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
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To version 15.1
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 +* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
9 9  
10 -//Level: beginner//
7 +=== **Beginner** ===
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 +=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
13 13  
14 -//Level: advanced//
11 +**Level**: beginner(%%) **Type**: user documentation
15 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 -
13 +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//
16 +**Level**: beginner(%%) **Type**: user documentation
35 35  
18 +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//
21 +**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"]] ===
23 +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
24 +=== [[A NEURON Programming Tutorial - Part D>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
41 41  
42 -//Level: advanced//
26 +**Level**: beginner(%%) **Type**: user documentation
43 43  
44 -=== [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
28 +After this tutorial, students will be able to add new membrane mechanisms to the simulator and incorporate them in our neurons.
29 +=== [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel=" noopener noreferrer" target="_blank"]] ===
45 45  
46 -//Level: advanced//
31 +**Level**: beginner(%%) **Type**: user documentation
47 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"]] ===
33 +A good beginner's tutorial to get an introduction to some of NEURON's basic GUI tools.
34 +=== [[A NEURON Programming Tutorial - Introduction>>https://web.mit.edu/neuron_v7.4/nrntuthtml/index.html||rel=" noopener noreferrer" target="_blank"]] ===
49 49  
50 -//Level: advanced//
36 +**Level**: beginner(%%) **Type**: user documentation
51 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"]] ===
38 +This is a web based tutorial in the NEURON Simulation package. It will hopefully take you step by step, through the process of creating a complex simulation of a small network of neurons.
39 +Starting by creating a single compartment neuron model with Hodgkin-Huxley conductances, how to run the simulator and how to display the simulation results, building multi-compartmental neurons, using different types of graphs to display the results, how to replicate neurons using templates, add new membrane mechanisms to the simulator and incorporate them into our neurons, increasing simulation speed and ways of getting data out of NEURON.
40 +=== [[Outline of "Construction and Use of Models: Part 1. Elementary tools">>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel=" noopener noreferrer" target="_blank"]] ===
53 53  
54 -//Level: advanced//
42 +**Level**: beginner(%%) **Type**: interactive tutorial
55 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"]] ===
44 +In this beginner tutorial you will learn how to make a simple model using hoc and how to use NEURON's graphical tools to create an interface for running simulations and to modify the model itself.
45 +=== [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel=" noopener noreferrer" target="_blank"]] ===
57 57  
58 -//Level: advanced//
47 +**Level**: beginner(%%) **Type**: slide deck
59 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"]] ===
49 +Slides from a presentation on hoc syntax. Clear and concise. Includes an example of program analysis (walkthrough of code for a model cell generated by the CellBuilder).
50 +=== [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
61 61  
62 -//Level: advanced//
52 +**Level**: beginner(%%) **Type**: user documentation
63 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"]] ===
54 +After this tutorial, students will be able to save data from the simulations and methods for increasing simulation speed.
55 +=== **Advanced** ===
65 65  
66 -//Level: advanced//
57 +=== [[Reaction-Diffusion – Radial Diffusion>>https://neuron.yale.edu/neuron/docs/radial-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
67 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"]] ===
59 +**Level**: advanced(%%) **Type**: -
70 70  
71 -//Level: advanced//
61 +Using NEURON Radial diffusion can be implemented in rxd using multicompartment reactions. By creating a series of shells and borders with reactions between them dependent the diffusion coefficient.
62 +=== [[Reaction-Diffusion Example – Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] ===
72 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"]] ===
64 +**Level**: advanced(%%) **Type**: interactive tutorial
75 75  
76 -//Level: advanced//
66 +The model presented in this tutorial generates Ca2+ waves and is a simplification of the model we used in Neymotin et al., 2015.
67 +=== [[Reaction-Diffusion – 3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] ===
77 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"]] ===
69 +**Level**: advanced(%%) **Type**: interactive tutorial
80 80  
81 -//Level: advanced//
71 +This tutorial provides an overview of how to set up a simple travelling wave in both cases.
72 +=== [[Reaction-Diffusion – Initialization strategies>>https://neuron.yale.edu/neuron/docs/initialization-strategies||rel=" noopener noreferrer" target="_blank"]] ===
82 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"]] ===
74 +**Level**: advanced(%%) **Type**: interactive tutorial
85 85  
86 -//Level: advanced//
76 +In this tutorial you will learn how to implement cell signalling function in the reaction-diffusion system by characterising your problems by the answers to three questions: (1) Where do the dynamics occur, (2) Who are the actors, and (3) How do they interact?
87 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 -