1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
|
.. _interactive_modeling:
Interactive Modeling
====================
Physical System
---------------
Giant axon from the squid: Loligo pealei
Conceptual Model
----------------
Hodgkin-Huxley cable equations
++++++++++++++++++++++++++++++
.. image:: img/hh.gif
:align: center
Simulation
----------
Computational implementation of the conceptual model
++++++++++++++++++++++++++++++++++++++++++++++++++++
We *could* implement this model in Python:
.. code::
python
from neuron import h, gui
axon = h.Section(name='axon')
axon.L = 2e4
axon.diam = 100
axon.nseg = 43
axon.insert(h.hh)
**But** for this exercise, let's instead use the CellBuilder tool to create the model:
.. image:: img/cbgeom.gif
:align: center
.. image:: img/cbbio.gif
:align: center
Save the model in ``hhaxon.ses`` using :menuselection:`NEURONMainMenu --> File --> savesession`
Using the computational model
+++++++++++++++++++++++++++++
If starting from a fresh launch of python, you can load the saved ses file by loading NEURON and its GUI: ``from neuron import h. gui`` and then selecting :menuselection:`NEURONMainMenu --> File --> loadsession`
Alternatively you can use NEURON to execute ``hhaxon.ses``
1. Change to the appropriate directory in your terminal
2. Start python, and at the >>> prompt enter the commands
.. code::
python
from neuron import h, gui
h.load_file('hhaxon.ses')
Exercises
---------
1.
Stimulate with current pulse and see a propagated action potential.
The basic tools you'll need from the :ref:`NEURON Main Menu <NEURONMainMenu>`
:menuselection:`Tools --> Point Processes --> Manager -->` :ref:`Point Manager <pointman>` to specify stimulation
:menuselection:`Graph -->` :ref:`Voltage axis <voltage_axis>` and :menuselection:`Graph -->` :ref:`Shape plot <shape_plot>` to create graphs of v vs t and v vs x.
:menuselection:`Tools -->` :ref:`RunControl <runctrl>` to run the simulation
:menuselection:`Tools --> Movie Run` to see a smooth evolution of the space plot in time
2.
Change excitability by adjusting sodium channel density.
Tool needed: :menuselection:`Tools --> Distributed Mechanisms --> Viewers -->` :ref:`Shape Name <shapename>`
3.
Use two current electrodes to stimulate both ends at the same time
4.
Up to this point, the model has used a very fine spatial grid calculated from the Cell Builder's d_lambda rule
.. image:: img/geometry.gif
:align: center
Change nseg to 15 and see what happens
|
