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 48.1
edited by abonard
on 2025/04/10 15:08
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"]] ===
13 +After this tutorial, students will be able to replicate neurons using templates and connect these neurons together.
14 +=== [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] ===
17 17  
18 -//Level: advanced//
16 +**Level**: beginner(%%) **Type**: user documentation
19 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"]] ===
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
19 +=== [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] ===
21 21  
22 -//Level: advanced//
21 +**Level**: beginner(%%) **Type**: user documentation
23 23  
24 -=== [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||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"]] ===
25 25  
26 -//Level: advanced//
26 +**Level**: beginner(%%) **Type**: user documentation
27 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"]] ===
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"]] ===
29 29  
30 -//Level: advanced//
31 +**Level**: beginner(%%) **Type**: user documentation
31 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 +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"]] ===
33 33  
34 -//Level: advanced//
36 +**Level**: beginner(%%) **Type**: user documentation
35 35  
36 -=== [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||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"]] ===
37 37  
38 -//Level: advanced//
42 +**Level**: beginner(%%) **Type**: interactive tutorial
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"]] ===
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"]] ===
41 41  
42 -//Level: advanced//
47 +**Level**: beginner(%%) **Type**: slide deck
43 43  
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).
44 44  === [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
45 45  
46 -//Level: advanced//
52 +**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"]] ===
54 +After this tutorial, students will be able to save data from the simulations and methods for increasing simulation speed.
55 +=== **Advanced** ===
49 49  
50 -//Level: advanced//
57 +=== [[Reaction-Diffusion – Radial Diffusion>>https://neuron.yale.edu/neuron/docs/radial-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
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"]] ===
59 +**Level**: advanced(%%) **Type**: -
53 53  
54 -//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"]] ===
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"]] ===
64 +**Level**: advanced(%%) **Type**: interactive tutorial
57 57  
58 -//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"]] ===
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"]] ===
69 +**Level**: advanced(%%) **Type**: interactive tutorial
61 61  
62 -//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"]] ===
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"]] ===
74 +**Level**: advanced(%%) **Type**: interactive tutorial
65 65  
66 -//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?
77 +=== [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||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"]] ===
79 +**Level**: advanced(%%) **Type**: user documentation
70 70  
71 -//Level: advanced//
81 +=== [[Using the CellBuilder – Introduction>>https://neuron.yale.edu/neuron/static/docs/cbtut/main.html||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"]] ===
83 +**Level**: advanced(%%) **Type**: interactive tutorial
75 75  
76 -//Level: advanced//
85 +The following tutorials show how to use the CellBuilder, a powerful and convenient tool for constructing and managing models of individual neurons. It breaks the job of model specification into a sequence of tasks:
86 +1. Setting up model topology (branching pattern).
87 +2. Grouping sections with shared properties into subsets.
88 +3. Assigning geometric properties (length, diameter) to subsets or individual sections, and specifying a discretization strategy (i.e. how to set nseg).
89 +4. Assigning biophysical properties (Ra, cm, ion channels, buffers, pumps, etc.) to subsets or individual sections.
90 +=== [[Using Import3D – Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||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"]] ===
92 +**Level**: advanced(%%) **Type**: user documentation
80 80  
81 -//Level: advanced//
94 +Import3D tool can be used to translate common varieties of cellular morphometric data into a CellBuilder that specifies the anatomical properties of a model neuron. This Tutorial will guide you through how to fix problems in your morphometric data.
95 +=== [[Randomness in NEURON models– The solution>>https://neuron.yale.edu/neuron/docs/solution||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"]] ===
97 +**Level**: advanced(%%) **Type**: user documentation
85 85  
86 -//Level: advanced//
99 +In this part of the tutorial we will show you how to give NetStim its own random number generator.
100 +=== [[Segmentation intro: 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"]] ===
87 87  
88 -=== [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
102 +**Level**: advanced(%%) **Type**: user documentation
89 89  
90 -//Level: advanced//
104 +How to deal with simulations that generate a lot of data that must be saved? We will showcase different approaches.
105 +=== [[Using the Channel Builder – Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
91 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"]] ===
107 +**Level**: advanced(%%) **Type**: interactive tutorial
93 93  
94 -//Level: advanced//
109 +Our goal is to implement a new voltage-gated macroscopic current whose properties are described by HH-style equations.
