Tutorial: Running Your First Plate Experiment in LabKey Biologics

This walkthrough covers the complete end-to-end flow for a multi-plate assay experiment in LKB Biologics. By the end, you'll have created plate templates, set up an assay design, plated samples, imported instrument data, reviewed results, and carried forward your best hits.

Prerequisites: You need Editor permissions in your project and at least one sample type with samples loaded.

Workflow at a Glance

1. Set up Plate Templates        ← define your well layouts (controls, replicates, zones)
2. Set up an Assay Design        ← define what you're measuring; must enable Plate Metadata
3. Create a Plate Set            ← from your sample table; assigns samples to plates
4. Verify plate layout           ← use the Plate Viewer to confirm well assignments
5. Import assay data             ← drag-and-drop your instrument file
6. Review results & mark hits    ← filter, analyze, mark candidates
7. Pick hits to a new plate set  ← carry forward for the next round

Steps 1 and 2 are one-time setup. Once templates and assay designs exist, you start from step 3 each experiment.

Step 1: Create Plate Templates

Plate templates define the layout of your plates — where samples, controls, standards, and replicates go — without any specific sample data. Set these up once and reuse them across experiments.

1. Go to Main Menu → Plate Templates.
2. Click Create New Plate Template.
3. Give it a name and select your plate type (e.g., 96-well 8×12).
4. Select groups of wells and click Edit in Bulk to assign well types and metadata values in batches. You can:
   • Designate wells as Sample, Control, Replicate, or other types.
   • Assign a group name (e.g., "Standards," "Unknowns").
   • Set concentration values or other metadata for the selected wells.
5. Repeat for each zone or well group in your design.
6. Click Save Plate when done.

If you're running a multi-plate experiment with different layouts per plate (e.g., four plates with different replicate patterns), create a separate template for each.

Tip: Template well groups directly affect how results aggregate in charts. If replicates aren't grouped correctly in the template, they may not roll up as expected in your results. Double-check your replicate group assignments before saving.

Step 2: Create an Assay Design

An assay design tells LKB what data your instrument produces and how to structure it.

1. Go to Main Menu → Assays.
2. Click Choose Standard Assay (or Create Assay Design).
3. Give it a name.
4. Check the box next to "Plate Metadata." This is required for all plate-based assay workflows. Without it, the plate-aware import and hit selection features will not be available.
5. Define your fields:
   • Run fields — properties that apply to the entire experiment (e.g., instrument ID, date, operator). Optional.
   • Result fields — the per-well measurements your instrument produces (e.g., Absorbance, Fluorescence, SNAP25). These are the values you'll analyze.
6. Save the assay design. It will now appear as an import option on your plate sets.

Important: The "Plate Metadata" checkbox is easy to miss and cannot be added to an existing assay design after creation. If you forget it, you'll need to create a new assay design.

Step 3: Create a Plate Set from Your Samples

1. Navigate to your sample type listing page (e.g., your protein batches or clones).
2. Check the boxes next to the samples you want to plate.
3. Click Plates → Add to Plate Set.
4. In the wizard:
   • Name: provide a name, or leave blank for auto-generation.
   • Plate Set Type: choose Assay (for running assays) or Primary (for stock samples).
   • Plate Type: select the Plate Template you created in Step 1. If you're using multiple templates across your plates, set the first one here.
5. Set the number of plates and click Add Plate for each additional plate.
6. In the Plate Type column, assign the correct template to each plate row if they differ.
7. In the Plate Name column, enter names that match the plate identifiers in your instrument's output file (see Step 5). For example, if your Excel file has sections labeled "Plate 1," "Plate 2," "Plate 3," and "Plate 4," enter those exact names here.
8. Click Submit. LKB generates the plates and navigates you to the new plate set via a green banner link.

Critical: The plate names you enter in LKB must match the plate identifiers in your instrument output file exactly. If they don't match, import will fail or data will be misaligned.

Step 4: Verify Your Plate Layout

Before importing data, confirm your plates look right.

1. Click any plate name from the plate set detail page to open the plate detail page.
2. Toggle to Map View to see the visual plate layout.
3. Check the tabs to review different metadata layers (Sample ID, Concentration, well groups).
4. Use the Summary tab to confirm all expected wells are filled — a well is colored only when all metadata is complete.

If anything looks wrong, you can edit well data directly in the Grid View (as long as no assay data has been imported yet).

Step 5: Import Assay Data

1. From the plate set or plate detail page, click Import Assay Data.
2. Select the assay design you created in Step 2.
3. Scroll to the Results section and drag-and-drop your instrument Excel file (or upload it).
4. Click Import.

On success, LKB links your instrument measurements to the samples in each well. You're taken to the Plate Set Assays page where results are ready to review.

Supported file formats:

• Graphical (plate-shaped): raw values arranged in plate grid format, optionally with plate ID headers above each grid. Works for one or multiple plates per file.
• Tabular (Tall Table): one row per well, with columns for Plate ID, Well Location, and your measure fields. A template is available for download from the import page.

Note on reimport: Reimporting data for a plate is not additive — it clears existing data for that plate and replaces it. This allows you to correct errors without creating duplicates.

Step 6: Review Results and Mark Hits

After import, results appear on the Assays tab of your plate set.

• The Sample ID and Hit Selection columns are always pinned to the left and cannot be hidden.
• Use the Hit Selection column filter to show only hits or non-hits.
• Select rows and click Mark as Hit to flag candidates, or Unmark as Hit to remove flags.

For routine assays, you can set automatic hit selection criteria in your assay design so that results are flagged on import without manual review. See the reference doc for details.

About replicates in results: If you set up replicate groups in your template, LKB calculates mean and standard deviation across replicate wells automatically. These aggregated values are available as columns in your results and can be used as hit selection criteria. If you're missing replicates in your analysis, check that the well groups in your template are correctly defined.

Step 7: Pick Hits to a New Plate Set

1. Go to the Hit Selection Summary tab on the plate set's Assays page. This shows all samples with hits rolled up across all assay types.
2. Select the rows you want to carry forward.
3. Click Pick Selected to New Plate Set.
4. Choose a layout (fill by row, fill by column, or preserve well positions).
5. The new plate set is created and appended to the plate hierarchy, ready for the next round of assays.

Common Questions

Why do I only see some of my replicates in charts or results?
Check the replicate group assignments in your plate template. Wells must be assigned to the same group to be treated as replicates. Also confirm none of the replicate wells are empty or QC-excluded.

Why did import fail saying the plate wasn't found?
The plate names in LKB must exactly match the plate identifiers in your instrument file (e.g., the section headers in your Excel output). Edit the plate names in the plate set detail page so they match.

I forgot to check "Plate Metadata" in my assay design. What do I do?
You'll need to create a new assay design with Plate Metadata enabled. This option cannot be added to an existing design after creation.

Can I add more samples to a plate set later?
Yes, if the plate set is eligible (not archived, no child plate sets). Select the additional samples from the sample grid and use Plates → Add to Plate Set, then choose the existing set. New samples are placed starting from the first available well after existing samples.

What happens when I reimport assay data?
Reimport clears existing results for the targeted plates and replaces them — it is not additive. Other plates in the plate set are unaffected.

Can I edit plate well assignments after running an assay?
No. Once an assay run is associated with a plate, that plate becomes read-only. You can reimport the assay data to update results, but the sample-well layout itself cannot be changed.