PKPD: pharmacokinetics simplified

PKPD is a graphical interface for pharmacokinetic and (work in progress) pharmacodynamic modelling. It's for people who want to model pharmacological metabolism without having to touch any code!

Quickstart

PKPD requires python 3.6+ and myokit. To get started, git clone the repository and run the setup.py to install it as a python module. The interface can then be called from the terminal or command line using python -m PKPD.

In-depth installation guide

This guide is split into sections:-
A) Install python
B) Install myokit
C) Install git
D) Install PKPD
E) Use PKPD
F) Troubleshooting

A) How to install Python

1. Open a terminal (iOS or ubuntu: search your apps for 'terminal') or command line (windows: open start menu & search 'cmd').
2. Check if you have python already by typing python --version. If the version is 3.6 or above then you can skip this section.
3. Go to www.python.org.
4. Go to 'Downloads' and click on any release 3.6 or higher to download it.
5. on windows or iOS, open your downloads folder and double-click the installer file. Follow the installer instructions. On ubuntu, python should be installed already; if it is not then something is horribly wrong.

B) How to install myokit

Full instructions for installing myokit on each operating system can be found here: www.myokit.org/install

C) How to install git

Type git --version to check if you have git already.

• On windows, you can download an installer from www.git-scm.com/download/win.
• On ubuntu, run sudo apt-get install git.
• On iOS, the command above will show you how to install it if it is not installed.

D) How to install PKPD

1. Make sure you have python and myokit installed.
2. Open the terminal (or command line, on windows) and go to the folder you want to download to (using cd).
3. Download PKPD using:-

git clone https://github.com/SABS-R3-projects/PKPD/

4. Enter the installed directory by typing

cd PKPD

5. Install the PKPD module and all dependencies with

pip install -e .

These commands should look like the picture below.

Congratulations! You successfully installed PKPD.

E) Use

Start the program by opening a terminal (or command line, on windows) and typing

python3 -m PKPD

F) Troubleshooting

I get the message Command 'git' not found

You might not have git installed: go to that section. Alternatively, you can download a .zip file from github, unzip it, and proceed with the instructions in the same way from there.

I get the message 'python' is not recognized as an internal or external command, operable program or batch file

Try replacing python with python3. If this doesn't work then you might not have python installed: go to that section.

I get the message Command 'pip' not found

Try replacing pip with pip3. If this doesn't work then you might not have python installed: go to that section.

I get the message ṫ̵̛͇̺͇͓͐̈́̀͒̿̏̆͝h̵̡̯̮̬̍͗̿̐̐̏̅͗̉̆̅̉͜ĕ̴͓̯͉͗̒̎͑͂̂̒̒͗̈́̓ṛ̶̡̭̗͕̀̄̅͐ę̶͔̹̥̖̠̼̎i̷̞̗̥̮̒̕s̵̲̱̭͔͙̑̐̾́̀̏̊̚͠â̶̧̫̣̗͔̘̹̝͓̬͇͒̿́̿̎ͅn̵̢̨̹̼̭̯͈̻̺̼̉̿̊̾͂̅͆͋̾̓͠ͅê̷̻͚̞̠̻̥̦͉̥͉̳̼̓͐̀́̓̌͗̃̕͠͝r̴̢̤͖̫͇̰̦̾͐̐̋͋͑̇͑͝r̸̛̛̼͔̺̹̯̼̻̅̾̐̅̋̋̉̍̀̚͝o̸͉̖̗̮̣͙͆̔̚r̵̠̳̖̟͉̞̰͕͍͂̋͒̾͗̿̋͜i̴̩̬͕̙̠͂̀̅n̴̢̢̳̤̥̣̠̻̹̥̼̮̞͑̍̒̈t̵̖̉̐̃́̊̌̋̚͝͝h̸̪̞͕̘̯̞͒̅̇e̴̠̓͌̒ṃ̷̧̭̞̬̳̹͔̹̙̈̊̑̓̇͛͒̓å̷͚̲̝͖̬̗̓͐̾̀̈͒͂̚͝ͅt̶͚̗͇̹̦̀͛̋ŗ̶̯͕̟̜͇̣̬̻̖̗̆̈́̍̊̀̎̈̑͑́͜͠i̸̡̡̛̟̺̮̤̽̒̋͒͝x̶̠̯͔̯̖̼̣̫͔̲̼̳̃̎

Your computer is haunted. Consider employing an exorcist.

Issues and contributions

If you find a bug or would like to contribute, then you are very welcome to get in contact through the github issues.