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Diffusive homeostasis in a spiking network model (Sweeney et al. 2015)
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<html><pre> 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 [email protected]. </pre></html>
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