| ... | ... | @@ -78,4 +78,96 @@ | 
              
                    | 78 | 78 |  | 
              
                    | 79 | 79 | **Level**: advanced(%%)  **Type**: user documentation | 
              
                    | 80 | 80 |  | 
              
                    |  | 81 | +=== [[Using the CellBuilder – Introduction>>https://neuron.yale.edu/neuron/static/docs/cbtut/main.html||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    | 81 | 81 |  | 
              
                    |  | 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 | +=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    |  | 152 | + | 
              
                    |  | 153 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 157 | + | 
              
                    |  | 158 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 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. | 
              
                    |  | 161 | +=== [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] === | 
              
                    |  | 162 | + | 
              
                    |  | 163 | +**Level**: advanced(%%)  **Type**: user documentation | 
              
                    |  | 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"]] === | 
              
                    |  | 169 | + | 
              
                    |  | 170 | +**Level**: advanced(%%)  **Type**: interactive tutorial | 
              
                    |  | 171 | + | 
              
                    |  | 172 | +How to make one or more biophysical properties vary systematically with position in space. | 
              
                    |  | 173 | + |