NEURON Hands-on Course

EXERCISES

Table of Contents

1. Introduction to the GUI
Lipid bilayer model

3

2. Interactive modeling
Squid axon model

7

3. The CellBuilder
Constructing a ball and stick model, saving session files

9

4. Using morphometric data
The Import3D tool

21

5. Using NMODL files
Single compartment model with HHk mechanism

29

6. HOC exercises
Introduction to the hoc programming language

31

7. Using ModelDB and Model View
Neuroinformatics tools for finding and understanding models

41

8. Specifying inhomogeneous channel distributions
with the CellBuilder

47

9. Bulletin board parallelization
Speed up embarrassingly parallel tasks

51

10. Multithread parallelization
Increase performance on multicore workstations

59

11. Custom initialization

63

12. Networks : discrete event simulations with artificial cells
Introduction to the Network Builder

67

13. Networks : continuous simulations of nets with biophysical model cells
Network ready cells from the CellBuilder

71

14. Hopfield Brody synchronization (sync) model
Networks via hoc

75

15. State and parameter discontinuities

83

16. Analyzing electrotonus
with the Impedance class

85

17. Introduction to the Linear Circuit Builder
A two-electrode voltage clamp

93



Informal extras

Some useful hoc idioms

99

Vectors and Matrices: reading data

101

Vectors and Matrices: processing data
Subtracting linear response

103

MyFirstNEURON
by Arthur Houweling

(remote)

Simulation control: a family of simulations
Automating the execution of a family of related simulations

105

Simulation control: forcing functions

111

Optimizing a model

115

Rectifying gap junction
implemented with the Linear Circuit Builder

131

MPI parallelization

137

Python

139


NEURON hands-on course
Copyright © 1998-2012 by N.T. Carnevale and M.L. Hines, all rights reserved.