110 +=== [[Using the Channel Builder – Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
95 95  
96 -=== [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] ===
112 +**Level**: advanced(%%) **Type**: interactive tutorial
97 97  
98 -//Level: advanced//
114 +Here we will implement a new voltage-gated macroscopic current whose properties are described by a family of chemical reactions.
115 +=== [[Randomness in NEURON models– Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] ===
99 99  
100 -=== [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
117 +**Level**: advanced(%%) **Type**: user documentation
101 101  
102 -//Level: advanced//
119 +=== [[Using the Network Builder – Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
103 103  
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"]] ===
121 +**Level**: advanced(%%) **Type**: user documentation
105 105  
106 -//Level: advanced//
123 +=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
107 107  
108 -=== [[Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
125 +**Level**: advanced(%%) **Type**: user documentation
109 109  
110 -//Level: advanced//
127 +This page provides a brief introduction to Python syntax, Variables, Lists and Dicts, For loops and iterators, Functions, Classes, Importing modules, Writing and reading files with Pickling.
128 +=== [[Reaction-Diffusion Example – RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] ===
111 111  
112 -=== [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
130 +**Level**: advanced(%%) **Type**: user documentation
113 113  
114 -//Level: advanced//
132 +NEURON's reaction-diffusion infrastructure can be used to readily allow intracellular concentrations to respond to currents generated in MOD files. This example shows you a simple model with just a single point soma, of length and diameter 10 microns, with Hodgkin-Huxley kinetics, and dynamic sodium (declared using rxd but without any additional kinetics).
133 +=== [[Segmenting a simulation of a model network - Introduction>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] ===
115 115  
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"]] ===
135 +**Level**: advanced(%%) **Type**: user documentation
118 118  
119 -//Level: advanced//
137 +=== [[Using the Network Builder – Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
120 120  
121 -=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
139 +**Level**: advanced(%%) **Type**: interactive tutorial
122 122  
123 -//Level: advanced//
141 +Learn how to Artificial Integrate and Fire cell with a synapse that is driven by an afferent burst of spikes.
142 +=== [[Reaction-Diffusion 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"]] ===
124 124  
125 -=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
144 +**Level**: advanced(%%) **Type**: user documentation
126 126  
127 -//Level: advanced//
146 +Implementation example for the restriction of the reaction to part of a region.
147 +=== [[Segmenting a simulation of a model cell - Introduction>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel=" noopener noreferrer" target="_blank"]] ===
128 128  
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"]] ===
149 +**Level**: advanced(%%) **Type**: user documentation
139 139  
140 -//Level: advanced//
151 +=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
141 141  
142 -=== [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
153 +**Level**: advanced(%%) **Type**: user documentation
143 143  
144 -//Level: advanced//
155 +The objectives of this part of the tutorial are to get familiar with basic operations of NEURON using Python. In this worksheet we will: Create a passive cell membrane in NEURON. Create a synaptic stimulus onto the neuron. Modify parameters of the membrane and stimulus. Visualize results with bokeh.
156 +=== [[Reaction-Diffusion – Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] ===
145 145  
146 -=== [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] ===
158 +**Level**: advanced(%%) **Type**: interactive tutorial
147 147  
148 -//Level: advanced//
160 +Learn how to scale reaction rates by a function of the form f(x) for suitably chosen a and m to approximately threshold them by a concentration.
161 +=== [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] ===
149 149  
150 -=== [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] ===
163 +**Level**: advanced(%%) **Type**: user documentation
151 151  
152 -//Level: advanced//
165 +We will touch upon the following subjects in this tutorial:
166 +How to create model specification code that employs randomization to avoid undesired correlations between parameters, and to produce a model cell or network that has the same architecture and biophysical properties, and generates the same simulation results regardless of whether it is run on serial or parallel hardware.
167 +How to generate spike streams or other signals that fluctuate in ways that are statistically independent of each other.
168 +=== [[Using the CellBuilder– Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
153 153  
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"]] ===
170 +**Level**: advanced(%%) **Type**: interactive tutorial
155 155  
156 -//Level: advanced//
172 +How to make one or more biophysical properties vary systematically with position in space.
