Demonstrations and Examples

Examples of NEURON in action

After installing NEURON, you can launch $NEURONHOME/nrn/demo/demo.hoc to examine models of Look here for screen shots of these models.

Here's a movie of spike conduction along an axon with a sudden increase of diameter. You should be able to recreate this quickly, without writing any code at all, by using the new CellBuilder and plotting Vm vs. distance in a Space Plot.

Pick up sizzle.zip, which contains ssc.hoc, a demonstration of how the site of spike initiation may be affected jointly by dendritic excitability and the strength and location of synaptic input. See movies of the effect of an input at the soma, the midpoint of a dendrite, and at the distal end of a dendrite.

For examples of computationally efficient methods for dealing with use-dependent synaptic plasticity, go to ModelDB http://senselab.med.yale.edu/senselab/ModelDB/ and get NEURON implementations of the models of short-term plasticity described by Varela et al. Journal of Neuroscience 17:7926-7940, 1997, and Tsodyks et al. Journal of Neuroscience 20:RC50:1-5, 2000. The mod files packaged with these runnable examples show how to use input events not only to produce postsynaptic conductance changes, but also how to modulate the amplitude of each conductance change as a function of the prior history of synaptic activation on a per-stream basis. This means that multiple afferent paths can drive the same point process (share the same postsynaptic mechanism) for computational efficiency, yet each can still have its own individual "memory" of prior activations (each path can facilitate or depress independently of the others).

Be sure to examine http://neuron.duke.edu where John Moore has posted many more examples.

Don't miss Arthur Houweling's MyFirstNEURON, which simulates experiments described in Huguenard and McCormick's book Electrophysiology of the Neuron (New York 1994, Oxford University Press). With MyFirstNEURON you can also design your own models of individual neurons and interconnected pairs of neurons.

Other programming examples

NEURON's on-line help files contain numerous examples of how to use specific features of hoc. Many of these can be executed directly from within your WWW browser, once you have configured it to use NEURON as a "viewer" for hoc files.

The directories under $NEURONHOME/nrn/examples/nrniv hold a rich collection of useful and informative files, including source code for many biophysical mechanisms ($NEURONHOME/nrn/examples/nrniv/nmodl is a great place to look when you start creating your own new mechanisms) and several illustrations of how to employ the new Network Connection class to build and manage networks ($NEURONHOME/nrn/examples/nrniv/netcon).

And did you know that the hoc code in $NEURONHOME/nrn/lib/hoc implements NEURON's GUI? It's all there, where you can examine it and use it to create your own customizations and new extensions.


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