The NeuronLab Simulator

The NeuronLab simulator only runs under Windows and runs best with a large monitor (or, better yet, two). This gives the user 'elbow' room to build the neuron and explore its operations.

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The NeuronLab 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 drop neuron components on your computer screen, connect them and see them in action.

The simulator allows you to construct an operating Neuron. Wire up the components by left-clicking near either end of the body part. As you add parts to the body plan, Its name will appear in the connection list to the left. This list is for reference only and should take care of itself.

The simulator is for Windows only 64 bit systems. The simulator is under constant revision so check in often.

This verion comes with a fully functional Izhikevich neuron as described in his book on page 293 Figure 8.22

 

To Download the NeuronLab simulator Click on the latest version below.
Full Izhikevich neuron supplied with download.
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Setup_NeuronLab_Simulator_64bit_Ver_2.4.0.2758.exe

After installation, the simulator will automatically start and may be used directly. You can find the simulator from the Windows START menu under NeuronLab [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:

Important: Before you start using a Soma you much chose a from a family of neurons. From the top menu chose Setup | Neuron Select and click on one of the neuron types [RS] is a good choice.

The body components available from the right side of the main screen are:

Step Functions - Generate a voltage spike to start the operation
Synapse Compartments - Sections of dendrite with some additional logic for some of the simulation tasks.
Dendrite Compartments - Compartments of dendrite that can be joined together to form a dendrite tree
Soma - Quadratic Integrate and fire based on the Izhikevich neurons
Axon Compartments - String compartments 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 if you wish. On restart the components will be remembered and restored.

Body parts in a family (Synapse, Soma, Dendrites) are all the same. The numbers are just for reference.

Connect components by Left Click on the edge of the body part and Left Click on the edge of a second body part. A wire line should appear between them.

More details next

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. The simulator will bitch at you if you try to connect components that are not logical or have no biological equivalent. For example:

• You cannot connect anything to the input of a Step or the Output side of a Scope
• You cannot connect the output of a Soma to a Dendrite. That doesn't happen in nature.
  

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.

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.

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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.

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.

Next: The Dendrite