Changes for page Neuron

Last modified by abonard on 2025/04/10 15:17
From version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
Change comment: There is no comment for this version
To version 5.1
edited by abonard
on 2025/04/10 15:07
Change comment: There is no comment for this version

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1 -XWiki.jessicamitchell
1 +XWiki.abonard
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1 -Available tutorials:
2 2  
3 -=== [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel=" noopener noreferrer" target="_blank"]] ===
4 4  
5 -//Level: beginner//
3 +* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
6 6  
7 -A good beginner's tutorial. Introduces some of NEURON's basic GUI tools.
8 -=== [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel=" noopener noreferrer" target="_blank"]] ===
5 +=== **Beginner** ===
9 9  
10 -//Level: beginner//
7 +=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
11 11  
12 -=== [[1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself-0||rel=" noopener noreferrer" target="_blank"]] ===
9 +**Level**: beginner(%%) **Type**: user documentation
13 13  
14 -//Level: advanced//
15 -
16 -=== [[2. Run a "complete" simulation and save its results>>https://neuron.yale.edu/neuron/docs/2-run-complete-simulation-and-save-its-results||rel=" noopener noreferrer" target="_blank"]] ===
17 -
18 -//Level: advanced//
19 -
20 -=== [[3. Run a segmented simulation and save its results>>https://neuron.yale.edu/neuron/docs/3-run-segmented-simulation-and-save-its-results||rel=" noopener noreferrer" target="_blank"]] ===
21 -
22 -//Level: advanced//
23 -
24 -=== [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] ===
25 -
26 -//Level: advanced//
27 -
28 -=== [[4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results||rel=" noopener noreferrer" target="_blank"]] ===
29 -
30 -//Level: advanced//
31 -
11 +After this tutorial, students will be able to replicate neurons using templates and connect these neurons together.
32 32  === [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] ===
33 33  
34 -//Level: advanced//
14 +**Level**: beginner(%%) **Type**: user documentation
35 35  
16 +After this tutorial, students will be able to know how to create a single compartment neuron model with Hodgkin-Huxley conductances, how to run the simulator and how to display the simulation results
36 36  === [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] ===
37 37  
38 -//Level: advanced//
19 +**Level**: beginner(%%) **Type**: user documentation
39 39  
40 -=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
21 +After this tutorial, students will be able to work with more advanced topics of building multi-compartmental neurons and using different types of graphs to display the results
41 41  
42 -//Level: advanced//
43 -
44 -=== [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
45 -
46 -//Level: advanced//
47 -
48 -=== [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel=" noopener noreferrer" target="_blank"]] ===
49 -
50 -//Level: advanced//
51 -
52 -=== [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] ===
53 -
54 -//Level: advanced//
55 -
56 -=== [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" noopener noreferrer" target="_blank"]] ===
57 -
58 -//Level: advanced//
59 -
60 -=== [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" noopener noreferrer" target="_blank"]] ===
61 -
62 -//Level: advanced//
63 -
64 -=== [[Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
65 -
66 -//Level: advanced//
67 -
68 -Here we will implement a new voltage-gated macroscopic current whose properties are described by a family of chemical reactions.
69 -=== [[Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
70 -
71 -//Level: advanced//
72 -
73 -Our goal is to implement a new voltage-gated macroscopic current whose properties are described by HH-style equations.
74 -=== [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
75 -
76 -//Level: advanced//
77 -
78 -Given a Channel Builder that implements a deterministic channel specified by a kinetic scheme, we create a new one that implements stochastic gating.
79 -=== [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
80 -
81 -//Level: advanced//
82 -
83 -Our goal is to build an extremely simplified model of a pyramidal cell.
