platekit

English | Русский

Open-source desktop tool for planning 96/384-well PCR, qPCR, PCR-RFLP and Sanger sequencing plates, calculating Master Mixes with dead-volume margins, normalizing DNA concentrations (C₁V₁ = C₂V₂) and exporting directly to real laboratory instruments. English/Russian interface, dark and light themes.

Features

1. Interactive Plate Designer

• Supported formats: 96-well (8×12), 384-well (16×24), 8-well and 12-well PCR strips, Qiagen Rotor-Gene rotors (36, 72, 100 positions).
• Rich well metadata: Sample name, stock DNA concentration (ng/µL), Assay / Target name, Well Role (Unknown, NTC, POS, STD, IPC, Empty), Replicate Group, Standard copy number/quantity, and custom notes.
• Smart Fill (Auto-Layout): Paste a list of samples (with optional NanoDrop/Qubit concentrations) and assays to populate replicates (×1..×12) row-wise or column-wise with automatic POS and NTC controls per assay.
• Serial Standards Generator: Create STD calibration dilution series (1:10, 1:5, 1:2, etc.) in replicates.
• Full editing workflow: Rubber-band selection, row/column header selection, copy/paste well blocks (Ctrl+C / Ctrl+V), unlimited Undo/Redo (Ctrl+Z / Ctrl+Y).

2. Master Mix Calculator

• Built-in & editable protocol presets:
  • Standard Taq PCR (25 µL)
  • qPCR SYBR Green 2× Mix (20 µL)
  • qPCR TaqMan Probe 2× Mix (20 µL)
  • PCR-RFLP Restriction Digest (15 µL) — pairs with rflppicker
  • Sanger Sequencing BigDye v3.1 (10 µL) — pairs with ab1kit
• Automatic per-assay grouping: Counts occupied wells for every Assay on the plate and computes exact reagent volumes and nuclease-free water to volume.
• Dead-volume modes: Percentage overfill (+10%), fixed extra reactions (+1, +2), or multichannel reservoir mode (+% with a minimum of +2 reactions).

3. DNA Normalization & Pipetting QC

• Two calculation modes:
  1. Per-reaction DNA mass (ng/rxn): Computes exact DNA template volume and water volume for each well.
  2. Dilution plate normalization (C₁V₁ = C₂V₂): Computes volumes to normalize stocks to a uniform target concentration (ng/µL) in a target final volume.
• Automated Pipetting QC flags:
  • OK — directly pipettable volume.
  • TOO_CONCENTRATED — required volume is below minimum reliable pipetting threshold (e.g. < 0.5 µL); automatically suggests a clean pre-dilution factor (1:5, 1:10, 1:20, 1:50).
  • TOO_DILUTE — stock concentration is too low to reach the target mass within the maximum template volume window.

4. Step-by-Step Pipetting Assistant & Printable Bench Sheet

• Interactive Bench Mode: Step through occupied wells one by one (single-channel), column by column (8-channel pipette), or row by row (12-channel pipette) using Space / Arrow keys while highlighting the active well/strip on the plate map.
• Printable A4 Bench Sheet (.html): Self-contained 1-page laboratory protocol with color-coded plate map, checkable [ ] Master Mix recipes, and DNA normalization table.

5. Instrument & Ecosystem Export / Import

• Bio-Rad CFX Maestro / CFX Manager (.csv Plate Setup)
• Applied Biosystems QuantStudio / StepOne (.csv Sample Setup)
• Qiagen Rotor-Gene Q (.csv rotor layout)
• ABI 3130 / 3500 Capillary Sequencer (.tsv Sample Sheet with systematic .ab1 file naming for ab1kit)
• Multi-sheet Excel Workbook (.xlsx): Colored Plate Map, Master Mix, DNA Normalization, and Well List sheets.

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Installation & Quick Start

Requires Python 3.11+.

python3 -m venv .venv
source .venv/bin/activate   # Windows: .venv\Scripts\activate
pip install -e ".[dev]"

Launch the desktop GUI:

platekit
# or
python plate_cli.py

Headless CLI export example:

platekit --demo \
  --save-project examples/demo_plate.platekit.json \
  --export-xlsx plate_report.xlsx \
  --export-bench bench_sheet.html \
  --export-cfx biorad_cfx.csv

Run tests:

pytest

License

MIT License — Copyright (c) 2026 Aleksey Drobin (@adrobi).