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How to get started modeling networks with NEURON?

Posted: Sun May 29, 2005 11:00 am
by ted
On 11/16/2004 a NEURON user wrote:
I have a student is not a programmer. How can he get started
using NEURON to implement simulations of neural circuits?

Posted: Sun May 29, 2005 11:01 am
by ted
On 11/16/2004 Michael Hines <> wrote:
I'd start with
exercises 13 and 14.
Also ... /main.html
And finally, Ted may be able to point you to a draft of the relevant chapter
in the NEURON book which we will be sending to the publisher at the end of the month.

I would emphasize that the gui tools are just for framework building
and your student will have to use the gui tool to create a framework
hoc file for actual construction of a large network.

material in the NEURON book relevant to modeling nets

Posted: Sun May 29, 2005 11:04 am
by ted
Chapter 11 ... xedref.pdf
shows how to use the hoc file emitted by a NetWork Builder to create a
large net. An indexed version should be available in a few days, but
the narrative is linear and cumulative, so lack of an index should
not be a serious problem.

Chapter 11 presumes familiarity with material in chapters 1, 4-10,
12 and 13.

Of these the most important for a beginner would probably be chapters
1 (general intro to NEURON), 5 and 6 (specifics about modeling
biological neurons), and 10 (key concepts underlying NEURON's
strategy for implementing synaptic connections).

12 and 13.are intros to basic hoc programming, and object oriented
programming in hoc, respectively.

4 is all "about numerical integration for the neuroscientist."

9 is the authoritative reference on NMODL (helpful for answering
questions that might arise in chapter 10).

7 and 8 deal with the run time system and initialization and how
to customize them.