Virtual Neurophysiology Workbench

The DIY Brain Lab! Developed to improve the accessibility of neuroscience education.

For these experiments, you'll need  the following items (for links to order many of these items, visit our "Useful Links and Other Resources" page):

To build your brain:*

  • One package of agar or gelatin
  • Water
  • A stove or electric kettle
  • A 1-2 quart container
  • Refrigerator

To simulate the neural signals and apply them to the brain:**

  • A computer with working headphone jack*
  • NEURON software
  • Matlab
  • One pair of earbud headphones with the earbuds cut off*

To record the signals from the surface of the brain:*

  • Backyard Brains Heart and Brains recording system
  • Backyard Brains Spike Recorder software or smart phone application
  • A computer or smartphone (this can be the same computer as is used for the simulations)


*If you are unable to purchase the Backyard Brains Heart and Brains recording system, you can still complete all of the simulations and play the audio files of your neural signals through any speaker or headphone set up you may have.  If you are doing this, you do not need to build a brain or cut any headphones.

**Even if you do buy the recording system, it may be fun to listen to the various neural signals you create!  Many neurosurgeons will record from the brain and listen to the neural signals to decipher where they are within the brain.  So try it out with a friend!  Make it a game!  See if you can tell the difference between the neurons you create and download only by what they sound like! Why do they sound different?  What changes did you make in the cell to change the signaling pattern? Why did that change the cell's behavior?  Post your findings, ideas, and questions here and discuss it with other virtual neurophysiologists!

Once you are familiar with simulating and recording neurons from your agar brain model, this experiment will show you how to download, manipulate, and record scientifically validated neuron models. With this experiment the possibilities are endless. Estimated time: 1-3 hours.

Now that you have had fun creating neurons and learning about their different components, it might be helpful to look at how real neural signals might look. ModelDB is a website with hundreds of realistic NEURON models.  Here we will show you an example of a pyramidal cell adapted from Kole, 2008, shown below [4]. For detailed instructions on downloading and running NEURON models on your operating system, please visit this page: https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.html

 layerV pyramidalThis model allows manipulation of the Na ion channel density on either the dendrite and soma or the axon.  Changing the Na channel density changes the conductance of the cell membrane in that segment.  Changing the conductance changes the ratio between the change in cell membrane's electrical potential and the amount of current flowing through the membrane.  This is dictated by Ohm's law:  
     ΔV = IG
Where ΔV is the change in membrane potential, I is the current flowing through the membrane, and G is the conductance of the membrane.  
 
You can play with this model and discover the different action potential and recording patterns you can create by changing the conductance at the axon and/or at the soma and dendrite.  The soma and dendrite are treated as the same segment in this model.  Below are three examples of different action potential patterns with their associated recordings and ion channel currents using this model. VNW recording example Parts a-c are action potentials propagated through the simulated neuron over 12 milliseconds of stimulation.  The cells were initiated with a resting potential of -88mV.  In part a, the Na conductance at the axon was 3000pS/μm and 50pS/μm at the somatodendritic segment.  In part b, the conductance at the axon was increased to 30000pS/μm, leaving the somatodendritic conductance at 50pS/μm and in part c, the axon conductance was returned to 3000pS/μm and the somatodendritic conductance was increased to 500pS/μm.  Parts d-f are the transmembrane currents for each of the action potential patterns with the same color scheme as shown above and parts g-i are the recordings obtained from the Backyard Brains recording system.  You can see the drastic difference in recording pattern caused by just changing one parameter on the cell! Fantastic!  You know how to create your own cell models, how to download and run simulations with realistic neuron models, and how to listen to and record your cells!  Now you can explore and discover all of the different ways changing your cells can change the signals you record!  Get creative!  Play a game with a friend and see if you can communicate with each other through only cell signals.  Pretend you're a neurosurgeon; save out a bunch of different cell simulations, have your Matlab code play a random file from those simulations each time it runs and see if you can tell which cell you're recording just by the extracellular recording.  Can you make a multicell model and play multiple recordings at the same time? what does that do to your recorded signal?   Create your own experiments and upload them here!  Interact with your fellow scientists in discussions!  Download others' experiments and play with what your peers have created!  Scientific collaboration helps everyone understand, learn, and have fun together!  We hope you've had a shockingly awesome time with your brains!  Check back regularly for new experiments and information from us about your brain, your body, and the nervous system!  Kole MH, Ilschner SU, Kampa BM, Williams SR, Ruben PC, Stuart GJ, 2008. Action potential generation requires a high sodium channel density in the axon initial segment. Nat Neurosci, 11, 178-86 

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Contact

For answers to questions regarding experiments and other information presented as part of the Virtual Neurophysiology Workbench, we encourage you to go to the Q&A forums and take part in discussions with your peers.  There are separate forums for general questions and for troubleshooting various issues.

For all other inquiries please email Christopher Butson, PhD at butson@sci.utah.edu or Shana Black at shana.black@sci.utah.edu 

Thank you for your interest!