PCR Plate Planner — 96-Well Layout, Opentrons Protocol & Echo Picklist Export
Lay out PCR reactions on a 96-well plate and export a runnable Opentrons protocol or Echo picklist.
🌐 Runs on the SeqBench API — also callable via REST & MCP, and in bulk from the batch tools
Paste a list of PCR reactions — a name, forward primer, reverse primer, and an optional template label per reaction — and see them laid out on a 96-well plate, row-major (A1 through A12, then B1, and so on). From that same layout you can download a real Opentrons Python Protocol API script that loads actual Opentrons labware and issues transfer calls for primers, template and master mix into each well, and a Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV in the standard Source/Destination-well, nanoliter-volume column convention. Both are a reviewable starting point — placeholder reaction volumes and plate-type codes are called out for you to adjust — not a certified, ready-to-run-unmodified protocol for your exact instrument and reagents.
0 valid reactions parsed. Also auto-detects pasted JSON from the Primer designer tool’s own output (its pairsarray). in_silico_pcr’s result doesn’t include primer sequences (they’re inputs to that tool, not outputs) — paste its request args instead, or use the line format above. Template is an optional name/id label, not a sequence.
How to use the PCR Plate Planner tool
- 1Paste one PCR reaction per line — name, forward primer, reverse primer, optional template label — or load the example.
- 2Review the plate diagram: hover any well for its reaction name and template, colored by which reactions share a template.
- 3Download the Opentrons protocol script (.py) and/or the Echo picklist (.csv), then review and adjust the placeholder volumes/plate types for your own instrument and enzyme before running.
Frequently asked questions
How are reactions assigned to wells?
Row-major order: the first reaction goes in A1, then A2, A3, … through A12, then B1, and so on down to H12 — up to 96 reactions on one plate.
Is the generated Opentrons script certified to run as-is?
No — treat it as a reviewable starting point. It uses real, current Opentrons Python Protocol API labware and pipette names (an OT-2 PCR plate, tip rack, and a P20-class pipette) and real load_labware/load_instrument/transfer call signatures, but the master-mix, primer, template and water volumes are clearly-labeled placeholder constants you should adjust for your own enzyme's recommended PCR recipe, and you should simulate it before running on real hardware.
What format is the Echo picklist, and what volume scale does it assume?
The standard Beckman/Labcyte Echo picklist column convention — Source Plate Name, Source Plate Type, Source Well, Destination Plate Name, Destination Well, Transfer Volume, Name — with volumes in nanoliters. It assumes a 5 µL Echo-scale PCR reaction (a commonly used acoustic-dispensing miniaturization scale, not a universal standard) and a placeholder source plate-type code you should replace with the exact type from your own Echo Plate Type Library.
Can I paste output from the Primer designer or in-silico PCR tools?
Pasting the Primer designer tool's own JSON output (its pairs array) is auto-detected and used directly. In-silico PCR's own result doesn't include the primer sequences themselves (they're inputs to that tool, not outputs), so that shape isn't auto-extracted — use its request arguments, or just paste reactions in the plain line format.
Is my data stored?
Your pasted reactions are sent to the SeqBench API to compute the well layout and generate the downloadable files; they are not stored. The same tools are available via the REST API and the MCP server.