GitHub - ModelDBRepository/243350: Model of the hippocampus over the sleep-wake cycle using Hodgkin-Huxley neurons (Aussel et al 2018)

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Model of the hippocampus over the sleep-wake cycle using Hodgkin-Huxley neurons (Aussel et al 2018)

modeldb.science/243350

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
Event_detection_Aussel.py		Event_detection_Aussel.py
hippocampus_Aussel.py		hippocampus_Aussel.py
readme.html		readme.html
screenshot1.png		screenshot1.png
screenshot2.png		screenshot2.png
topology_Aussel.py		topology_Aussel.py

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<html>
<p>This is the readme for the models associated with the paper:
</p>
<p>Aussel A, Buhry L, Tyvaert L, Ranta R (2018) A detailed anatomical and mathematical model of the hippocampal formation for the generation of sharp-wave ripples and theta-nested gamma oscillations. J Comput Neurosci 45:207-221
</p>
<p>These models were contributed by A. Aussel. The python scripts require the freely available brian2 package:
<a href="https://brian2.readthedocs.io/en/stable/index.html">https://brian2.readthedocs.io/en/stable/index.html</a></p>
The model also requires at least python version 3.6.  In addition EEG data files must be
supplied (unfortunately the ones used for the paper are not allowed to be released).  See the hippocampus_Aussel.py around line 505 for filenames. The sampling rate was 1024 Hz. </p>
To run on a linux cluster you may need to execute commands like (if when you
try running the python script it reports missing requirements, add those names to the pip3 command like the examples below:</p>
module load Python/3.6<br/>
pip3 install --user --upgrade pip<br/>
pip3 install --user brian2<br/>
pip3 install --user matplotlib<br/>
python3 -i hippocampus_Aussel.py<p/>
Then type into the python prompt:<p/>
main_process([0], 60*psiemens,600*psiemens,0.1,0.06)<br/>
<p/>
Although the simulation will stop when it needs the real data for stimulation it
will generate these graphs:<p/>
<img src="./screenshot1.png" alt="screenshot 1" width="650">
<p/>
<img src="./screenshot2.png" alt="screenshot 2" width="650">
<p/>
</html>