Neural Networks B, SS06 1

UA Dr. Robert Legenstein, WiMAus Prashant Joshi, M.S.

Institute for Theoretical Computer Science
Technische Universität Graz
A-8010 Graz, Austria
{legi, joshi}

NACHNAME Vorname Matrikelnmr Teammitglieder

Exercise 9: Compartmental modelling in NEURON

NOTE: You can download this exercise in pdf or postscript(ps) format here.

This exercise is based on the neuron tutorial availaible here2. This exercise uses part A and B of the tutorial only.

  1. First follow the instructions of part A. At the end you must be able to get a plot of the membrane potential of the soma. Submit this plot. If it is not clear as to how to print your plots, then please read the section ``The Print and File Window Manager'' from tutorial part B.
  2. Now please read pages 9-14 of ``NEURON: a Tool for Neuroscientists'' which can be found here3 (section ``Choosing the spatial grid''). As you can see choosing the correct spatial resolution (i.e. the no. of compartments) is very important for accuracy of simulations.

    Now go ahead to section ``Cables'' in Part B of the tutorial. Compute the values of $ \lambda_{100}$ for dendrite[0], dendrite[1] and the soma.

  3. In part B, section ``Making the neurons subthalamic'' check that your code is running correctly. At the end of this section it says ``This is a good time to run the model and explore ...''. Now try moving the current injection to $ 30\%$ and $ 70\%$ down the length of dendrites4. Plot the voltage at the center of soma, and at these 4 injection locations on a single plot(so you will have 4 plots with 5 traces on each plot). Set the stimulus as ( $ del = 10ms, dur = 100ms$ and $ amp = 0.5nA$). Write a small note about your observations.

  4. Now experiment with different fractions of $ \lambda_{100}$ for compartment lengths. Write your script such that nsegs is set automatically to make compartment lengths a fraction of $ \lambda_{100}$. You can start with $ 30\%$, but make this a sensibly named variable. located somewhere on the top of your script file.

  5. (For 5 BONUS points!) Rerun the simulation making the segments $ < 20\%, 40\%, 60\%, 80\%$ and $ 100\%$ of $ \lambda_{100}$. For each fraction of $ \lambda_{100}$ run the simulation with different input currents, e.g. $ 0.005, 0.01,
0.05, 0.1$ and $ 0.5 nA$. You may need to make the duration for current injection longer to make it fire for small current amplitudes. Also try it with the current injection in the soma, and $ 30\%$ and $ 70\%$ of the way down the longer dendrite. Submit a few of these plots which illustrate the difference that you see for using:
    • Different fractions of $ \lambda_{100}$ for compartment lengths.
    • Different levels of current injections.
    • Different locations of current injections.
    Write a small paragraph discussing your observations.

  6. Submit a printout of the script that you used for your simulations.

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Neural Networks B, SS06 1

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The translation was initiated by Joshi Prashant on 2006-06-13


... SS061
Class Website:
... here2
... here3
... dendrites4
i.e. 4 different IClamp locations, dendrite[0](0.3), dendrite[0](0.7), dendrite[1](0.3) and dendrite[1](0.7)

Joshi Prashant 2006-06-13