What is a Run?

A Benchling run is an experiment performed through an assay instrument, robot, or software analysis pipeline. For example, runs can be used to model NGS sequencing runs, flow cytometry experiments, or liquid handling methods. The associated structured data collected from the experiment can then be linked back to the run and viewed within the Notebook.

What is a Run Schema?

A run schema defines the metadata that should be tracked on a run. For example, the run schema may include fields for attaching raw instrument output files, or parameters adjusted directly on the instrument.

Who can configure Run schemas?

Only organization level admins are able to configure run schemas.

Create a result schema: Step-by-step Instructions 

1. Access the Result Schemas

From your Benchling workspace, click on your avatar (bottom left corner) and select Feature Settings → Result Schemas. This will take you to the result schemas page.

Next, in the “Result Schemas” section in the sidebar, click on “Run Schemas."

2. Create a new Run Schema

Click on the create icon to initialize your new schema. You will be redirected to a page that asks for more information:

On this page, you will be need to enter the name of the new schema before clicking the Create button. Do not touch the JSON Spec Box.

Make sure to double-check the schema name before clicking Create! Once a schema is created, you will not be able to change the name.

3. Link a result schema

In order to upload results from the API that are associated with a run, the result schema must be linked to the run schema.

  1. First, look at the URL of your run schema. It should be something like this: https://example.benchling.com/your_username/assay-schemas/runs/assaysch_i2sX8NGy
  2. Extract the run schema's ID from the last part of the URL, for example “assaysch_i2sX8NGy”.
  3. Then, make sure to configure the result schema that you want to link.
  4. Edit the JSON Spec to add the following field:
{
    "isMulti": false,
    "isRequired": false,
    "schemaId": your_run_schema_id,
    "type": "assay_run_link",
    "name": "run"
}
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