Product Bulletin: Fall 2020

BY Prem Mohanty
November 19, 2020

With fall almost over, the life science industry continues to persevere through this global pandemic. We’ve seen our customers adopting new digital strategies, leveraging shift-based time in the lab, and driving innovation on needed therapeutics and vaccines, including those directly targeted at COVID-19. The importance and impact of the research that our customers do has never been greater.

Benchling released dozens of new features and enhancements across all of our applications to continue driving our mission of accelerating life sciences R&D. One feature that we’re really excited about is bulk codon optimization and back translation, which helps our customers dramatically increase their sequence design throughput. Read on to learn more about this and other new features below.

Accelerate Throughput With Bulk Codon Optimization And Bulk Back Translation

What it is:

Benchling’s codon optimization and back translation tool streamlines the process of designing a DNA sequence to optimize protein expression in a target organism. This tool leverages a trusted algorithm, balances codon prevalence with other important input parameters, and provides powerful customization for GC content, uridine depletion, and other advanced parameters to provide high quality results.

What’s new:

We now support the use of codon optimization and back translation in a high throughput manner boosting productivity significantly. Additionally, we added a new parameter and made several user interface enhancements to make this tool even more user friendly and relevant to your research.

New features that make it possible:

  • Bulk codon optimization and back translation: This new feature allows users to select existing DNA sequences or AA sequences from the expanded toolbar view and generate corresponding codon optimized sequences in bulk. This highly requested feature increases sequence design throughput significantly, saving users time and effort. It is especially useful for power users who work with a large number of sequences.

New bulk codon optimization modal

  • New “patterns to reduce” parameter: We added a new “patterns to reduce” parameter to codon optimization. This parameter reduces the usage of user specified nucleotide patterns across the entire sequence. For example CpG motifs in pDNA are known to contribute to immune response and would be a pattern that can be reduced with this new parameter. This powerful new parameter makes the codon optimization tool much more flexible as users can fine tune the output to better fit their research needs.


    “Pattern to reduce” configuration menu

  • User interface enhancements:  As part of the recent updates, we also upgraded several aspects of the codon optimization tool’s user interface (marked in the accompanying screenshot. These changes together make it easier to set up a codon optimization analysis.
    1. Organism is now an optional parameter: This helps users perform codon optimization based on their preferred parameter selection without having unnecessary competing constraints.
    2. Added visual counts to the tabbed parameters:  For the tabbed parameters such as “Avoided cut sites”, “Preserved cut sites”, “Protected regions”, and “Patterns to reduce”, users can now see a count of the constraints configured across these parameters. This helps users keep track of their selections while setting up the tool.
    3. Added a “Remove all” button to quickly clear out existing constraints: All the tabbed parameters such as “Avoided cut sites”, “Preserved cut sites”, “Protected Regions” and “Patterns to Reduce”, now have a “Remove all” button. This helps clear out existing constraints with the click of a button.

Three new UI enhancements to the codon optimization modal

  • Saving codon optimization parameters to sequence description tab: With this new update, the detailed history of codon optimization and results from the analysis are automatically added to the description tab of the corresponding codon optimized sequence. This makes it easy to trace and understand all the changes made by the codon optimization tool.

Codon optimization details added to the description tab of a sequence

What you can do with it:

Codon optimization and back translation are useful across a variety of research areas and industries where protein expression needs to be optimized in a host system.

  • Antibody production
  • Enzyme technologies
  • Fermentation optimization
  • Plant biotechnology
  • Vaccine development
  • Viral vector production

To learn about other new features and enhancements by product, click on the product links below.

Notebook
Molecular Biology
Registry and Inventory
Insights
Lab Automation
Platform

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NOTEBOOK

Benchling’s Notebook was designed to promote higher quality data capture with an exceptional and intuitive user experience. Recent releases significantly improve the usability of the transfer table and add the option to integrate with Box.

