PyHTE

A python package for high-throughput experiments and laboratory automation.

Features

• Compositions of solvent volumes and solute amounts, with mixed solvents and dissolved solids
• Labware: containers and plates with capacities and dead volumes
• Plans that are simulated before dispensing, and designs that create them, e.g. titrations
• Devices: protocols for the UK Robotics D2 dispenser, measurements from the JASCO V-750 spectrophotometer
• Records of what was actually dispensed, and the state derived from them
• Storage of plates, plans, runs and measurements in an SQLite (or other SQL) database

Installation

python3 -m pip install pyhte

The package is published as pyhte and imported as hte.

Optional RDKit support (molecule objects on substances):

python3 -m pip install "pyhte[chem]"

Development tools (including pytest, ruff and pyright, and sphinx) from a clone of the local package:

python3 -m pip install -e .[chem] --group dev

Usage

Volumes are given in L, amounts in mol, concentrations in mol/L, masses in g and molar masses in g/mol. The factors in hte.units convert from and to these base units: multiply to enter a value (250*uL), divide to read one (state[well].volume/uL).

Containers and plates describe the labware only. What they contain is a LabState: an immutable snapshot that maps containers to their Composition. A Plan starts from an initial state and never modifies it; plan.simulate() derives the final state and checks every transfer on the way.

from hte import Composition, Container, LabState, Plate, PlateType, Substance, TitrationDesign, TitrationSeries
from hte.units import mL, mM

water, dmso = Substance("water"), Substance("DMSO")
analyte, titrant = Substance("analyte"), Substance("titrant")

analyte_stock = Container(capacity=10*mL, label="analyte")
titrant_stock = Container(capacity=10*mL, label="titrant")
solvent = Container(capacity=50*mL, label="solvent")
plate = Plate.create(PlateType.well_24())

initial = LabState.create(
    {
        analyte_stock: Composition.solution(dmso, 5*mL, {analyte: 10*mM}),
        titrant_stock: Composition.solution(water, 5*mL, {titrant: 20*mM}),
        solvent: Composition.solution(water, 30*mL),
    },
    plates=[plate],  # registers the (empty) wells
)
design = TitrationDesign(
    series=TitrationSeries(
        analyte_concentration=[1*mM] * plate.size,
        titrant_concentration=[i * 4*mM / (plate.size - 1) for i in range(plate.size)],
    ),
    analyte=analyte_stock,
    titrant=titrant_stock,
    solvent=solvent,
    volume=1*mL,
    plate=plate,
)

plan = design.create_plan(initial)
final = plan.simulate()  # raises at the first transfer that is not possible

well = plate["B3"]
print(final[well].concentration(titrant)/mM)  # 1.391...
print(final[well].solvent_fractions)  # 10 % DMSO, 90 % water
print(initial[well].is_empty)  # True: the initial state is unchanged

The documentation covers dispensing with the D2, recording runs, importing measurements from the V-750 and saving to a database; see the tutorial for a complete walk-through.

Invalid input and violated domain rules raise hte.exceptions.ValidationError, a subclass of both HTEError and ValueError.