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OpticalBlock simulation

This is a simulation of optical block in an unmylenated axon in NEURON.

The code is currently in an early stage of development and it is likely that many parameters are not yet properly set; thus we recommend caution in interpreting any model results at this time.

Running the simulation

To run the simulation, first open a shell window and compile the conductances (fhm1.mod) using nrnivmodl:

cd OpticalBlock
nrnivmodl

You can then run the code using NEURON, specifying which configuration file to use, e.g.:

nrngui nrnaxon.py demo_block.yaml

The above example will produce the file "demo_block.csv".

Advanced usage

If you have R installed, Rscript on your path, and R yaml installed, you can build all of the figures by running

make

or individual results using make, e.g.

make demo_block.pdf

or

make demo_block.csv

License

This code is licensed under the GNU General Public License; see LICENSE.txt for details.

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NEURON model of optical block

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