is the main window of this software. It consists of

1) A text box that displays the name of currently-used model file, which is "Ex_03_simple_axon" in this example.

2) Menus that allows users to operate the simulation. The functions of menus are described below.

In order to run the simulation, user must specify first which model file will be used. Within the File menu, there is a submenu Open model. Use this submenu to open a model file you want to use for the simulation.

Within the Setting menu, there are six submenus. 

1) Time: set the value of time step and time length for simulation.

2) Environment: set the value of Temperature and extra- cellular resistivity. 

3) Parameters: access to the parameters of any vaiable. 

4) Channel: access to the membrane kinetic parameters if you have one in your model.

5)& 6) Intracellular Stim and Extracellular Stim bring up a graphic user interface for adjusting parameters of intracellular and extracellular stimulator respectively. These parameters are first assigned within a model file. If the model file does not contain any stimulator parameter, these menus will not work. For more information, please refer to the how to create model file section.   

No need to explain what they are.

is created from  Neurocal -> Setting -> Time menu for adjusting the simulation parameters.

Time(ms) : The length of simulation

Time step : There are three options for time step size.

     1)-Fixed step (1-20)(us):  Users define the step size on the edit box.

     2)-Variable (Coarse) : The step size is automatically calculated with Coarse accuracy

     3)-Variable (Fine) : The step size is automatically calculated with Fine accuracy

is created from  Neurocal -> Setting -> Environment menu for adjusting the simulation parameters.

1) R extra-cel (Ohm-Cm) : The extracellular resistivity in the model. It is used only when the extracellular stimulator is assigned in the model file. It has no effect on the model that has only intracellular stimulator.

2)  Temperature : The temperature in the system

Allow uses to change the parameters of variables in the model file. Please read it carefully.

·         The length of variable (L) can be either "a constance number" or "a function of the diameter". The latter is useful for modeling the myelinated axon.

·         The Rm (membrane resistance) is normally a number. However, if the variable has any active channel, Rm will be replaced by 1/G_Lk (leakage current).

·         If there is any extracellular stimulator in the model, all segments need to have a "coordinate" so that the extracellular voltage can be calculated accordingly. The coordinates can be automatically assigned by vectors [XYZi] and [XYZc]. [XYZi] represents the vector of the variable (axon) and the [XYZc] is the coordinate of its center node. In this example, the axon is on the X axis with the center node on the origin. After a simulation is performed, you can check the coordinate at "axon.xyz".

·         If there is NO extracellular stimulator in the model, [XYZi] or [XYZc] won't be used.

Please refer to How to create a variable section to see what each parameter means.

Allow uses to change the parameters of membrane kinetics of any Variable.

is created from Neurocal -> Setting -> Intracellular Stim  menu for adjusting parameters of intracellular stimulator(s) first assigned within a model file. Each intracellular stimulator has 5 parameters that can be adjusted ;Variable, Position, Amplitude, Duration, and Delay. The position is a value between 0 and 1, which represent two ends of a variable. For a variable that has only 1 segment. This value has no effect. For more information, please refer to the How to create a model file section.  In this example, there are 3 intracellular stimulators in the model.

is created from Neurocal -> Setting -> Extra cellular Stim menu for adjusting parameters of extracellular stimulator(s) first assigned within a model file.

Each extracellular stimulator has 6 parameters that can be adjusted ;X, Y, Z, Amplitude, Duration, and Delay.  In this example, there is one extracellular stimulators in the model. Multiple extracellular stimulators can be implemented.

is created from Neurocal -> Graph -> 2DViewer menu for displaying simulation result in 2 dimension mode. Clicking the Plot menu brings up a plot control window (2D-Viewer:Plot).

The display properties of the result can be changed by clicking    on the toolbar and then selecting any plot you want to make changes. You can delete or change the plot style of the result. For more information, please refer to Matlab user guide..

is created from 2D-Time -> Plot menu. This window allows users to select what to plot on the 2D-Time window. The first (left) column is the list of variables in the model. The second (middle) column is the list of segments associated with the variable in the first column. The third (right) column is the list of parameters associated with the variable in the first column.. There are 4 buttons.

Color : specify a color for the next plot.

Replace :    erase old plots and plot  new values.

Add :    keep old plots and add new values. 

Close : close the window

The time to be plotted can be chosen either by the slide bar or the edit box.

is created from Neurocal -> Graph -> 3DViewer menu for displaying simulation result in 3 dimension mode. There are 3 menus on this window.

Plot          : Brings up a plot control window (3D-Viewer:Plot).

Duplicate : Plot the current result on a new window.

Export      : Save the current result into a text file in ASCII format with tab delimiter. In the output file, the first column is Time and the rest are the current plot.

is created from 3D-Viewer-Plot. This window allows users to select what to plot on the 3D-Viewer window. The first (left) column is the list of variables in the model. The second (right) column is the list of parameters associated with the variable in the first column.. There are 2 buttons.

Replace:    plot the variable and parameter selected.

Close    :    close the window.

%Ex_01_Simple_soma

1:create('soma');                            %create a variable named soma with default parameters.

2:global soma                                %required for all variable created

3:insert(soma,'hh')                         %insert HH channel into SOMA    [variable model]      

4:Iinstim(soma,0.5,0.1,100,100)    %intracellular stimulation   

                                                       % [variable positon(0-1) amp(uA) pulsewidth(us)  delay(us)]

%Ex_03_Simple_axon_active

1:create('axon');                                  %create a variable named axon with default parameters.

2:global axon                                      %required for all variable created

3:axon.nseg=55;                                 % change the number of segments

4:axon.L=10*axon.dia*axon.nseg;   % um    change the length of axon

5:insert(axon,'hh')                               %insert HH channel into AXON    [variable model] 

6:Iinstim(axon,0.5,0.1,100,0)             %intracellular stimulation     [variable positon(0-1) amp(uA) pw(us)  delay(us)]

%Ex_08_Simple_Neuron

1:create('axon');

2:create('soma');

3:create('dendrite',3)                         %create dendrite(1),dendrite(2),dendrite(3)

4:global axon soma dendrite

5:axon.L=2500;

6:axon.nseg=20;

7:dendrite{1}.L=2000;

8:dendrite{1}.nseg=20;

9:dendrite{2}.L=4000;

10:dendrite{2}.nseg=20;

11:dendrite{3}.L=2000;

12:dendrite{3}.nseg=20;

13:connect(soma,0,dendrite{1},0); %[main, position(0-1), branch, position (0 OR 1)]

14:connect(soma,0,dendrite{2},0); %the branch position is either 0 or 1

15:connect(soma,0,dendrite{3},0); %the branch position is either 0 or 1

16:connect(axon,0,soma,0);        %the branch position is either 0 or 1

17:insert(axon,'hh')

18:Iinstim(soma,1,0.5,200,0) %[variable positon(0-1) amp(uA) pw(us)  delay(us)]