This topic is under construction for the 23.3 (March 2023) release of LabKey Biologics. For the previous version of this documentation, click here.
Within the Biologics application, you can import assay data from a file or by entering values directly into the grid. Both individual run and bulk insert options are available. You can also initiate assay data from a grid of samples, making it easy to enter data for those samples.
Import Assay Data
To import new assay data:
- From the main menu, under Assays, click the name of the assay design you wish to import into.
- On the next page fill out the form:
- Batch Details: (Optional) If the assay design includes batch fields, you will be prompted to enter values for them here.
- Run Details: (Optional) Run fields include the Assay Id (name for this run) and also capture the characteristics of this assay experiment defined as run fields in the assay design. These may include such the instrument settings, special circumstances, or which request this data fulfills.
- Assay Id: If no id is supplied, then the assay file name will be used. If no file name is used, then an id will be created from the assay design name plus a time stamp.
- Comments: Add text to record special circumstances connected to this assay run.
- Workflow Task: Select the workflow task associated with this run, if any.
- Other fields to populate may be shown here.
- Results - There are two tabs in this panel. To help your data conform to the assay design, click Template to download a template to use.
- Import Data from File (Default) - On this tab (shown in the screencap above), you can either click to select your assay data file or you can drag and drop it directly onto the upload area.
- Enter Data Into Grid - On this tab, you can manually enter data into a grid. Select the desired number of rows and click Add rows, then populate with data. For lookup fields like Sample ID, you can type ahead and choose the right option.
- You can export the contents of any grid by clicking the button. Choose CSV, TSV, or Excel format exports. Fields from all tabs of the editable grid will be included in the export.
- You can click Bulk Insert to add a batch of assay rows that will share some set of properties.
- After entering properties that will be shared, click Add Rows to Grid; you will then be able to customize individual rows in the grid editing interface.
- After adding rows to the grid, either individually or via bulk insert, you can select one or more runs and choose Bulk Update.
- In the popup, you can click the Disabled slider to Enabled, then enter a value for any row that the selected rows should share. For example, to give all selected rows the same Day, you might use the following. No values will be changed for fields left Disabled. Scroll down and click Finish Editing Rows.
- After bulk editing rows, you will return to the grid view where you can make adjustments to individual rows if needed.
- Once your data has been uploaded or rows entered, click Import.
Import Assay Data Associated with a Sample
An alternative way to import assay data lets you directly associate assay data with some sample(s) in the registry.
From the Samples grid, select one or more samples, and then select Assay
(on narrower browsers this will be a section of the More >
menu). Expand the Import Assay Data
section, then click the [Assay Design Name]
. Scroll to select, or type into the filter box to narrow the list.
The assay import form will be pre-populated with the selected samples, as shown below.
Enter the necessary values and click Import
In cases where you need to revise assay data after uploading to the server, you can replace the data by "re-importing" a run.
To re-import a run of assay data:
- Go the details page for the target run. (For example, go to the runs table for an assay, and click one of the runs.)
- Click the Manage menu and select Re-import Run.
Note that re-import of assay data is not supported for: file-based assay designs, ELISA, ELISpot, and FluoroSpot. If the re-import option is not available on the menu, the only way to re-import a run is to delete it and import it again from the original source file.
- For instrument-specific assay designs (such as NAb and Luminex), you will be directed to the specific assay’s import page in LabKey Server. Follow the procedure for re-import as dictated by the assay type: Reimport NAb Assay Run or Reimport Luminex Run.
- For general purpose assay designs, you will stay within the Biologics application:
- Revise batch and run details as needed.
- Enter new Results data. The first few lines of the existing results are shown in a preview. Choose Import Data from File or Enter Data Into Grid as when creating a new run.
- Click Re-Import.
- The data replacement event is recorded by the "Replaced By" field.
Delete Assay Runs
To delete one or more assay runs, you have several options:
- From the overview page for the assay, select the run(s) to delete using the checkboxes.
- Select Edit > Delete.
You can also delete a single run directly from the detail page for the run.
- Go to the runs table for an assay, and click the run to delete.
- Click the Manage menu and select Delete Run.
For either option, you will be reminded that deletion of runs is permanent and cannot be undone. If any runs cannot be deleted because of data dependencies this will also be mentioned in the popup.
You can enter a comment regarding the Reasons for deleting
that will be audited.
Confirm the action by clicking Yes, Delete
Learn about editing and deleting individual results rows within a run in the topic Biologics: Work with Assay Data