Discussions on development, Auryn's inner workings, adding new features and how to change things at the core
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Joined: Fri Jan 11, 2019 1:34 pm


Post by k47h4 »

I reimplemented sim_background in brian2.
This was well possible with the information from the publication 'Zenke, Hennequin, Gerstner et al in PlosCB 2013' together with the code 'sim_background' provided online. Thanks for providing the code online!

While the manuscript was clear about the values for inhibitory and excitatory resting potentials, as well as the excitatory membrane time constant, I could not find where these were set in the code, or whether Auryn provides default values for those? The documentation nicely mentions default values for different synaptic time constants (AMPA, GABA, NMDA).
The simulation code revealed that membrane voltages were initialised normally distributed around -60mV with a standard deviation of 10mV.

I get an asynchronous irregular regime, as desired, with an alpha (AMPA to NMDA ratio) of .5 as in the manuscript.
inhibitory_neurons.png (40.57 KiB) Viewed 16445 times
excitatory_neurons.png (60.45 KiB) Viewed 16445 times
However, with the random initialisation of membrane voltages I expected to get into the regime a bit quicker? So there might still be discrepancies between the two implementations.

As zenke pointed out himself, in Eq. (13) and (14) of the manuscript, only the conductance term (g_inh and g_ampa, respectively) is supposed to be divided by the synaptic time constant (tau_inh and tau_ampa, respectively).

Here's the code: ...
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