Compatibility with pyNN

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lopez.ber...@gmail.com

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Jul 20, 2020, 10:20:10 AM7/20/20
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Hello,

I checked both the documentation of pyNN and Brian2. Focusing on the first one, I saw that pyNN is only compatible with Brian 1.4. Checking the documentation of Brian2, there is no information indicating this situation. I only found this old post, apparently for Brian1: https://briansimulator.org/posts/brian-is-in-pynn/

Could you please confirm if Brian2 is compatible with pyNN?

I am trying to run a neuronal topology modeled in SONATA and, for that, the only option I see feasible is to convert the SONATA model into pyNN, and then import it in Brian. If it is not possible, do you have any alternative to use it in Brian?

Thanks in advance!

Marcel Stimberg

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Aug 4, 2020, 6:12:05 AM8/4/20
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Hi,
Brian2 is currently not supported by PyNN, but work is underway to change this (https://github.com/NeuralEnsemble/PyNN/pull/671). I am not very familiar with SONATA, but if you only want to import the connection information then I guess it should be possible with SONATA tools to generate a list of pre-synaptic and post-synaptic indices which you can then use in Brian with the synapses.connect(i=..., j=...) syntax.
Best,
  Marcel

lopez.ber...@gmail.com

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Aug 4, 2020, 11:06:43 AM8/4/20
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Thanks Marcel for your response, I will explore the possibility you suggest.

Best,
Sergio
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