1 - A tour of the NEURON simulation environment

Summary

… so, entering, the first thing I did was to stumble over an ash-box in the porch. Ha! thought I, ha, as the flying particles almost choked me, are these ashes from that destroyed city, Gomorrah?

Modeling and understanding

Modeling can have many uses, but its principal benefit is to improve understanding. The chief question that it addresses is whether what is known about a system can account for the behavior of the system. An indispensable step in modeling is to postulate a conceptual model that expresses what we know, or think we know, about a system, while omitting unnecessary details. This requires considerable judgment and is always vulnerable to hindsight and revision, but it is important to keep things as simple as possible. The choice of what to include and what to leave out depends strongly on the hypothesis that we are studying. The issue of how to make such decisions is outside the primary focus of this book, although from time to time we may return to it briefly.

The task of building a computational model should only begin after a conceptual model has been proposed. In building a computational model we struggle to establish a match between the conceptual model and its computational representation, always asking the question: would the conceptual model behave like the simulation? If not, where are the errors? If so, how can we use NEURON to help understand why the conceptual model implies that behavior?

Introducing NEURON

NEURON is a simulation environment for models of individual neurons and networks of neurons that are closely linked to experimental data.