orena1 / neuron_tutorial

Tutorial for understanding how to use NEURON simulation environment

This tutorial will help you understand how to use The NEURON simulation environment

Instructions

In order to use this tutorial, you need to install NEURON (How_to_Install_NEURON.txt); after installing NEURON, you can decide whether to use jupyter notebook or Python scripts.

You will also need to compile to mod files. For example, if you decide to use the Jupyter_notebooks

Linux/Mac:

1. Open Terminal
2. Go to Jupyter_notebooks directory
3. Type: nrnivmodl mods

Windows:

1. Move all files from the folder mods to the base-directory
2. Use the following instructions (second section - Compiling mod files in NEURON 5.1 and later), choose the base-directory that now contains all the mod files

After completing the installations download the NEURON_tutorial.pptx and follow the instructions in the presentation. Suggested exercises are available in the slides notes (The presentation is also available here: https://1drv.ms/p/s!ApfBr7JWIT35mj3A1Sjcw3hKNCdF?e=4yG34n)

Feel free to open Issues if you find any bugs, or have any suggestions.

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neuron_tutorial's Issues

Do not understand how to insert mechanism

For example, soma.insert('kv') gives me an error message "not a density mechanism".
I do not find how to do it. I tried insertin "hh" and then change conductancies but the results are not the one i find in the tutorial.
Thank you

LookupError: 'tstop' is not a defined hoc variable name

Hi,

I followed the instruction and have compiled the mods.However ,a LookupError happened when I tried to run the example in Jupyter Notebook.

---------------------------------------------------------------------------
LookupError                               Traceback (most recent call last)
<ipython-input-6-0f2c77b59e6a> in <module>
----> 1 h.tstop = 220
      2 h.dt = 0.025
      3 h.v_init=-70
      4 h.run()

LookupError: 'tstop' is not a defined hoc variable name.

Any idea what I'm doing wrong? Otherwise,I use pip3 install neuron instead of downloading the NEURON installer.