Benchling Product Bulletin: Winter 2021

BY Caitlin La Honta
March 3, 2021

Data is the currency of life sciences R&D. Its value to your company depends on its completeness, accuracy, and ease of use. A key highlight of our most recent product release makes it easier to derive insights from scientific and operational data by placing it in context with your company’s entities, samples, and processes.

Embedding Insights Dashboards in Registry

With Insights, teams can visualize and share their R&D data in Benchling through robust dashboards. Now you can embed relevant dashboards within the Registry to easily query, view, and analyze data without the need to navigate to Insights.

Once you configure the Registry schema to include Insights dashboards, a new “dashboard” tab will appear in the Registry entity view so you can access related dashboards directly within Registry.

How this feature helps you

Embedding Insights in Registry combines the analytical power of Insights with sample traceability in Registry. By surfacing context-relevant intelligence alongside entities, teams can make faster, more informed decisions about data across Benchling.

Embedding Insights in Registry is especially useful for analyzing scientific or operational entity data in the context of an entity. For example, you can show:

  • The location of plasmid tubes in the lab when looking for a particular plasmid entity
  • The performance of a particular cell line against other reference cell lines
  • All downstream entities that are connected to a selected gene, such as the gene in a plasmid or linked to an AA sequence
  • A specific results-based analysis for a given entity, for instance, a growth curve for a selected bacteriophage

Key functionality

Here is the key functionality that will help you get the most out of this new feature:

Dynamic updates:  Insights dashboards dynamically update as entity results change. Flexible parameters:  The dashboards support both static and dynamic parameters.
New configuration UI:  You can now access a new interface for configuring a dashboard to examine a particular entity. Block templates:  You can now run a SQL query or use a quick start template to create dashboards linked to registry schemas.

Example use cases for Insights embedding in Registry

Insights embedding in Registry is a flexible feature that supports many use cases. It is especially helpful for analyzing experimental or operational entity data alongside that particular entity.

For example, you can configure dashboards to show:

  • The location of plasmid tubes in the lab when searching for a particular plasmid entity
  • The performance of a particular cell line against other reference cell lines, in the context of the selected cell line
  • All downstream entities that are connected to a selected gene, such as the gene in a plasmid or linked to an AA sequence
  • A specific results-based analysis for a given entity, for instance, a growth curve for a selected bacteriophage

Learn about other features by clicking through the links below:

Notebook
Molecular Biology
Registry and Inventory
Insights
Lab Automation
Platform

 

Notebook

Benchling Notebook’s easy-to-use interface lets you log experiments, track information, and capture sample results, all while driving unified data capture across Benchling. We’ve made the Notebook more intuitive by enhancing the transfer table UI and surfacing review statuses for Notebook entries.

Tabbed interface for transfer tables

Transfer tables now have a more streamlined UI so you can create tables faster. The new tabbed interface makes it easy to create new containers or use existing ones.

Transfer tables in Notebook

Visibility into Notebook review status

The Notebook entries list now has a column for Notebook status to depict the review state for an entry. This gives you the ability to quickly see a Notebook’s review status as well as understand the state of Notebook reviews across all relevant entries.

Statuses in 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. Recent upgrades to the tool provide greater flexibility for managing oligo and sequence data.

Oligo search and bulk import

You can now conduct more precise searches on your DNA bases by looking for registered oligos. When searching within a DNA base, set the type to “Oligo” and the filter to “Nucleotide String.” Toggle the “includes text” field, and fill in the specific oligo.

Search by Oligo

In addition to executing more precise oligo searches, we’ve also replaced the bulk oligo creation workflow with the standard CSV workflow. This gives you the ability to upload oligos in bulk from a spreadsheet. The CSV workflow also allows for more flexibility when mapping data to Benchling, since you can choose which columns align to which base sequence.

Bulk unlinking and unfilling parts in DNA sequences

You can now unfill and unlink DNA sequences in bulk. Previously, to sever part links, you needed to unlink the parts and delete these pieces from the metadata, one sequence at a time. Now, you can select multiple entities at once and toggle to “analyze” → “unlink parts” to remove them in bulk. This increases throughput and reduces repetitive, manual tasks.

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Registry and Inventory

Benchling Registry and Inventory work together to power your experiments through connected data — whether sequences, samples, or experimental results. With Benchling Registry, you can standardize, connect, model, and track samples across your experiments. Benchling Inventory provides a digital window into your physical lab, enabling you to track vials, wells, batches, and more while linking them to relevant results. In this release, we’re increasing the number of supported values in mixture tables and adding new ways to configure mixture experiments.

New values for mixture tables and containers

With the addition of the “QS” value and microbiology concentration units, you can now execute more detailed experiments for a wider variety of use cases.

QS value for solvents: “QS,” meaning “quantum satis” or “enough” in Latin is now a supported value for solvents in mixtures. Instead of a numerical value, QS indicates that enough of the solvent should be added in order to reach the total desired quantity. QS enables use cases across media and formulation where this value is often used when preparing samples.

Concentration units for microbiology: containers now allow for three additional concentration units – CFU/g, CFU/kg, and (x10^6) cells/mL. Adding these categories permits new microbiology use cases for estimating the number of viable bacteria or fungal cells in a sample.

QS value

Preparation instructions in Notebook

You can now include preparation instructions for mixtures and insert them into Notebook entries. When creating a mixture from a mixture schema in the “Media Recipe Instructions” section, toggle to the “Insert” button to add the prep. This provides more direct access to relevant preparation instructions and makes it easier to trace the history of the recipe.

