scrolling through a sequence

  • Feature libraries with more than 5,000 features were being imported

Access Management

  • A vague error message displayed when users created folders without having sufficient access

  • Schema access policy messaging needed improving

  • Users will no longer have archived locations as a destination option. Archived locations now need to be unarchived to be viewed

  • Removed unnecessary warning dialog about changed permissions when moving an item within the same project

  • Benchling emails are no longer sent to users’ spam folders

  • Removed an additional verification step for users who have already been authenticated by Google and use their Google account to sign into Benchling. Now, users who are verified by Google’s authentication process can automatically log into Benchling

  • Improved accessibility and messaging so users can more easily view and accept invitations to join organizations on Benchling. Previously, users had to scroll through a list of organizations to view pending invitations

Application Platform

  • Entity links were not properly loading

Developer Platform

  • The URL was missing when performing a GET/workflow-task-groups call

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