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

23

5. Python + NEURON

31

6. Using NMODL files
Single compartment model with HHk mechanism

35

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

37

8. Reaction diffusion

43

9. Specifying inhomogeneous channel distributions
with the CellBuilder

45

10. Custom initialization

49

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

51

12. State and parameter discontinuities

57

13. Bulletin board parallelization
Speed up embarrassingly parallel tasks

59

14. HOC exercises
Introduction to the hoc programming language

67

15. Multithread parallelization

77

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

81

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

85

17. Synchronization network in Python

89

18. MPI parallelization

97

19. Using the Neuroscience Gateway Portal

99


Informal extras

Some useful hoc idioms

101

Vectors and Matrices: reading data

103

Vectors and Matrices: processing data
Subtracting linear response

105

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

107

Simulation control: forcing functions

113

Optimizing a model

117

Rectifying gap junction
implemented with the Linear Circuit Builder

133

Analyzing electrotonus
with the Impedance class

139

Hopfield Brody synchronization (sync) model
Networks via hoc

147

Numerical Methods Exercises

155


NEURON hands-on course
Copyright © 1998-2019 by N.T. Carnevale, M.L. Hines, and R.A. McDougal, all rights reserved.