Wiki source code of Neuron

Version 88.1 by abonard on 2025/04/10 15:16
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3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
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5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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7 === **Beginner** ===
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9 === [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
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11 **Level**: beginner(%%) **Type**: user documentation
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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"]] ===
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16 **Level**: beginner(%%) **Type**: user documentation
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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"]] ===
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21 **Level**: beginner(%%) **Type**: user documentation
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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
26 **Level**: beginner(%%) **Type**: user documentation
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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"]] ===
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31 **Level**: beginner(%%) **Type**: user documentation
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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"]] ===
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36 **Level**: beginner(%%) **Type**: user documentation
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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"]] ===
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42 **Level**: beginner(%%) **Type**: interactive tutorial
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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"]] ===
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47 **Level**: beginner(%%) **Type**: slide deck
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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"]] ===
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52 **Level**: beginner(%%) **Type**: user documentation
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54 After this tutorial, students will be able to save data from the simulations and methods for increasing simulation speed.
55 === **Advanced** ===
56
57 === [[Reaction-Diffusion – Radial Diffusion>>https://neuron.yale.edu/neuron/docs/radial-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
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59 **Level**: advanced(%%) **Type**: -
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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"]] ===
63
64 **Level**: advanced(%%) **Type**: interactive tutorial
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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"]] ===
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69 **Level**: advanced(%%) **Type**: interactive tutorial
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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
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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"]] ===
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79 **Level**: advanced(%%) **Type**: user documentation
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81 === [[Using the CellBuilder – Introduction>>https://neuron.yale.edu/neuron/static/docs/cbtut/main.html||rel=" noopener noreferrer" target="_blank"]] ===
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83 **Level**: advanced(%%) **Type**: interactive tutorial
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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"]] ===
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92 **Level**: advanced(%%) **Type**: user documentation
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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"]] ===
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97 **Level**: advanced(%%) **Type**: user documentation
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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"]] ===
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102 **Level**: advanced(%%) **Type**: user documentation
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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"]] ===
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107 **Level**: advanced(%%) **Type**: interactive tutorial
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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"]] ===
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112 **Level**: advanced(%%) **Type**: interactive tutorial
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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"]] ===
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117 **Level**: advanced(%%) **Type**: user documentation
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119 === [[Using the Network Builder – Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
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121 **Level**: advanced(%%) **Type**: user documentation
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123 === [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
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125 **Level**: advanced(%%) **Type**: user documentation
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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"]] ===
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130 **Level**: advanced(%%) **Type**: user documentation
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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).