Configure the Output File Processor to Capture Results

  • Updated

Benchling has the ability to capture Results using Connect output file processor. The functionality is convenient for use cases where raw data files from an analytical instrument are associated with registered entities in your Benchling Registry.

Populated run and associated Results

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Screen Shot 2021-03-04 at 2.39.09 PM.pngProcess overview

  1. Create the Result schema you want to use in the Benchling Registry if it doesn’t already exist

  2. Create a Run schema to process the output file

  3. Create an output file with Result field information, one row for each new Result

  4. Insert the Run object into a Benchling notebook entry and create a new Run

  5. Upload the output file to the Run and click the process button, the user must have write permissions agains the result schema in order to process

  6. Results are now associated with relevant entities and linked within the Run

Example output file


Date and Time

Concentration (mg/mL)






















Output files should be comma separated UTF-8 plain text format. Each row represents the one unique Results input.

Note: Multiple output files can be processed within the same Run allowing for multiple captures of the same Result that may came from different raw output files.

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Example Run configuration

  1. Navigate to the Run schema in the Configuration settings
  2. Click the “+” in the Output file configurations section to configure how Benchling processes your output files

  1. Configure the display name. This will be the section header for the output file section in the run.
  2. Select “Record results” in the “Bencling action” section

  1. Click on “Configure result schema” to select from the existing results schema or create a new result schema
  2. To configure new result schema in the run:
    • Click on “Create new result schema”

  • Add the result schema columns and select column type then click “Create result schema”

  • Add a Name to the new result schema and select the Benchling organization.
  • Specify the result field names, required fields, multi-select fields, and field definitions. Click “Next”

  • Change the new result schema collaborators and change access policies if needed. Click “Create result schema”

  1. Configure column mapping to specify how Benchling interprets the columns in your output file.
  2. Toggle column mapping by column name (expects the exact header in data file) or column order (expect the exact order in data file).



For runs that process >= 700k cells of results, File Queuing can be enabled to improve the convenience of uploading very large files into Benchling.

Benchling supports ingestion of localized numbers and dates. You can configure the Locale in your user settings. To learn more, visit Updating user locale.

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