I'm starting work on a computational neuroscience project where I want to create my own model of a spiking Hodgkin-Huxley neuron and connect many instances (about 400) of this model through synapses. Is there a generally accepted way to do this? I have experience in Python and Matlab but I'm wondering if there are any good packages or other software to create neurons and connecting them into a network?
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$\begingroup$ don't use HH neurons unless you absolutely have to. First implement a rate model network, then once that's working switch to a integrate and fire network, and only once that's working switch to HH neurons. No point in making things hard for yourself unless you absolutely have to and you've gone step by step through simpler versions. $\endgroup$– honiCommented Apr 10, 2019 at 18:21
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$\begingroup$ I'm continuing a project from a PhD dissertation so I guess they were at that point. They used pretty old software and I'm mostly looking for currently supported packages/software that I can create networks with and run on the super computer at my school. Thanks! $\endgroup$– markagriosCommented Apr 15, 2019 at 0:50
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$\begingroup$ Just an idea: to determine what is "generally accepted", you could potentially use Google Trends or Google Scholar result counts to get an impression of what is in use after having identified potential candidates. Alternatively, you rely on the opinion of someone who is currently active in the field. 🙂 $\endgroup$– Steven Jeuris ♦Commented Apr 23, 2019 at 21:54
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$\begingroup$ More options here. $\endgroup$– Arnon Weinberg ♦Commented Oct 6, 2022 at 2:07
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2 Answers
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I am old and my experience with this area is 20 years out of date, but I would still go with https://neuron.yale.edu/neuron/
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$\begingroup$ Well, the website definitely doesn't look 20 years old. 😉 $\endgroup$– Steven Jeuris ♦Commented Apr 23, 2019 at 21:52
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You can simulate a network of hodgkin huxley neurons quite easily with Brian, a python package for simulating networks of neurons. http://briansimulator.org/demo/ <- there's actually a demo of what you want here, I think.
There is also Neuron, as a previous poster answered, but I don't think you need this unless you are doing morphologically detailed simulations.
