Changes for page Neuron

Last modified by abonard on 2025/04/10 15:17

From version 92.1
edited by abonard
on 2025/04/10 15:16
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To version 104.1
edited by abonard
on 2025/04/10 15:16
Change comment: There is no comment for this version

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148 148  
149 149  **Level**: advanced(%%) **Type**: user documentation
150 150  
151 +=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
151 151  
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 +=== [[Using Import3D – An introduction>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
174 +
175 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
180 +
181 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
184 +
185 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
188 +
189 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
192 +
193 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
196 +
197 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
201 +
202 +**Level**: advanced(%%) **Type**: interactive tutorial
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"]] ===
206 +
207 +**Level**: advanced(%%) **Type**: -
208 +
209 +Learn how to build an extremely simplified model of a pyramidal cell.
210 +