pbpk-lite 1.1.4

This is a simple implementation of PBPK modeling in python.

pbpk-lite

pbpk-lite is a lightweight Python package for basic physiologically based pharmacokinetic (PBPK) modeling.

It provides a simple programmatic interface for defining substance properties, patient physiology, elimination kinetics, and solving the resulting ODE system.

The implementation is intended to be used with a consistent unit system based on mass units for doses and amounts, milliliters (mL) for volumes, and minutes for time. When using the model, doses, volumes, flows, and clearances should all be expressed in compatible units within that framework.

Features

• Substance partition coefficient calculation using logP and fraction unbound
• Patient blood flows and tissue volumes derived from body weight
• Linear liver and kidney elimination pathways
• ODE solution via scipy.integrate.solve_ivp
• Plotting helpers for whole-model, venous-blood, and selected-compartment concentration profiles
• Support for different administration routes, including intravenous, intra-arterial, and inhalation dosing

Installation

Install from PyPI:

pip install pbpk-lite

Quick Start

from pbpk_lite import model

m = model()
m.set_substance(log_p=6.97, fu=0.0022448)
m.set_patient(bw=70)
m.set_elimination(cl_l=748.6643482986731, cl_k=0)

# example dose: 0.053 mg/kg for a 70 kg patient, converted to ng
# dose = 0.053 * 70 * 1e3 * 1e3

dose = 0.053

doses = [dose]
times = [0, 480]

t, c = m.simulate(doses, times, route_of_administration='iv')

m.graph_whole('concentrations.png')
m.graph_venous('venous.png', limit_of_detection=0.15)
m.graph_compartments(['liver', 'kidney'], 'selected.png')

Route of Administration

The simulate() method accepts a route_of_administration argument to control where each dose is introduced into the model.

Supported values are:

• iv: intravenous dosing into the venous blood compartment (default)
• ia: intra-arterial dosing into the arterial blood compartment
• inh: inhalation dosing into the lung compartment

Example:

m.simulate([dose], [0, 24*60], route_of_administration='inh')

Dosing Schedule

The simulate() method expects:

• doses: array-like of administered doses
• times: array-like of dosing times plus a final endpoint

Important: times must have exactly one more element than doses. Each dose at index i is administered at times[i], and the final value in times is the last observation or endpoint. Times are interpreted in hours, so dosing schedules and simulation endpoints should be provided in hours.

Example with one dose:

# one dose at time 0, observation at 480 minutes
doses = [dose]
times = [0, 480]

Example with two doses:

# two identical doses spaced 480 minutes apart, with a final observation at 960 minutes
doses = [dose, dose]
times = [0, 480, 960]

API Summary

pbpk_lite.model

set_substance(log_p, fu)

Set the substance physicochemical properties.

• log_p: log octanol-water partition coefficient
• fu: fraction unbound in blood

set_patient(bw)

Set patient physiological parameters using body weight in kilograms.

set_elimination(cl_l=0, cl_k=0)

Set linear clearance from liver and kidney compartments.

simulate(doses, times, route_of_administration='iv')

Simulate the PBPK model and return time points t and compartment concentrations c.

• route_of_administration: administration route used for each dose ('iv', 'ia', or 'inh')

graph_whole(name)

Save a multi-panel plot of concentrations across all compartments.

graph_venous(name, limit_of_detection=None)

Save a plot of venous blood concentrations, optionally marking a detection limit.

graph_compartments(compartments, name)

Save a plot of selected compartments by name or index.

License

pbpk-lite is licensed under the MIT License.