New transfer table
Transfer table is one of the key types of structured tables in Benchling. It is used to transfer samples into or between containers directly within your Notebook entry enabling you to manage samples in the context of your experiment. With the recent releases we have revamped the transfer table to make it more intuitive and user friendly.

  • New tabbed configuration user interface with more configuration options
  • More descriptive column layout
  • Ability to add samples and rows in multiple ways
  • Replacing “Number of Containers” column with “Unified Add Samples” modal to improve metadata tracking of replicates

Click on the corresponding links to learn more about the transfer table and the new updates.

External file integration with Box
Benchling has always supported the integration of Notebook with external file storage systems to fit the unique data storage needs of our customers. We already support integration with file storage systems such as Google Drive and Dropbox. With the latest release, we now support external file integration with Box. This integration allows you to easily connect your Box account, browse Box files directly in Benchling, and drag and drop files directly into Notebook entries.


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MOLECULAR BIOLOGY

Benchling Molecular Biology is a cutting edge, in silico design tool that supports the latest scientific workflows. In addition to the changes to codon optimization discussed at the beginning of this article, recent product updates also add more options to export sequences and sequence-based information.

More export options for sequences
The ability to export sequences and sequence-based information such as annotations is a critical part of how Benchling enables collaboration and sharing of information between scientists. We added to this capability with recent releases.

  • Ability to select “Export Annotation Colors” and “Convert Non-Standard Annotation Types” for bulk genbank annotation export
  • Addition of a “Copy to” button to AA sequences

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REGISTRY AND INVENTORY

Registry and Inventory are core to modeling data on Benchling and managing critical in-lab samples. With the recent releases we added features related to the new entity type “Mixtures”, expanded support for more bulk actions through spreadsheet uploads, and further improved worklists.

Deeper integration of “mixtures” across Benchling
Mixtures is a new entity type in Benchling used for managing and tracking samples made up of two or more ingredients such as media, buffers, and formulations. We have added several new functionality to expand the utility of “mixtures” to better meet the needs of your experiments across Benchling.

  • New mixture preparation table to allow prep creation directly in the Notebook entry
  • The data warehouse now supports mixture ingredient data and related metadata
  • Added ability to use new units such a QS, CFU/g, CFU/kg, and (x10^6) cells/mL
  • New “Notes” column has been added to the mixtures tables in both Registry and Notebook to allow for freeform text entry
Improved collaboration with worklists
Worklists help users work with large sets of samples such as entities, batches, containers, and plates and save scientists time and effort by facilitating bulk actions on large numbers of samples. With the new update, worklists can now be shared with other users, teams, or orgs. This streamlines sample handoffs between users and extends the benefits of worklists across an entire team.
Expanded functionality with spreadsheet uploads
Spreadsheet uploads is one of the most flexible ways to create or update data in Benchling. This feature is especially more powerful when dealing with large numbers of samples. Recent releases add to this capability.

  • Ability to change registry ID in bulk via spreadsheet upload
  • Bulk import locations via spreadsheet upload
  • Bulk update plates and boxes via spreadsheet

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INSIGHTS

Benchling Insights enables users to leverage their data and run analytics natively. This opens up access to comprehensive operational and scientific insights. We have added several new features to the Insights application which enhance the user experience.

Insights dashboard embedding in Registry is now in limited availability
Benchling Registry helps centralize all results related to an entity automatically, while Insights helps visualize the results. With this new feature, the Insights dashboards with data visualizations can now be linked to the appropriate Registry entry. This makes it easy to not only centralize but also share results with accompanying analysis. This feature is in limited release. Contact [email protected] to enable this feature for your tenant.
Improvements to the user experience
We continue to release features that make Insights even more user friendly. 

  • Added “storage” as a new parameter configuration type which allows users to access all storage related schemas while setting up a query
  • Table sorting is now enabled in Insights tables which allows users to sort information in a column in ascending or descending order
  • Headers of Insights tables are now frozen which helps keep the headers in view while scrolling down the table

Insights now shows a message when there are no blocks in the dashboard

More relationships in dynamic warehouse diagram
Dynamic warehouse diagram allows users to understand the relationship between different entities, results, requests, workflows, and other schemas. As part of the recent releases, we have added even more relationships to the diagram so that users can set up effective queries quickly. To view the list of supported relationships check this release note.

