pbpk-lite 1.1.0

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.

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

Install from source:

pip install .

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=10, cl_k=0)

doses = [10]
times = [0, 24]

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

m.graph_whole('concentrations.png')
m.graph_venous('venous.png', limit_of_detection=1.0)
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([10], [0, 24], 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.

Example with one dose:

# one dose at time 0, observation at 24 hours
doses = [10]
times = [0, 24]

Example with two doses:

# doses at 0 and 12 hours, observation at 24 hours
doses = [10, 10]
times = [0, 12, 24]

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.