An open-source Python-based ontology and tool for designing, implementing, and reproducing high-throughput experiments (HTE).
PyPlate provides tools for the design and implementation of high-throughput chemistry and biology experiments (e.g., reaction screening, cell assays, chromatography screening). It allows the user to define a space of experimental parameters to be explored, select points in that space for experimentation, and design liquid/solid handling steps to implement those experiments in 96 well plates.
PyPlate requires Python 3.10 or later.
pip install pyplate-hte
To view plate visualizations, you will need an interactive Python shell like Jupyter.
Note: A similarly named package pyplate also exists on PyPi. Be sure to install pyplate-hte and not pyplate.
Here is a simple example that illustrates some of the core features of PyPlate:
from pyplate import Substance, Container, Plate, Recipe
triethylamine = Substance.liquid(name="triethylamine", mol_weight=101.19, density=0.726)
water = Substance.liquid(name="water", mol_weight=18.015, density=1.0)
triethylamine_50mM = Container.create_solution(solute=triethylamine, solvent=water, concentration='50 mM',
total_quantity='10 mL')
plate = Plate(name='plate', max_volume_per_well='50 uL')
recipe = Recipe().uses(triethylamine_50mM, plate)
recipe.transfer(source=triethylamine_50mM, destination=plate[2:7, 2:11], quantity='10 uL')
results = recipe.bake()
triethylamine_50mM = results[triethylamine_50mM.name]
plate = results[plate.name]
recipe.visualize(what=plate, mode='final', unit='uL', timeframe=0)
Online documentation is available at ReadTheDocs. To build the documentation locally, please follow these steps:
make -C docs html
The resulting HTML files will be in docs/build/html.
In order to build the documentation successfully, you must install the packages listed in docs/requirements.txt. You can do this by running:
pip install -r docs/requirements.txt
Licensed under the Apache License, Version 2.0 (the "License").
PyPlate was designed and written by James Marvin, Eugene Kwan, Corin Wagen, Aryamaan Dhomne, and Pravin Mahendran.
Please open a GitHub issue! We respond regularly. Please also feel free to contribute!