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
Create the Result schema you want to use in the Benchling Registry if it doesn’t already exist
Create a Run schema to process the output file
Create an output file with Result field information, one row for each new Result
Insert the Run object into a Benchling notebook entry and create a new Run
Upload the output file to the Run and click the process button
Results are now associated with relevant entities and linked within the Run
Configuration details
Example output file
Prep | Date and Time | Concentration (mg/mL) |
PR1982 | 3/4/2021 | 0.797 |
PR1999 | 3/4/2021 | 0.915 |
PR2003 | 3/4/2021 | 0.851 |
PR2190 | 3/4/2021 | 0.312 |
PR2199 | 3/4/2021 | 0.412 |
PR2156 | 3/4/2021 | 0.489 |
PR2174 | 3/4/2021 | 0.722 |
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.
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.