These screen shots give an idea of the appearance of NEURON's GUI. These were generated with models that are distributed with NEURON.
- Voltage clamped membrane patch with Hodgkin-Huxley channels.
- Stochastic gating of voltage-dependent channels.
- Calcium accumulation in the presynaptic terminal at a neuromuscular junction.
- Synaptic integration and spike propagation in a stylized ("ball and multiple sticks") motoneuron model.
- Spike initiation and propagation in an anatomically detailed model of a pyramidal cell.
- Synchronizing network of integrate and fire neurons.
Here's a movie of spike conduction along an axon that has a sudden increase of diameter. You should be able to recreate this quickly with the GUI, without writing any code at all, by using the CellBuilder and plotting membrane potential vs. distance in a Space Plot.
Pick up sizzle.zip, which contains ssc.hoc, a demonstration of how the site of spike initiation is affected 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.
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.
Also, check out ModelDB (modeldb.yale.edu), which contains a large number of published models that address a wide range of topics. Many of these were implemented with NEURON and are ready to run. For instance, you might want to try the 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 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 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).
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 directory $NEURONHOME/nrn/examples/nrniv/nmodl (for all you MSWin users, that's c:\nrn\examples\nrniv\nmodl) hold a rich collection of useful and informative files, including source code for many biophysical mechanisms. It's a good place to look when you start creating your own new mechanisms with the NMODL programming language.
And did you know that the hoc code in $NEURONHOME/nrn/lib/hoc (c:\nrn\lib\hoc for MSWin) implements NEURON's GUI? It's all there, where you can examine it and use it to create your own customizations and new extensions.