Changes for page Neuron

Last modified by abonard on 2025/04/10 15:17
From version 51.1
edited by abonard
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To version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
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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 -* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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  
7 -=== **Beginner** ===
10 +//Level: beginner//
8 8  
9 -=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
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"]] ===
10 10  
11 -**Level**: beginner(%%) **Type**: user documentation
14 +//Level: advanced//
12 12  
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"]] ===
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"]] ===
15 15  
16 -**Level**: beginner(%%) **Type**: user documentation
18 +//Level: advanced//
17 17  
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"]] ===
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"]] ===
20 20  
21 -**Level**: beginner(%%) **Type**: user documentation
22 +//Level: advanced//
22 22  
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"]] ===
24 +=== [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] ===
25 25  
26 -**Level**: beginner(%%) **Type**: user documentation
26 +//Level: advanced//
27 27  
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"]] ===
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"]] ===
30 30  
31 -**Level**: beginner(%%) **Type**: user documentation
30 +//Level: advanced//
32 32  
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"]] ===
32 +=== [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] ===
35 35  
36 -**Level**: beginner(%%) **Type**: user documentation
34 +//Level: advanced//
37 37  
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"]] ===
36 +=== [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] ===
41 41  
42 -**Level**: beginner(%%) **Type**: interactive tutorial
38 +//Level: advanced//
43 43  
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"]] ===
40 +=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
46 46  
47 -**Level**: beginner(%%) **Type**: slide deck
42 +//Level: advanced//
48 48  
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 50  === [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
51 51  
52 -**Level**: beginner(%%) **Type**: user documentation
46 +//Level: advanced//
53 53  
54 -After this tutorial, students will be able to save data from the simulations and methods for increasing simulation speed.
55 -=== **Advanced** ===
48 +=== [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel=" noopener noreferrer" target="_blank"]] ===
56 56  
57 -=== [[Reaction-Diffusion – Radial Diffusion>>https://neuron.yale.edu/neuron/docs/radial-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
50 +//Level: advanced//
58 58  
59 -**Level**: advanced(%%) **Type**: -
52 +=== [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] ===
60 60  
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"]] ===
54 +//Level: advanced//
63 63  
64 -**Level**: advanced(%%) **Type**: interactive tutorial
65 -
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"]] ===
68 -
69 -**Level**: advanced(%%) **Type**: interactive tutorial
70 -
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"]] ===
73 -
74 -**Level**: advanced(%%) **Type**: interactive tutorial
75 -
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 77  === [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" noopener noreferrer" target="_blank"]] ===
78 78  
79 -**Level**: advanced(%%) **Type**: user documentation
58 +//Level: advanced//
80 80  
81 -=== [[Using the CellBuilder – Introduction>>https://neuron.yale.edu/neuron/static/docs/cbtut/main.html||rel=" noopener noreferrer" target="_blank"]] ===
60 +=== [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" noopener noreferrer" target="_blank"]] ===
82 82  
83 -**Level**: advanced(%%) **Type**: interactive tutorial
62 +//Level: advanced//
84 84  
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"]] ===
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"]] ===
91 91  
92 -**Level**: advanced(%%) **Type**: user documentation
66 +//Level: advanced//
93 93  
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"]] ===
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"]] ===
96 96  
97 -**Level**: advanced(%%) **Type**: user documentation
71 +//Level: advanced//
98 98  
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"]] ===
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"]] ===
101 101  
102 -**Level**: advanced(%%) **Type**: user documentation
76 +//Level: advanced//
103 103  
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"]] ===
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"]] ===
106 106  
107 -**Level**: advanced(%%) **Type**: interactive tutorial
81 +//Level: advanced//
108 108  
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"]] ===
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"]] ===
111 111  
112 -**Level**: advanced(%%) **Type**: interactive tutorial
86 +//Level: advanced//
113 113  
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"]] ===
88 +=== [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
116 116  
117 -**Level**: advanced(%%) **Type**: user documentation
90 +//Level: advanced//
118 118  
119 -=== [[Using the Network Builder – Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
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"]] ===
120 120  
121 -**Level**: advanced(%%) **Type**: user documentation
94 +//Level: advanced//
122 122  
123 -=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
96 +=== [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] ===
124 124  
125 -**Level**: advanced(%%) **Type**: user documentation
98 +//Level: advanced//
126 126  
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"]] ===
100 +=== [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
129 129  
130 -**Level**: advanced(%%) **Type**: user documentation
102 +//Level: advanced//
131 131  
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"]] ===
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"]] ===
134 134  
135 -**Level**: advanced(%%) **Type**: user documentation
106 +//Level: advanced//
136 136  
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"]] ===
108 +=== [[Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
138 138  
139 -**Level**: advanced(%%) **Type**: interactive tutorial
110 +//Level: advanced//
140 140  
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"]] ===
112 +=== [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
143 143  
144 -**Level**: advanced(%%) **Type**: user documentation
114 +//Level: advanced//
145 145  
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"]] ===
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"]] ===
148 148  
149 -**Level**: advanced(%%) **Type**: user documentation
119 +//Level: advanced//
150 150  
151 -=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
121 +=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
152 152  
153 -**Level**: advanced(%%) **Type**: user documentation
123 +//Level: advanced//
154 154  
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"]] ===
125 +=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
157 157  
158 -**Level**: advanced(%%) **Type**: interactive tutorial
127 +//Level: advanced//
159 159  
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.
