Changes for page Neuron

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edited by abonard
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165 165  We will touch upon the following subjects in this tutorial:
166 166  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.
167 167  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"]] ===
168 168  
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 +=== [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] ===
211 +
212 +**Level**: advanced(%%) **Type**: user documentation
213 +
214 +=== [[Reaction-Diffusion Example – Circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
215 +
216 +**Level**: advanced(%%) **Type**: user documentation
217 +
218 +Here we develop a NEURON implementation of the Leloup-Goldbeter model for circadian rhythms in Drosophila. In this example NEURON's h library and its standard run system are being used as well as matplotlib to plot concentrations of circadian proteins over time.
219 +