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Changes for page Neuron

Last modified by abonard on 2025/04/10 15:17
From version 65.1
edited by abonard
on 2025/04/10 15:15
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To version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
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Summary

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1 -XWiki.abonard
1 +XWiki.jessicamitchell
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1 +Available tutorials:
1 1  
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"]] ===
2 2  
3 -* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
5 +//Level: beginner//
4 4  
5 -=== **Beginner** ===
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"]] ===
6 6  
10 +//Level: beginner//
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"]] ===
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 +
32 +=== [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] ===
33 +
34 +//Level: advanced//
35 +
36 +=== [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] ===
37 +
38 +//Level: advanced//
39 +
7 7  === [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
8 8  
9 -**Level**: beginner(%%) **Type**: user documentation
42 +//Level: advanced//
10 10  
11 -After this tutorial, students will be able to replicate neurons using templates and connect these neurons together.
44 +=== [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
12 12  
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 +