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.

The Basics

When Runs are created and configured, they can be inserted into the body of Notebook entries via Insert. After the Run is inserted, users will have the option to fill out the different fields of the Run, generate an input file, or upload and process an output file. Depending on the purpose of the Run schema, you may have all of these components configured, or only one or two of them. In any case, the basic configuration of a Run involves three components:

  • Run Fields

  • Input File Config

  • Output File Config

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Run Fields
Run schema fields can be configured to allow users to enter any necessary information to be captured with the Run itself and/or to provide information that will be used in the generated input file. The available schema field types that can be used include:

  • Text

  • Dates

  • Entity links

  • Storage links

  • Dropdowns

  • Floating points

  • Integers

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 files based on information entered in 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 .csv file (e.g., transfer instructions for a liquid handler, or a sample sheet for a qPCR instrument). See the image below for a simple 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 of a Run is a configurable portion of a Run schema that will process .csv files and translate it to Benchling actions. These translated actions can be as simple as moving samples from one plate to another plate or as complex as creating newly assembled plasmids with automatically filled-in sequence links while maintaining the movement of liquid from tubes to plates. In addition to translating the file into Benchling actions, this component can also be used to capture analytical data similar to Results tables.

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 captured within 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 data 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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