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Neuron Software Package: A Basic Introduction

Neuron Software Package: A Basic Introduction. NMD Lab Jose M. jmatt005@fiu.edu. What is Neuron . Neuron is a simulation environment designed for modeling neurons and networks of neurons, developed by Yale University, Scientists.

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Neuron Software Package: A Basic Introduction

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  1. Neuron Software Package:A Basic Introduction NMD Lab Jose M. jmatt005@fiu.edu

  2. What is Neuron. • Neuron is a simulation environment designed for modeling neurons and networks of neurons, developed by Yale University, Scientists. • Neuron provides tools for building, managing and using models specifically for the neuronal system.

  3. Installation Guide • Visit: http://www.neuron.yale.edu/neuron/download • Select your relevant operating system and install to selected location on your hard-drive.

  4. Utilizing Neuron:Single Compartment Cell • The neuron software architecture works off of .hoc files that define the majority of the parameters of the neuronal cell environment. • Our first example is that of an isopotential spherical cell with Hodgkin-Huxley currents, the surface area of the cell is 100um^2

  5. A single compartment Spherical Cell • We will learn how to • Create the model • Attach a stimulating electrode • Evoke an action potential • Show the time course of V_m

  6. Step 1: Build the Interface Required for Simulation • We will need 4 controls: • Controls for running simulation • This is the Neuron Main Menu, it controls all major facets of the environment • Controls for adjusting model parameters • Tools-> RunControlcreates a window that determines the parameters of how the simulation is run temporally. • Graphical Display of the simulation result • Graph-> Voltage Axis • Stimulation of the Model • Tools-> Point Processes-> Managers-> Point Manager • Here we define an Iclamp (current clamp)

  7. Step 2 • Generate the geometry of the cell via the gui: • Build single compartment • Here we add HH, these are the Hodgkin-Huxley gating regime.

  8. Step 3 • Once we have the cell geometry defined and the stimulation electrode. We can begin to perform experiments!

  9. Step 4: Using the Interface we Just built • Setting Stimulus Parameters: • Point process manager allows for modification of the stimulating process: • Use the spinner to increase and decrease “del” in ms. • Use direct entry to enter a value into the “dur” field in ms. • Type a mathematical expression into the “amp” 0+1 and then enter.

  10. Recapitulation • We now have: • RunControl Window: that delieneates the parameters of the simulation. • Graph Window: that serves to display the dependence of voltage on time. • PointProcessManagerWindow: that serves to modify the parameters of the process driving the simulation, in the current case a current clamp

  11. Assignment. • First part: • Brief analysis on Nernst Potentials of most relevant ions. • Second part: • Linearized GHK Equation, solve for the relation algebraically. • Third part Neuron Simulation: • Simulate the Neuron for 100 ms with varying amplitudes. • Set the time via Tstop (100ms), this is total simulation time. • Set the duration of the Iclamp to (50ms) • Vary the current from 0.001 nA to the threshold where the cell can no longer respond (oscillations, no AP’s)

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