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. Specifying inhomogeneous channel distributions
with the CellBuilder

29

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

33

7. Using NMODL files
Single compartment model with HHk mechanism

39

8. State and parameter discontinuities

41

9. Multithread parallelization

43

10. Python

47

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

49

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

53

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

57

14. Custom initialization

63

15. MPI parallelization

67


Informal extras

Some useful hoc idioms

69

Vectors and Matrices: reading data

71

Vectors and Matrices: processing data
Subtracting linear response

73

MyFirstNEURON
by Arthur Houweling

(remote)

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

75

Simulation control: forcing functions

81

Optimizing a model

85

Rectifying gap junction
implemented with the Linear Circuit Builder

101

Analyzing electrotonus
with the Impedance class

107

HOC exercises
Introduction to the hoc programming language

115

Hopfield Brody synchronization (sync) model
Networks via hoc

125

Bulletin board parallelization
Speed up embarrassingly parallel tasks

133


NEURON hands-on course
Copyright © 1998-2014 by N.T. Carnevale and M.L. Hines, all rights reserved.