PyPlate

An open-source Python-based ontology and tool for designing, implementing, and reproducing high-throughput experiments (HTE).

Introduction

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.

Installation

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.

Quick Start

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)

Documentation

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

License

Licensed under the Apache License, Version 2.0 (the "License").

Contributors

PyPlate was designed and written by James Marvin, Eugene Kwan, Corin Wagen, Aryamaan Dhomne, and Pravin Mahendran.

Getting Help

Please open a GitHub issue! We respond regularly. Please also feel free to contribute!