https://github.com/matthiaskoenig/pkpd-course
PK/PD Tutorial
https://github.com/matthiaskoenig/pkpd-course
Last synced: 4 months ago
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PK/PD Tutorial
- Host: GitHub
- URL: https://github.com/matthiaskoenig/pkpd-course
- Owner: matthiaskoenig
- Created: 2017-02-02T09:39:17.000Z (over 8 years ago)
- Default Branch: develop
- Last Pushed: 2022-02-14T11:14:33.000Z (over 3 years ago)
- Last Synced: 2025-01-04T20:25:17.294Z (5 months ago)
- Language: Jupyter Notebook
- Homepage: https://livermetabolism.com
- Size: 159 MB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
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README
pkpd-course: A python introduction to PK/PD models
===================================================
Matthias König, `https://livermetabolism.com `__
The introductory lecture is available here
.. image:: ./presentation/presentation.png
:target: https://docs.google.com/presentation/d/e/2PACX-1vQG8vtoCVWW3yOQFczrevLZmluhHrKpGVztJho-SY-nbTis8XNYNQyZ3src6AkrL5n3Sv2F6tlL3Fyu/pub?start=false&loop=false&delayms=3000
This course provides resources for a simple introduction to PK/PD models
using a `caffeine` physiological-based whole body model.
The course contains the following information::
./notebooks: tutorial notebooks
./presentation: introductory presentation
./literature: relevant literature
Installation
============
We need an environment with the libraries listed in `requirements.txt`
These are standard python libraries and `libroadrunner` for simulation of SBML models.
Conda
-----
The easiest way to use this tutorial is to use conda/bioconda.
After installation add the additional library `libroadrunner` via::
pip install libroadrunner
Virtualenv
----------
One possible solution is to setup a virtual environment with all system dependencies.
Create a virtual environment via::
mkvirtualenv pkpd-course
Install requirements::
(pkpd-course) pip install -r requirements.txt --upgrade
(pkpd-course) pip install ipykernel jupyterlab
Register the virtualenv as a kernel::
python -m ipykernel install --user --name pkpd-course
Funding
=======
Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054),
by the German Research Foundation (DFG) within the Research Unit
Programme FOR 5151 "QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex
Resection - A Systems Medicine Approach)" by grant number 436883643 and by grant no. 465194077
(Priority Programme SPP 2311, Subproject SimLivA).
License
=======
* Source Code: `LGPLv3 `__
* Documentation: `CC BY-SA 4.0 `__
© 2018-2022 Matthias König