 

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LAB AUTOMATION

Benchling for Lab Automation unlocks the potential of your laboratory hardware by integrating Benchling with liquid handlers and analytical instruments. We recently released updates which expand functionality of the Lab Automation product by adding new processing steps, configuration options, and lookup steps.

Additional processing step options We continue to add more options to the processing step of a run schema to better suit user needs.

  • Processing step to remove trailing rows from an output file
  • Processing step to filter out rows that contain certain values (“notin”)
  • Processing step to filter values based on numerical ranges, including less/greater than, less/greater than or equal to, equals, not equal, and between
  • “SPLIT” processing step to separate a combined value from a single cell into two columns by a delimiter
  • “ADD_COLUMN” processing step to add a column with a constant value looked up via a lookup config
  • “MERGE” processing step to merge two columns in the output file together, separated by a delimiter

 

New configuration options We released several updates that provide a greater range of options while configuring your lab automation runs. 

  • Configuration to allow user to select project folder and location in the lab automation run
  • Lab automation input and output files support configurable delimiter and file extension
  • Lab automation runs can be configured to allow the user to select folder and inventory location at runtime
  • User can select a folder (rather than project) when creating a workflow

 

Lookup step updates
A handful of new lookup steps were added as part of the recent updates.

  • COUNT lookup step returns the count of values in a schema field
  • REGISTRY_ID lookup step can find an entity’s registry ID
  • BOX_CONTAINERS lookup step can find containers within a box

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PLATFORM

Benchling’s platform is designed to provide a unified experience and help you easily manage and quickly access your research across Benchling applications. We released several updates that significantly improve search functionality and audit capabilities. We also introduced a brand new way to integrate with Benchling (still in public beta) and added new APIs and new filters for APIs.

Improved audit capabilities
The audit features on Benchling are critical to enabling enterprise control and regulatory compliance. Benchling already provides robust audit tracking throughout each application. With the new updates, Benchling makes it easy to export these audit logs. 

  • Export the audit log for a project
  • Export the audit log for a single user or multiple users
  • Export the audit log for a team
  • Export the audit log for an organization
Search improvements
Benchling search allows users to access their and their team’s research data easily. We continue to add to the search capabilities to increase performance and enhance user friendliness.

  • DNA sequence (DNA string and reverse complement base) search performance has been significantly improved

Searches can now be saved which helps you access and replicate your favorite searches quickly

 

Events public beta Events (beta) is the newest addition to our developer platform. Benchling’s Events allows external services to subscribe to events that are triggered in Benchling (e.g. plasmid registration, request submission, etc.) through the AWS EventBridge system. This brand new class of integrations that react to actions in Benchling has become a necessity for many of our customers working with advanced use cases and related IT infrastructure. After successful adoption of Events in the early access program, we are excited to open up the functionality to a wider audience as part of this beta release. You are eligible to access Events (beta) if you already have access to our developer platform. Contact [email protected] to have this feature activated for your team’s use. Learn more with this getting started guide.
New APIs Benchling’s APIs are built to match the flexibility and speed of modern life science R&D. We continue to add new APIs that extend functionality and provide new ways to interact with data in Benchling. As part of the recent releases, we have added APIs for Run, Request, and Result schemas that allow you to retrieve the information by their unique ID.
New filters for APIs
Benchling allows you to filter API calls to identify the specific information required. With the latest updates, we have expanded these filters.

  • Added schemaId filter to experimental /search-bases endpoint
  • Added API ids filters for Listing endpoints
  • Added barcodes filter for storage List endpoints

For a more comprehensive list of all the features released refer to our product release announcement section at help.benchling.com.

Published by Prem Mohanty
VIEW ALL POSTS BY Prem Mohanty

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