PK Modelling (SABS:R3 2020)

This is a package that allows the user to calculate drug pharmacokinetics for two different non-physiological models:

• Intravenous Bolus dosing (dose administered directly to a central compartment)
• Subcutaneous dosing (dose administered to a separate compartment from which it is absorbed into the central one)

Modelling Assumptions

For both of the above-mentioned models, we assume that the organism can be divided into kinetically homogeneous compartments. After the drug enters the central compartment (either by direct infusion or through the subcutaneous compartment), it is both cleared at a constant rate and diffuses into an arbitrary number of peripheral compartments. This is meant to model the circulatory concentration of a drug to check whether it exceeds certain toxicity and efficacy thresholds.

In the case of a simple instance with only one peripheral compartment, the models are described by the following systems of equations.

intravenous dosing	subcutaneous dosing

The case for more than one peripheral compartment is calculated accordingly.

Installing the Package

The latest release of the package can be installed directly by opening a console and typing:

$ pip3 install -i https://test.pypi.org/simple/ pkmodelling-sabs-group1

The package is maintained for python 3.6 and newer.

Using the Package

When initialising the Model class, the package creates a model that consists solely of the central compartment.

import pkmodelling_sabs_group1 as pk

model = pk.model.Model(clearance_rate=1.0, vol_c=1.0)

You are then able to add one subcutaneous and/or arbitrarily many peripheral compartments with different volumes [ml] and initial drug quantities [ng].

model.add_subcutaneous_compartment(absorption_rate=2.0)
model.add_peripheral_compartment(pc_name="Compartment 1", vol_p=2.0, q_p=3.0)
model.add_peripheral_compartment(pc_name="Compartment 2", vol_p=4.0, q_p=5.0)

You are then able to specify a dosing protocol that can be either

• A number of instantaneous does at specific times
• A steady dose over a given period of time
• A combination of the above

protocol = pk.protocol.Protocol(dose_amount=1)
protocol.make_continuous(time_start=0, time_finish=0.5)

In order to solve the model you specified above, you initialise a Solution class that takes both the model and dosing protocol as parameters and then run the solve method. The standard initial values are 0 for the drug concentrations in all compartments and a timespan of 1hr, divided into 1000 time steps.

sol = pk.solution.Solution(model=model, protocol=protocol)

You are then able to generate a plot that shows you the change in drug concentration for each compartment over time.

sol.plot("MyModel")

A demo of a subcutaneous model can be found in the demo.py script.

Useful links

• Project description - https://sabs-r3.github.io/2020-software-engineering-projects/01-introduction/index.html
• GitHub repo - https://github.com/SABS-Group-1/pkmodelling
• TestPyPI - https://test.pypi.org/project/pkmodelling-sabs-group1/
• ReadTheDoc - https://readthedocs.org/projects/pkmodelling/