GitHub - ModelDBRepository/183371: Diffusive homeostasis in a spiking network model (Sweeney et al. 2015)

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This is the readme for the Brian code associated with the paper:

Y Sweeney, J Hellgren-Kotaleski, and M Hennig (2015). 
A diffusive homeostatic signal maintains neural heterogeneity and
responsiveness in cortical networks. PLoS Comp. Biol. DOI:
10.1371/journal.pcbi.1004389

An up-to-date version of the code may be found at
<a href="https://github.com/yannaodh/sweeney-2015">https://github.com/yannaodh/sweeney-2015</a>

To see the code used to implement the numerical diffusion method, see
code/diffusion_minimal_example.py . Brief instructions on how to
include this in an existing brian model are contained within.

To see a simplified python script containing a spiking network model
with diffusive homeostasis implemented (written in brian) see
code/network_minimal_example.py .

To generate the data for each figure run the run_simulations_figX.py
script from command line using 'python run_simulations_figX.py', where
X is the figure number. A lot of text output will be created showing
the progress. You will need to be in the same directory as the
'network_simulation.py' file, and other .py files.

Python with numpy (<a href="http://www.numpy.org/">http://www.numpy.org/</a>) and the brian simulator
(<a href="http://www.briansimulator.org">http://www.briansimulator.org</a>) will need to be installed. These scripts were
tested on a machine with OSX 10.10, Python v2.7.10, numpy v1.9.2, and
brian v1.4.1

IPython Notebook (http://ipython.org/notebook.html) will be required in order to interact with the IPython Notebooks containing the plots.

As the simulations can take quite a long time to run (several hours on
a multicore machine) and the resulting datafiles are quite large (~1
GB total), sample data generated from the code are provided for each
figure and may be downloaded from figshare.

Figure 1: <a href="http://dx.doi.org/10.6084/m9.figshare.1454450">http://dx.doi.org/10.6084/m9.figshare.1454450</a>

Figure 4: <a href="http://dx.doi.org/10.6084/m9.figshare.1454455">http://dx.doi.org/10.6084/m9.figshare.1454455 </a>

Figure 5: <a href="http://dx.doi.org/10.6084/m9.figshare.1454469">http://dx.doi.org/10.6084/m9.figshare.1454469</a>

For any queries, comments or requests please do not hesitate to
contact me at yann.sweeney@ed.ac.uk.
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