Welcome to the sixth 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 May 2022.

Notebook

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

Updated entry creation options

When creating entries, users can now include entry schema selection and completion.

To request this feature, contact a Benchling representative.

Insert custom columns in structured tables

Users can now add custom columns to any structured table via templates or modifiable entries. With custom columns, users can capture non-schematized, contextually relevant data in tables.

To request this feature, contact a Benchling representative.

Printing templates

Similar to entries, users can now print templates.

Registry and Inventory

The Registry and Inventory applications 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.

Inventory tables

Users can use Inventory tables to archive containers or plates and change the quantity of existing containers and plate wells via automated addition and subtraction. Previously, users leveraged transfer tables to create new containers, but with Inventory tables, users can create new containers, archive old containers, and change quantities within existing containers. Inventory tables are now live for all users.

Additional quantity units

Users can now select these quantity units:

  • 10^3 cells

  • 10^4 cells

  • 10^5 cells

  • 10^7 cells

  • 10^8 cells

Design and print labels with BarTender

Users can now design labels and print them using the BarTender integration. Using BarTender reduces the steps to print since you don’t need to manually upload label templates into Benchling.

Workflows

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.

Flowcharts

Users can visualize their linear workflows to plan and execute more complex and interdependent tasks and activities, improving efficiency, traceability, and collaboration among teams. Teams can visualize their workflows and manage interdependent processes that span multiple steps and users.

To request this feature, contact a Benchling representative.

Modify execution templates

Users can now modify execution templates while creating a workflows schema.

Print barcodes shortcut

Users can print barcodes by right-clicking task and output tables.

Sort functionality

Users can now sort by functionality on the Workflows page.

Start lookup from an associated task

When configuring snapshot fields in output schemas, users can now lookup information from an associated task.

Clone direct execution tasks

Users can now clone tasks within the Execute tasks modal by right-clicking on a task table.

Flowcharts and direct execution tasks are no longer executed into entries

Since users cannot execute flowcharts or direct execution tasks into entries, the Entry column will no longer display on the dashboard.

Expanded view in direct execution and output table submission modals

Users can now expand tables to view larger portions of their workflows tables.

Auto-fill direct execution modal

Users can now auto-fill the direct execution modal with one row per task, preventing the need to copy and paste.

Standardized messages on task and output submission modals

Messages on the task and output submission modals now include information about flowchart propagation to inform users of the consequence of this action.

Output table submission triggers task status modal change

Users are now prompted to change their task statuses after submitting an output table.

Improved date selector

Date and datetime schema fields in task and output tables now use an improved date selector.

Edit option on task table

The option to edit a tasks table will no longer display for users without edit access.

Insights

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

Redesigned bar charts

Users can now configure bar charts to contain aggregates (count, mean, and sum), error bars, grouped or stacked bar chart modes, and configurable y-axis ranges.

To request this feature, contact a Benchling representative.

Four new parameter types

Users can now configure the following parameter types in Insights: folders, teams, workflow task, and workflow task group.

Edit parameters option

Users can configure all parameters and their values at the same time in the dashboard’s overflow menu by clicking Edit parameters.

Lab Automation

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

Container concentrations in file upload

Users can now define a container’s concentration directly through a Lab Automation output file. Previously, this required an additional transfer step.

Plate well coordinates defined using separate row and column values

Users can now set well coordinates using row and column values when creating input files. For example, well A1 would be defined as row A, column 1.

Schemas

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.

Large-scale schemas for Results

Benchling can now ingest results up to seven times faster and entities up to two times faster. Additionally, Benchling can now store millions of entities and billions of results.

Access Management

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

Run and Result schema permissions

Schema access policies now apply to entity, entry, run, and result schemas. To help users ensure the right collaborators are added programmatically to schemas, there are now custom permission defaults for the entity, result, and run schema types.

To request this feature, contact a Benchling representative.

Updated invite limit for unverified free users

Academic users are now limited to sending four invites per day. If a user exceeds this amount, this message displays: “You may not invite more people today unless you're a verified academic. If you work at an academic institution, please verify your email and try again. Contact support@benchling.com with any questions.”

Update folder location in expanded view

Users can now change a folder’s parent location while viewing its settings.

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.

SDK docs

Users can now access Benchling’s public reference documentation for the Benchling Python SDK. The SDK docs allow developers to explore every function in the SDK, what it does, and its inputs and outputs. The SDK Docs can be found at https://benchling.com/sdk-docs.

Bulk-upsert APIs have been promoted to beta

Bulk upsert APIs are supported for AA and DNA sequences and custom entities.

Sort by createdAt field within assay-result endpoint

Users can now sort the assay-results listing endpoint using a createdAt field.

Bug Fixes

The following bugs were fixed in this release:

Notebook

  • The add from structured table feature no longer crashes when pulling items from results filled with formulas

  • .tiff images no longer fail to preview

  • @-mentioning a user in a text-based task field no longer causes error

  • Bulk entry exports no longer incorrectly use one entry ID across all pages.

  • Cloned tables no longer miss default values within templates.

Molecular Biology

  • Default colors are no longer incorrectly assigned in .csv parser for feature libraries

  • Users are now able to use two different lengths of homology regions during two-fragment assembly. Previously, the HR lengths could only be one base pair apart

Workflows

  • Task finder button option no longer displays on read-only output tables

  • Error messages no longer display when adding tasks to a flowchart task group

Insights

  • Tooltips in scatter plots no longer render away from where a user was hovering

  • Legend labels in charts no longer overlap

  • Pie chart legend labels are no longer sized incorrectly

  • Configured schemas were not saved in Workflows task parameter

  • Long legend labels no longer render over the chart with gradient legends in Heatmaps and Scatter plots

  • Legends with one item no longer render a scroll wheel

  • Numbers in heatmaps, pie charts, and scatter plots are now correctly formatted

Schemas

  • Benchling no longer duplicates a lookup if an entity is present twice in a results row

  • Benchling no longer returns results for lookups that are linked by any field

Access Management

  • Users could not consistently drag and drop imported files into folders

Application Core

  • Resolved an issue with long latency for loading entity links

Developer Platform

  • Bulk-registered entities in the SDK no longer handle a list of strings incorrectly

  • Listing mixtures in the SDK now works appropriately

  • Retry Strategy no longer breaks when paging in the SDK

  • Custom Entities endpoint now returns a 400 error code when a null is passed as an alias

Lab Automation

  • The output processor no longer shows a “Failed - Click to Sync Run” error before processing was initiated

  • Resolved errors in column mapping modal within the Output File Config UI

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