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.
161 161  === [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] ===
162 162  
163 -**Level**: advanced(%%) **Type**: user documentation
140 +//Level: advanced//
164 164  
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"]] ===
142 +=== [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
169 169  
170 -**Level**: advanced(%%) **Type**: interactive tutorial
144 +//Level: advanced//
171 171  
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"]] ===
146 +=== [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] ===
174 174  
175 -**Level**: advanced(%%) **Type**: user documentation
148 +//Level: advanced//
176 176  
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"]] ===
150 +=== [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] ===
180 180  
181 -**Level**: advanced(%%) **Type**: user documentation
152 +//Level: advanced//
182 182  
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"]] ===
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"]] ===
184 184  
185 -**Level**: advanced(%%) **Type**: user documentation
156 +//Level: advanced//
186 186  
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"]] ===
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"]] ===
188 188  
189 -**Level**: advanced(%%) **Type**: user documentation
160 +//Level: advanced//
190 190  
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"]] ===
162 +=== [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] ===
192 192  
193 -**Level**: advanced(%%) **Type**: user documentation
164 +//Level: advanced//
194 194  
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"]] ===
166 +=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
196 196  
197 -**Level**: advanced(%%) **Type**: user documentation
168 +//Level: advanced//
198 198  
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"]] ===
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"]] ===
201 201  
202 -**Level**: advanced(%%) **Type**: interactive tutorial
177 +//Level: advanced//
203 203  
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"]] ===
179 +=== [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] ===
206 206  
207 -**Level**: advanced(%%) **Type**: -
181 +//Level: advanced//
208 208  
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"]] ===
183 +=== [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] ===
211 211  
212 -**Level**: advanced(%%) **Type**: user documentation
185 +//Level: advanced//
213 213  
214 -=== [[Reaction-Diffusion Example – Circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
187 +=== [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
215 215  
216 -**Level**: advanced(%%) **Type**: user documentation
189 +//Level: advanced//
217 217  
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"]] ===
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"]] ===
220 220  
221 -**Level**: advanced(%%) **Type**: user documentation
194 +//Level: advanced//
222 222  
223 -=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
196 +=== [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
224 224  
225 -**Level**: advanced(%%) **Type**: user documentation
198 +//Level: advanced//
226 226  
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"]] ===
200 +=== [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
229 229  
230 -**Level**: advanced(%%) **Type**: user documentation
202 +//Level: advanced//
231 231  
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"]] ===
204 +=== [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
233 233  
234 -**Level**: advanced(%%) **Type**: user documentation
206 +//Level: advanced//
235 235  
236 -=== [[Using NEURON's Optimization Tools – Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
208 +=== [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
237 237  
238 -**Level**: advanced(%%) **Type**: user documentation
210 +//Level: advanced//
239 239  
240 -We will look into how to bring up a Multiple Run Fitter, load the Experimental Data into the Multiple Run Fitter, specify the function we want to optimize, specify the parameters that will be adjusted, specify the criteria we want the function to satisfy and finally perform the optimization.
241 -=== [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" noopener noreferrer" target="_blank"]] ===
212 +=== [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
242 242  
243 -**Level**: advanced(%%) **Type**: user documentation
214 +//Level: advanced//
244 244  
245 -=== [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
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"]] ===
246 246  
247 -**Level**: advanced(%%) **Type**: interactive tutorial
220 +//Level: advanced//
248 248  
249 -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?
250 250