Reproduction of: Fast-Activating Voltage- and Calcium-Dependent Potassium (BK) Conductance Promotes Bursting in Pituitary Cells: A Dynamic Clamp Study
A reference implementation of "Fast-Activating Voltage- and Calcium-Dependent Potassium (BK) Conductance Promotes Bursting in Pituitary Cells: A Dynamic Clamp Study, J. Tabak, M. Tomaiuolo, A. Gonzalez-Iglesias, L. Milescu and R. Bertram, Journal of Neuroscience 31.46 (2011), 10.1523/JNEUROSCI.3235-11.2011"
We have created a Docker environment
with all dependencies installed.
This Docker environment can be started, and the
article directory mounted
by running the bash script
run_docker.sh from within the
All results have been created in this Docker environment.
The required dependencies are:
These can be installed with:
pip install numpy pip install matplotlib pip install uncertainpy pip install chaospy pip install tqdm
Additionaly the Neuron simulator with the Python interface is required. NEURON must be manually installed by the user.
The content is:
article/- Contains the description of the reproduction.
code/- Contains the code for reproducing the results.
Running the code
The code is found in the
To create Figure 1 and Figure 2 in Tabak et al. run from
This runs in parallel and takes around 10 hours on a workstation computer.
This reproduction can be speed up by increasing the time step
dt = 0.25 gives results similar to the results in the paper,
and only takes around 23 minutes.
To perform the uncertainty quantification and sensitivity analysis of the model
This takes around 20 minutes on a workstation computer.