Wiki source code of Neuron
Version 2.1 by jessicamitchell on 2023/09/11 11:44
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| author | version | line-number | content |
|---|---|---|---|
| 1 | Available tutorials: | ||
| 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 | |||
| 5 | //Level: beginner// | ||
| 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"]] === | ||
| 9 | |||
| 10 | //Level: beginner// | ||
| 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"]] === | ||
| 13 | |||
| 14 | //Level: advanced// | ||
| 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"]] === | ||
| 17 | |||
| 18 | //Level: advanced// | ||
| 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"]] === | ||
| 21 | |||
| 22 | //Level: advanced// | ||
| 23 | |||
| 24 | === [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] === | ||
| 25 | |||
| 26 | //Level: advanced// | ||
| 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"]] === | ||
| 29 | |||
| 30 | //Level: advanced// | ||
| 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 | |||
| 34 | //Level: advanced// | ||
| 35 | |||
| 36 | === [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 37 | |||
| 38 | //Level: advanced// | ||
| 39 | |||
| 40 | === [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 41 | |||
| 42 | //Level: advanced// | ||
| 43 | |||
| 44 | === [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 45 | |||
| 46 | //Level: advanced// | ||
| 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"]] === | ||
| 49 | |||
| 50 | //Level: advanced// | ||
| 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"]] === | ||
| 53 | |||
| 54 | //Level: advanced// | ||
| 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"]] === | ||
| 57 | |||
| 58 | //Level: advanced// | ||
| 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"]] === | ||
| 61 | |||
| 62 | //Level: advanced// | ||
| 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"]] === | ||
| 65 | |||
| 66 | //Level: advanced// | ||
| 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"]] === | ||
| 70 | |||
| 71 | //Level: advanced// | ||
| 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"]] === | ||
| 75 | |||
| 76 | //Level: advanced// | ||
| 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"]] === | ||
| 80 | |||
| 81 | //Level: advanced// | ||
| 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"]] === | ||
| 85 | |||
| 86 | //Level: advanced// | ||
| 87 | |||
| 88 | === [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] === | ||
| 89 | |||
| 90 | //Level: advanced// | ||
| 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"]] === | ||
| 93 | |||
| 94 | //Level: advanced// | ||
| 95 | |||
| 96 | === [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] === | ||
| 97 | |||
| 98 | //Level: advanced// | ||
| 99 | |||
| 100 | === [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] === | ||
| 101 | |||
| 102 | //Level: advanced// | ||
| 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"]] === | ||
| 105 | |||
| 106 | //Level: advanced// | ||
| 107 | |||
| 108 | === [[Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 109 | |||
| 110 | //Level: advanced// | ||
| 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"]] === | ||
| 113 | |||
| 114 | //Level: advanced// | ||
| 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"]] === | ||
| 118 | |||
| 119 | //Level: advanced// | ||
| 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"]] === | ||
| 122 | |||
| 123 | //Level: advanced// | ||
| 124 | |||
| 125 | === [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] === | ||
| 126 | |||
| 127 | //Level: advanced// | ||
| 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"]] === | ||
| 139 | |||
| 140 | //Level: advanced// | ||
| 141 | |||
| 142 | === [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] === | ||
| 143 | |||
| 144 | //Level: advanced// | ||
| 145 | |||
| 146 | === [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] === | ||
| 147 | |||
| 148 | //Level: advanced// | ||
| 149 | |||
| 150 | === [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] === | ||
| 151 | |||
| 152 | //Level: advanced// | ||
| 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"]] === | ||
| 155 | |||
| 156 | //Level: advanced// | ||
| 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"]] === | ||
| 159 | |||
| 160 | //Level: advanced// | ||
| 161 | |||
| 162 | === [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] === | ||
| 163 | |||
| 164 | //Level: advanced// | ||
| 165 | |||
| 166 | === [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] === | ||
| 167 | |||
| 168 | //Level: advanced// | ||
| 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"]] === | ||
| 176 | |||
| 177 | //Level: advanced// | ||
| 178 | |||
| 179 | === [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] === | ||
| 180 | |||
| 181 | //Level: advanced// | ||
| 182 | |||
| 183 | === [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] === | ||
| 184 | |||
| 185 | //Level: advanced// | ||
| 186 | |||
| 187 | === [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 188 | |||
| 189 | //Level: advanced// | ||
| 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"]] === | ||
| 193 | |||
| 194 | //Level: advanced// | ||
| 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"]] === | ||
| 197 | |||
| 198 | //Level: advanced// | ||
| 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"]] === | ||
| 201 | |||
| 202 | //Level: advanced// | ||
| 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"]] === | ||
| 205 | |||
| 206 | //Level: advanced// | ||
| 207 | |||
| 208 | === [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] === | ||
| 209 | |||
| 210 | //Level: advanced// | ||
| 211 | |||
| 212 | === [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] === | ||
| 213 | |||
| 214 | //Level: advanced// | ||
| 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"]] === | ||
| 219 | |||
| 220 | //Level: advanced// |