chondrocyte
Description
Model of the fundamental electrophysiological characteristics of human articular chondrocytes, focused on K+ selective ion channels and ion pumps, but also including the contributions of Na+, Ca2+, and Mg2+ on the chondrocyte membrane potential (Em).
Installation
The following python modules are needed to use chondrocyte,
- NumPy (developed with Version: 1.18.1)
- SciPy (developed with Version: 1.6.0)
- Matplotlib (developed with Version: 3.4.1)
To use chondrocyte, please clone the repository:
git clone https://github.com/mmaleck/chondrocyte.git
cd chondrocyte
Usage
chondrocyte was originally developed with MATLAB and can be found in the matlab_code folder. It has been reimplemented in python with some improvements and model expansions. Therefore, we encourage users to use python_code, and also we only write instructions on how to use chondrocyte in python for that matter.
Inside python_code, there are four python files, chondrocyte.py, functions.py, params.py, modelpopulations.py, and postprocess.py in addition to four jupyter notebooks demo_*.ipynb.
These jupyter notebooks are examples of how to use the chondrocyte interactively, and the demos include replications of figures from the published papers.
chondrocyte.py is the core part of the chondrocyte model.
It imports necessary functions from functions.py and parameters from params.py to execute the program, and postprocess.py demonstrates one way to process the results. modelpopulations.py illustrates how to use population of models to explore high dimension parameter space.
For detailed instructions about the code, we ask users to have a look at the code as it contains the explanation as comments.
Authors
chondrocyte is developed by
- Kei Yamamoto
- Sophie Fischer
- Maria Perona Fjeldstad
- Molly Maleckar
License
chondrocyte is licensed under the MIT License.
chondrocyte is Copyright (2021) by the authors.
Citation
If you use chondrocyte and want to cite it, you can either cite this website or one of the following papers.
@article{Maleckar2018,
title = {{The resting potential and K+ currents in Primary Human articular chondrocytes}},
author = {Maleckar, Mary M. and Clark, Robert B. and Votta, Bartholomew and Giles, Wayne R.},
doi = {10.3389/fphys.2018.00974},
journal = {Frontiers in Physiology},
volume = {9},
year = {2018}
}
@article{Maleckar2020,
title = {{ Physiological Effects of the Electrogenic Current Generated by the Na + /K + Pump in Mammalian Articular Chondrocytes }},
author = {Maleckar, Mary M. and Mart{\'{i}}n-Vasallo, Pablo and Giles, Wayne R. and Mobasheri, Ali},
doi = {10.1089/bioe.2020.0036},
journal = {Bioelectricity},
volume = {2},
year = {2020}
}
Contact
Please report bugs and other issues through the issue tracker