84 -=== [[Dealing with simulations that generate a lot of data>>https://neuron.yale.edu/neuron/docs/dealing-simulations-generate-lot-data||rel=" noopener noreferrer" target="_blank"]] ===
85 -
86 -//Level: advanced//
87 -
88 -=== [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
89 -
90 -//Level: advanced//
91 -
92 -=== [[Example: restricting a reaction to part of a region>>https://neuron.yale.edu/neuron/docs/example-restricting-reaction-part-region||rel=" noopener noreferrer" target="_blank"]] ===
93 -
94 -//Level: advanced//
95 -
96 -=== [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] ===
97 -
98 -//Level: advanced//
99 -
100 -=== [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
101 -
102 -//Level: advanced//
103 -
104 -=== [[How to generate independent random spike streams>>https://neuron.yale.edu/neuron/docs/how-generate-independent-random-spike-streams||rel=" noopener noreferrer" target="_blank"]] ===
105 -
106 -//Level: advanced//
107 -
108 -=== [[Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
109 -
110 -//Level: advanced//
111 -
112 -=== [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
113 -
114 -//Level: advanced//
115 -
116 -We use the CellBuilder to specify the spatial grid (nseg) and biophysical properties of a model based on detailed morphometric data.
117 -=== [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel=" noopener noreferrer" target="_blank"]] ===
118 -
119 -//Level: advanced//
120 -
121 -=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
122 -
123 -//Level: advanced//
124 -
125 -=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
126 -
127 -//Level: advanced//
128 -
129 -This page provides a brief introduction to:
130 -Python syntax
131 -Variables
132 -Lists and Dicts
133 -For loops and iterators
134 -Functions
135 -Classes
136 -Importing modules
137 -Writing and reading files with Pickling.
138 -=== [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] ===
139 -
140 -//Level: advanced//
141 -
142 -=== [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
143 -
144 -//Level: advanced//
145 -
146 -=== [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] ===
147 -
148 -//Level: advanced//
149 -
150 -=== [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] ===
151 -
152 -//Level: advanced//
153 -
154 -=== [[Reaction-Diffusion: varying initial concentrations and parameters>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-varying-initial-concentrations-and-parameters||rel=" noopener noreferrer" target="_blank"]] ===
155 -
156 -//Level: advanced//
157 -
158 -=== [[Reading a morphometric data file and converting it to a NEURON model>>https://neuron.yale.edu/neuron/docs/import3d/read_data||rel=" noopener noreferrer" target="_blank"]] ===
159 -
160 -//Level: advanced//
161 -
162 -=== [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] ===
163 -
164 -//Level: advanced//
165 -
166 -=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
167 -
168 -//Level: advanced//
169 -
170 -The objectives of this part of the tutorial are to get familiar with basic operations of NEURON using Python. In this worksheet we will:
171 -Create a passive cell membrane in NEURON.
172 -Create a synaptic stimulus onto the neuron.
173 -Modify parameters of the membrane and stimulus.
174 -Visualize results with bokeh
175 -=== [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel=" noopener noreferrer" target="_blank"]] ===
176 -
177 -//Level: advanced//
178 -
179 -=== [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] ===
180 -
181 -//Level: advanced//
182 -
183 -=== [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] ===
184 -
185 -//Level: advanced//
186 -
187 -=== [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
188 -
189 -//Level: advanced//
190 -
191 -How to make one or more biophysical properties vary systematically with position in space.
192 -=== [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel=" noopener noreferrer" target="_blank"]] ===
193 -
194 -//Level: advanced//
195 -
196 -=== [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
197 -
198 -//Level: advanced//
199 -
200 -=== [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
201 -
202 -//Level: advanced//
203 -
204 -=== [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
205 -
206 -//Level: advanced//
207 -
208 -=== [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
209 -
210 -//Level: advanced//
211 -
212 -=== [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
213 -
214 -//Level: advanced//
215 -
216 -Reading a morphometric data file and converting it to a NEURON model
217 -Exploring morphometric data and fixing problems
218 -=== [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel=" noopener noreferrer" target="_blank"]] ===
219 -
220 -//Level: advanced//
221 -
222 -