| ... | 
        ... | 
                @@ -120,4 +120,76 @@ | 
      
              
                    | 120 | 
          120 | 
            | 
        
              
                    | 121 | 
          121 | 
           **Level**: advanced(%%)  **Type**: user documentation | 
        
              
                    | 122 | 
          122 | 
            | 
        
              
                     | 
          123 | 
          +=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] === | 
        
              
                    | 123 | 
          123 | 
            | 
        
              
                     | 
          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 | 
          +=== [[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 | 
          + |