Provenance Module: Run Builder

LabKey Server's provenance module is available with all Premium Editions of LabKey Server, but is not currently included in all distributions. Please contact LabKey to inquire about obtaining and using the Run Builder feature described here.

The run builder captures experiment processes by linking together a set of inputs, some process or "run", and a set of outputs. A user-friendly tool prompts the user for information about the run: the inputs (samples and of files), metadata on the run that was performed, and the output (samples and/or files). Any combination of samples and files can be linked to a run, either as inputs or outputs, making this a flexible tool that can be applied to many use cases.

The run builder can be useful for capturing "at the bench" experimental information. For example, a lab technician might use the run builder to record that a process has happened, where samples were the input and files were the output. The run builder lets you form relationships between individual input samples/files (or any other LSID record) with individual outputs. In the run depicted below, a blood sample is the input to the experiment and two CSV files form the output:

The samples added to a run must pre-exist on the server, but the files need not (as you can upload files as you build a new run).

Run inputs and outputs create lineage/parentage relationships, which are reflected in the lineage views as parents (inputs) and children (outputs).

Once they are related within a run, the files and samples cannot be deleted without first deleting the run.

Note that the "runs" referred to here cannot be used with Assay runs.

Enable Run Builder

To enable the run builder, you must enable both the provenance and experiment modules within the container where you plan to use it.

Access Run Builder

The run builder is accessed via the URL. Navigate to the desired container and replace the end of the URL with:


Add Properties

In the Properties section, give your run a name, enter a description, and add any Vocabulary Properties with values that you need. These values will be applied to the run as a whole, not to individual inputs or outputs.

Under Inputs and Outputs, add the samples and files required.

You can Save while building the run, and click Save & Finish when finished.

Add Samples

To add samples, either to the Inputs or Outputs section of the run builder, click the Add Samples button. Select the sample set and the grid below will populate.

The omnibox (where you see "Select..." text above the grid) lets you filter, sort, or search to locate the samples you want to include. Click in the box to use it to locate your samples of interest.

Check the boxes for the desired samples and click Add Samples. The samples you added will now appear in a grid in the run builder:

You can now click Add Samples to add more, Move Selected Samples to Output or if necessary, select and Remove Selected Samples.

You can Save work in progress while building the run, and click Save & Finish when finished.

Add Files

Click Add Files to choose files to add to either the input or output sections. Use the File Select tab to browse the file root for files already uploaded. Use the checkboxes to select one or more files to add to the run you are building.

Click the File Upload tab to switch to a drag-and-drop interface for uploading new files.

Click Add Files when ready.

The files you've added will be listed, each with a for deleting. Click Add Files to add more as needed.

You can Save work in progress while building the run, and click Save & Finish when finished.

Run-related Web Parts

Runs created by the run builder are available on the Experiment Runs web part.

The lineage relationships established by the run are displayed on the Run Details panel.

Related Topics


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