Prep instructions in Notebook

Optional parent fields for mixture experiments

When creating mixture preps in Notebook, you are no longer required to fill out the parent field. Now, you can track mixture experiments that don’t yet have a defined recipe. For example, if you are conducting a new experiment, you can track the mixture prep without needing to trace back to a parent formulation or recipe.

Optional parent fields for mixture experiments

Surfacing information on box position via API

Using the API, you can now identify the number of positions of a box that don’t contain existing containers. This gives you greater visibility into your Benchling Inventory for integration or automation purposes.

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Insights

Insights lets you visualize, query, and share Benchling data to help answer important questions about your R&D pipeline, experiments, team productivity, and resource allocation. In addition to Insights Registry Embedding mentioned above, we’ve released features that make it easier to find important information in your data warehouse and SQL queries.

More options for sorting, tracking, and finding information

  • Get the information you need faster with new functionality for configuring how you sort and view data:
  • Sort by column:  you can now sort Insights tables by column.
  • Sort by storage type:  add specific storage-type parameters based on schema (containers, boxes, plates, locations).
  • Frozen table headers:  Insights table headers are now frozen, making it easier to keep track of each column.
  • Search an entire SQL query:  we’ve also expanded the “find” shortcut to include the entire SQL query. Search for keywords throughout the SQL editor – not just what’s on screen.
Search an entire SQL query
Search an entire SQL query

 

New ways to model entity relationships

We now support eleven new relationships within dynamic warehouse diagrams, extending coverage to additional entity and result types:

  • container_content
  • container_transfer
  • request_assignee
  • request_fulfillment
  • request_sample
  • entity
  • workflow
  • stage_run_sample
  • stage_run
  • workflow
  • field

New entity relationships

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Lab Automation

Lab Automation lets you integrate lab instruments — like liquid handlers and plate readers — into Benchling to scale experiments, increase scientist productivity, and sync research across software and hardware. In this release, we are continuing to focus on simplifying data entry and management to improve efficiency for users.

More ways to sort, search, and filter data

  • Sort by columns alphanumerically:  previously, sorting by well position led to A1, A10, A11, A12, A2. Now, well positions sort alphanumerically:  A1, A2, A3…A9, A10, A11.
  • Look up more than one value by using the ADD_COLUMN filter:  previously, you could only return a single value in a given column. Now, if a field contains two entities, you can use a multi-entity link to generate one row for each entity.
  • Use new parameters to filter results:  we’ve added new parameters for filtering on type of entity, container, or plate. The FILTER lookup now supports >, <, <=, >=, “is null”, and “not null” filter types to help you identify a wider range of values.

New options for configuring runs

  • Interleave four source plates onto one:  configure Lab Automation runs to interleave four source plates onto one destination plate. For example,  you can interleave a 96-well plate onto a 384-well plate.
  • Leave primary samples blank:  you can now upload results with a blank primary sample through a Lab Automation run. This supports results schemas that don’t require a primary sample.

Request entities directly within tables

Within a run output table, you can create a request for entities or containers directly within the table using the “create request” shortcut.

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Platform

The Benchling Platform connects capabilities and data across Benchling to provide a simple, unified user experience. In this release, we’re excited to announce Benchling Validated Cloud which makes it possible for R&D teams to operate from a unified, validated informatics solution. We’ve also extended the flexibility of the developer platform through Events and other API updates.

Benchling Validated Cloud

The Benchling Validated Cloud extends the Benchling platform for use in GxP validated environments. This solution improves the tech transfer between research and development to help accelerate product development. With quarterly validated releases and robust user access controls, organizations can seamlessly unify research and development teams while adhering to the latest regulations. Learn more about Benchling Validated Cloud from our recent webinar and blog.

Events API

The Events API functionality triggers external systems from events in Benchling. This allows for a seamless flow of information across your systems by notifying external tools of changes happening in Benchling.

Developers can subscribe to Events for a variety of different use cases, such as when a user registers an entity, creates a Notebook entry, or Requests a submission. (View the list of available Events here.) Subscribing to such Events enables Benchling to stay connected to external tools in near real time — for example, to support live syncing between databases. Empowering developers with this robust API interface offers greater agility for managing advanced IT infrastructure use cases. Learn more about getting started with Events in our API user guide.

Additional API updates

Benchling APIs are built to match the speed and agility of modern R&D so you can easily extend Benchling into your broader digital ecosystem. We continuously add APIs to increase flexibility in integrations to Benchling. In this release, we’ve included new functionality to help you simplify certain tasks — like registering IDs and requesting tasks — through the API.

  • Create and register entities in a single API call:  when you create entities via API, you can optionally register them as well, saving time by grouping tasks. If the registration fails, the entities are not created at all. This prevents the creation of invalid entities, which is especially useful when bulk importing data.
  • Set Registry IDs via API:  you can now define an entity’s Registry ID via API, in one of two ways:
    • bulk register entities endpoint
    • various create and bulk create endpoints under DNA sequences, AA sequences, oligos, and custom entities
  • Directly call an API for a full object:  apiURL is now available in API resources, allowing you to call the API for a full object if you need additional context or resource sub-references.
  • Create request tasks in bulk via API:  use the new endpoint to create bulk Request tasks.
  • Use list endpoints for ID filters and barcode filters:  you can now use list endpoints instead of bulk-get endpoints, which aligns more to traditional RestAPI conventions. You can leverage list endpoints for two tasks:
    • Using the ‘IDs’ filter, return a list of comma-separated IDs from all list endpoints
    • Using the ‘barcodes’ filter, return a list of comma-separated storage barcodes from all list endpoints

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Published by Caitlin La Honta
VIEW ALL POSTS BY Caitlin La Honta

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