GitHub - katsu1110/Hierarchical_network: Attractor model with valleys in the energy profile (Wimmer et al., Nature Communications, 2015)

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Attractor model with valleys in the energy profile (Wimmer et al., Nature Communications, 2015)

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integration_circuit.py		integration_circuit.py
integration_circuit.pyc		integration_circuit.pyc
loop_network_single_run.png		loop_network_single_run.png
readme.html		readme.html
run_hierarchical_model.py		run_hierarchical_model.py
sensory_circuit.py		sensory_circuit.py
sensory_circuit.pyc		sensory_circuit.pyc

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<font size="10">This repository is entirely from Klaus Wimmer's website (https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=168867).
I (katsu1110) modified his script for the computation of psychophysical kernel.</font>

Copyright (C) 2014 Klaus Wimmer

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not,
see <a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>.

SUMMARY:

This program implements the model of: K Wimmer, A Compte, A Roxin, D
Peixoto, A Renart & J de la Rocha. Sensory integration dynamics in a
hierarchical network explains choice probabilities in cortical area
MT. Nat. Commun. 6:6177 doi: 10.1038/ncomms7177 (2015).

A complete description of the model is provided in the methods of the
paper and the supplementary material (in particular the Supplementary
Tables 1-4).

The program runs a single simulation and outputs a figure, similar to
the one shown in Fig 1b in the paper:

<img src="./loop_network_single_run.png" alt="Output of a single simulation run." width="550">

The code is not at all optimized in order to keep it simple, clean and
platform independent. Depending on your CPU, the execution can take
several minutes.

REQUIREMENTS: You will need Python and
the <a href="http://www.briansimulator.org">Brian simulator</a>
installed. Plotting requires matplotlib, a Python plotting library.


USE:
To run the simulation, just execute the command:

python run_hierarchical_model.py

CONTACT:
wimmer.klaus@gmail.com

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