173 +=== [[Using Import3D – An introduction>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
157 157  
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"]] ===
175 +**Level**: advanced(%%) **Type**: user documentation
159 159  
160 -//Level: advanced//
177 +Import3D tool can be used to translate common varieties of cellular morphometric data into a CellBuilder that specifies the anatomical properties of a model neuron. This Tutorial will guide you in reading a morphometric data file and converting it to a NEURON model as well as
178 +exploring morphometric data and fixing problems.
179 +=== [[Segmenting a simulation of a model network – 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"]] ===
161 161  
162 -=== [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] ===
181 +**Level**: advanced(%%) **Type**: user documentation
163 163  
164 -//Level: advanced//
183 +=== [[Segmenting a simulation of a model network – 2. Run a "complete" simulation and save its results>>https://neuron.yale.edu/neuron/docs/2-run-complete-simulation-and-save-its-results-0||rel=" noopener noreferrer" target="_blank"]] ===
165 165  
166 -=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
185 +**Level**: advanced(%%) **Type**: user documentation
167 167  
168 -//Level: advanced//
187 +=== [[Segmenting a simulation of a model cell – 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"]] ===
169 169  
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"]] ===
189 +**Level**: advanced(%%) **Type**: user documentation
176 176  
177 -//Level: advanced//
191 +=== [[Segmenting a simulation of a model cell – 1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself||rel=" noopener noreferrer" target="_blank"]] ===
178 178  
179 -=== [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] ===
193 +**Level**: advanced(%%) **Type**: user documentation
180 180  
181 -//Level: advanced//
195 +=== [[Using NEURON's Optimization Tools – Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
182 182  
183 -=== [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] ===
197 +**Level**: advanced(%%) **Type**: user documentation
184 184  
185 -//Level: advanced//
199 +We will go over how to create an "unoptimized" model, set up a current clamp experiment on this model, configure a MultipleRunFitter to do a "run fitness" optimization, load the Experimental Data into the iclamp Run Fitness Generator, specify the parameters that will be adjusted and finally perform the optimization.
200 +=== [[Reaction-Diffusion – Hodgkin-Huxley using rxd>>https://neuron.yale.edu/neuron/docs/hodgkin-huxley-using-rxd||rel=" noopener noreferrer" target="_blank"]] ===
186 186  
187 -=== [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
202 +**Level**: advanced(%%) **Type**: interactive tutorial
188 188  
189 -//Level: advanced//
204 +In this tutorial you will learn how to set the proper parameters for the Hodgkin–Huxley model in NEURON.
205 +=== [[Using the CellBuilder – Creating a stylised ("stick-figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
190 190  
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"]] ===
207 +**Level**: advanced(%%) **Type**: -
193 193  
194 -//Level: advanced//
209 +Learn how to build an extremely simplified model of a pyramidal cell.
210 +=== [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] ===
195 195  
196 -=== [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
212 +**Level**: advanced(%%) **Type**: user documentation
197 197  
198 -//Level: advanced//
214 +=== [[Reaction-Diffusion Example – Circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
199 199  
200 -=== [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
216 +**Level**: advanced(%%) **Type**: user documentation
201 201  
202 -//Level: advanced//
218 +Here we develop a NEURON implementation of the Leloup-Goldbeter model for circadian rhythms in Drosophila. In this example NEURON's h library and its standard run system are being used as well as matplotlib to plot concentrations of circadian proteins over time.
219 +=== [[Segmenting a simulation of a model cell – 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"]] ===
203 203  
204 -=== [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
221 +**Level**: advanced(%%) **Type**: user documentation
205 205  
206 -//Level: advanced//
223 +=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
207 207  
208 -=== [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
225 +**Level**: advanced(%%) **Type**: user documentation
209 209  
210 -//Level: advanced//
227 +This example demonstrates how ModelView can explore a NEURON model.
228 +=== [[Segmenting a simulation of a model network – 3. Run a segmented simulation and save its results>>https://neuron.yale.edu/neuron/docs/3-run-segmented-simulation-and-save-its-results-0||rel=" noopener noreferrer" target="_blank"]] ===
211 211  
212 -=== [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
230 +**Level**: advanced(%%) **Type**: user documentation
213 213  
214 -//Level: advanced//
232 +=== [[Segmenting a simulation of a model network – 4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results-0||rel=" noopener noreferrer" target="_blank"]] ===
215 215  
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"]] ===
234 +**Level**: advanced(%%) **Type**: user documentation
219 219  
220 -//Level: advanced//
221 221  
222 -