| ... | ... | @@ -64,4 +64,88 @@ | 
              
                    | 64 | 64 | **Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    | 65 | 65 |  | 
              
                    | 66 | 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"]] === | 
              
                    | 67 | 67 |  | 
              
                    |  | 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 | +=== [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    |  | 78 | + | 
              
                    |  | 79 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 80 | + | 
              
                    |  | 81 | +=== [[Using the CellBuilder – Introduction>>https://neuron.yale.edu/neuron/static/docs/cbtut/main.html||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    |  | 82 | + | 
              
                    |  | 83 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 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"]] === | 
              
                    |  | 91 | + | 
              
                    |  | 92 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 96 | + | 
              
                    |  | 97 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 101 | + | 
              
                    |  | 102 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 106 | + | 
              
                    |  | 107 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 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"]] === | 
              
                    |  | 111 | + | 
              
                    |  | 112 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 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"]] === | 
              
                    |  | 116 | + | 
              
                    |  | 117 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 120 | + | 
              
                    |  | 121 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 122 | + | 
              
                    |  | 123 | +=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    |  | 124 | + | 
              
                    |  | 125 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 129 | + | 
              
                    |  | 130 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 134 | + | 
              
                    |  | 135 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 138 | + | 
              
                    |  | 139 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 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"]] === | 
              
                    |  | 143 | + | 
              
                    |  | 144 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 148 | + | 
              
                    |  | 149 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 150 | + | 
              
                    |  | 151 | + |