Configure a Lab Automation Run

  • Updated

Before proceeding, be sure to review “What is a Lab Automation Run?”.


Who can configure a lab automation Run?

Only organization-level admins can create and configure lab automation Runs.


Lab Automation runs can be inserted into the body of Notebook entries, templates or sub-templates via the Insert dropdown. Runs have three components:

  • Run Fields
  • Input File Config
  • Output File Config

Depending on the purpose of the Run schema, you may have all of these components configured, or only one or two of them.

Run Fields

Run fields are optional, depending on the actions being performed by the Lab Automation Run. When used, run fields allow users to enter the necessary information to perform an action such as creating a file for a liquid handler transfer or creating and filling new containers. Run fields can also be used to provide additional context for an output file being ingested. For example, adding the contents per well from a plate reader file when creating the results in Benchling. 


The available schema field types that can be used include:

  • Text
  • Number (integer or decimal)
  • Date
  • Boolean
  • Entity links
  • Inventory link
  • Dropdown
  • Attachment

For more information on how to configure run fields, please read Configure the fields for a Lab Automation run.

Input File Config

Run schemas can be configured in a way that allows Benchling users to automatically generate .csv, .tsv or .txt files based on information entered in, or obtained through, the run fields. There is flexibility in how the file is generated that allows the run to remain agnostic to the actual instrument that will ingest the file (e.g., transfer instructions for a liquid handler, or a sample sheet for a qPCR instrument). See the image below for an example of a .csv file generated.

For more information on how to configure the input file config, please read Configure the Input File Config of a Lab Automation Run.

Output File Config

The output file config component will process .csv, .tsv or .txt files and translate it to Benchling actions. These actions can range from moving samples from one plate to another to creating new entities with results and containers. 

At its core, the output file processing capability enables users to capture the context of what happens in the lab and ensure that it’s recorded in Benchling. Some common use cases include, but are not limited to:

  • Record a plate stamping method that was just performed on a liquid handler
  • Register new bacterial samples after a high throughput transformation method
  • Upload plate reader results for multiple 384-well plates

For more information on how to configure the output file config, please read Configure the output file config of a lab automation run.

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