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First the homework from Lab Y.

I promised at the beginning of class that you would do original research as part of a "project." I am going to deliver on that promise on the last day of class. But don't worry, your project will take between 5 and 15 minutes and then you can enjoy your summer. And grades for the class will be only based on homework: the last-day-of-class project will be a 10 point homework like the others.


What does the likelihood function look like for Hodgkin-Huxley (current based) models? Does it look like the LS-cost function or the UG-cost function? Few, if any, people, besides me, have looked at this, and I have done woefully few numerical experiments. I don't know the answer to this question and I don't think anyone else does either, but we are going to find out.

How the Project will work

You are going to program the computer to plot a likelihood function. This will be easy, because you are just going to download then edit one of three key files. Each key file correspond to a different model.

  • The Hodgkin-Huxley model
  • A single compartment, many-current, model of the LP cell in the lobster stomatogastric ganglion.
  • The two compartment Ghostburster model.

The first model was written by me, the other two were written by students in this class as an extra (non-credit) project.

When you edit the key file, you will specify which two parameters to vary in the contour plot (the two axes), the values of the parameters to generate the data, and the erroneous assumptions about the parameters that don't vary. Then you are going to send the file you created to me. That is all you will be required to do. Over the summer I will use your file to generate the likelihood plot with my own computer (this may take a month, or more, for all 12 plots). When I am done I will post the key files and the plots on this website, and send out an email telling everyone in the class to take a look. With 12 experiments we should have a good answer to our problem!

What to do?

Download one of the following key files:

As explained in Lab I, the key files are used to interpret the corresponding template files. (You don't need to download the template files but feel free to look at them to understand what the parameters do):

In the key file you downloaded, search for the word CHANGE and make the changes requested.

  • Change the name of the key file ??plot.m to your first name.m or whatever name you want your code identified with on the web.
  • Make the two changes indicated to the code to reflect the new name of the function.
  • Change choice of plot range.
  • Change add or remove parameter and state assumptions about the other parameters.

Homework Z: After editing, email the file to me.