Configure the Output File Processor to Capture Results

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

Populated run and associated Results

Process 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

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

Example output file

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.

Example JSON configuration

Note: fields from the run schema can be accessed with a lookupConfig and used to populate fields of the new entities that are created.

{
	"fields": [],
	"automationOutputFileConfigs": [
		{
			"name": "Quant",
			"resultSchemaInfo": {
				"fields": {
					"concentration": {
						"columnName": "Concentration (mg/mL)",
						"type": "DIRECT"
					},
					"date_and_time": {
						"columnName": "Date and Time",
						"type": "DIRECT"
					}
				},
				"schema": "assaysch_p13pJSRU"
			},
			"columnTypes": [
				"ENTITY_NAME",
				"SCHEMA_FIELD",
				"SCHEMA_FIELD"
			],
			"delimiter": ",",
			"fileExtension": "csv",
			"tableType": "SAMPLE"
		}
	]
}

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