The Neuron SimulatorThe Neuron simulator only runs under Windows and runs best with a large monitor (or better yet two) that give the user 'elbow' room to build the neuron and to explore its operations.
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The SETI Net Neuron Simulator was developed specifically to learn by doing. It allows you to create a custom neuron to your specifications with as little effort as possible. With it you can drag and place neuron components on your computer screen, connect them and see them in action..
Download and install instructions
The simulator was designed to be as straight forward as possible. It is for Windows only and will work on either Windows 32 or Windows 64 bit systems.
(1) Windows Start select Settings then Update & Security
(2) Select Windows Security
(3) Select App & browser control
(4) Turn off SmartScreen for Microsoft Edge
Download this EXE file and then click on it to open. SelectSetup_Neuron_Simulator.exe to install.
After installation the simulator will automatically start and may be used directly. You can find the simulator from the Windows START menu under SETI Net
[Hint: using all the default setting works best.]
The simulator Body Plan work area will look something like this after download and installation
There will also be an Oscilloscope that will look like this:
The body components available from the right side of the main screen are:
|Step Functions - Generate a voltage spike to start the operation|
|Dendrite Compartments - Sections of dendrite that can be joined together|
|Soma - Quadratic Integrate and fire|
|Axon Compartments - String together for the complete axon.|
|Scope Probes - Allows you to connect at various points and view the results|
Feel free to drag and drop body components onto the blue working area. You may move the Body and 'Scope to different parts of your monitor or onto a second monitor it you wish.
Connect components by Left Click on edge of the component and the Left Click on the edge of a second component. A wire line should appear between them.
More details next.
Using the Simulator - first time
Move Components - Drag and drop a Step and a Scope probe as in this picture. Any step and any scope they are all the same.
Wiring Components - LEFT click near the edge of the two components to connect them as shown. Notice that there names appear in the Connection List.
Wire your components from left to right just as you would expect the signal flow to go.
This is important for proper operation of the simulator
Saving the Plan - You can save this setup from the top menu on the Body Plan (Body Plan | Save Plan). it will be save on your machine under file name you chose. You can reload it anytime from Body Plan | Load Plan. If you get tangled up you can reset the whole thing from
Body Plan | Reset. This will give you a clean start.
Wiring Refresh - From time to time the connecting lines on the body components may get out of place. When this happens hit the Refresh Connections button. The lines are for reference only and the simulator will work through ugly.
Scope Range - You should see the step function on the scope. Slide the two thumbs left and right until you get the portion of the trace you are interested in.
Connect List - This table shows the current set of connections. You should be able to ignore this for the most part.
Setting Step and Scope Parameters
Right click on the Step and then right click on the 'Scope probe. You should get something like this:
Scope Params - Click the Up/Down and notice that the Scope trace moves along with the Blue scale Next to it. This allows each of the probes to live on the scope with minimal confusion.
Unset the Output Enable and notice that the 'Scope shuts off and the 'Scope probe changes to a neutral color to remind you that it is off. Dismiss the Params box by clicking on the body of the Scope probe or the "X" of the parameter display.
Press the Dock button The Scope returns to the right side and the trace shuts off.
Step Params - Right click the Step. The top spinner sets the amplitude above VRest which is normally -60 mVolts. The next two set the start time and the width of the pulse.
The slider will move the entire pulse where you want it on the Oscilloscope.
You will want to make time and amplitude measurements on the Oscilloscope using the markers.
Open up the 'Scope and adjust the thumbs to get a display something like this:
Click the Marker Select color to match your 'Scope probe.
Left click somewhere on the trace and right click some where else. The X is the time in mSec the Y is the voltage in mVolts When you hit the Up/Down on the 'Scope probe parameters box and the markers will move with the trace;There is more to the Simulator but this will be explained as we come to it.