NEURON implementation of Vogels & Abbott model

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lneisenman
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NEURON implementation of Vogels & Abbott model

Post by lneisenman » Fri Aug 05, 2011 10:17 am

I have a question about Brette and colleagues' implementation of the COBA model. Both the original description of the model by Vogels and Abbott (J Neurosci 25:10786, 2005) and the description by Brette and colleagues (appendix B) state that the decay time constants for excitatory and inhibitory inputs are 5 ms and 10 ms, respectively. However, in the cell template, the time constants appear to be set at 10 ms and 20 ms, respectively (see below), and I don't see anywhere else in the code that they are changed. Can someone help me understand the discrepancy? Thanks.

Larry

The following code is from the cell template in the file cobacell.hoc in the coba folder in the NEURON implementation of the model from the ModelDB package.

Code: Select all

...
proc synapses() {
  /* E0 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 10
  /* I1 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 20
    syn_.e = -80
}
...

ted
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Re: NEURON implementation of Vogels & Abbott model

Post by ted » Fri Aug 05, 2011 11:58 am

Brette and colleagues' implementation of the COBA model.
Well, the error isn't in "Brette and colleague's implementation"--it's in the NEURON implementation, which was done by Michael Hines and me. Our "coba" version of the Vogels & Abbott model has synaptic time constants that are twice as large as they should be. Sorry about that mistake, but thanks for bringing it to my attention. Fortunately it does not affect the qualitative results published in Brette et al. 2007. The fix, of course, is simply to change the assignment statements that you quoted. We will make revised source code available on ModelDB http://senselab.med.yale.edu/modeldb via accession number 83319.

The "cobahh" and "cuba" implementations have correct time constants. There is no issue with the "cubadv" model, in which the time course of all synaptic transients is governed entirely by the "membrane" time constant. Also, the time constants were correct in the PyNN implementation (which generated NEURON and NEST models that were used for Fig. 24).

Final note: the discovery and correction of this error provide yet another demonstration of the importance of the general principle of sharing model source code, and of the specific value of ModelDB as a mechanism for model sharing.

tom_morse
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Re: NEURON implementation of Vogels & Abbott model

Post by tom_morse » Fri Aug 05, 2011 3:01 pm

Ted's time constants update has been uploaded to ModelDB:

http://senselab.med.yale.edu/ModelDB/sh ... odel=83319

lneisenman
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Re: NEURON implementation of Vogels & Abbott model

Post by lneisenman » Fri Aug 05, 2011 5:24 pm

Thanks for the rapid clarification. I was worried about re-using code I wasn't sure I understood.

Larry

ted
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Re: NEURON implementation of Vogels & Abbott model

Post by ted » Sat Aug 06, 2011 9:42 am

Thank you for bringing this discrepancy to our attention so we could fix it.

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