Course Instructor: | Mark Kramer (email, 3-4591) |

Course Hours: | 12:30-2 PM / TTh / MCS B23 |

Office Hours: | 2:00-3:30 PM / TTh, or by appointment |

Textbook: | MATLAB for Neuroscientists |

Handouts . . . |

The plan - it's still flexible . . .

**Week 1 (8)**

Lecture: Introduction + Measures of coupling.

- New students: You'll need to create an AD account to use the computers in Engineering. Fill out the forms here.

Sample data - Case_Study_1.mat and Case_Study_2.mat.

Optional Reading:

- New students: Be comfortable using MATLAB. See the course text, and make sure you can complete Ch 2.
- Pereda et al. Prog Neurobiol, 2005. First 3 pages only.
- Bruns. J Neurosci Methods, 2004. First 3 pages only.

**Week 2 (9)**

Lecture: Cross frequency coupling and bicoherence.

Lab: Application of cross frequency coupling and bicoherence code and bicoherence.m.

Sample data - data_1.mat and data_2.mat.

Optional Reading:

- Tort et al, PNAS, 2008.
- Canolty et al, Trends Cogn Sci, 2010.
- Kramer et al, J Neurosci Method, 2008.

**Week 3 (10)**

Lecture: Relating spikes and fields through coherence.

Lab: The spike train spectrum and spike-field coherence code and my_cc_circ_shift.m.

Sample data - case_study_1.mat and case_study_2.mat.

Optional Reading:

- A technical paper (Jarvis and Mitra, Neural Comp, 2001) about spike-field coherence.
- An application paper (Gregoriou et al, Science, 2009) using spike-field coherence.
- The Chronux software package.

**Week 4 (11)**

Lecture: The FitzHugh-Nagumo model.

Lab: Analysis of the FitzHugh-Nagumo model.

Motivation - MATLAB code to first explore the Hodgkin-Huxley model.

Download and install XPPAUT binary from here.

Assignment for this week. The FitzHugh_Nagumo.ode file for XPPAUT. The FitzHugh_Nagumo.nb file for Mathematica.

Optional Reading:

- FitzHugh-Nagumo model on Scholarpedia.
- XPPAUT Tutorial on Bard Ermentrout's website.
- Mathematica documentation from Wolfram's website.

**Week 5 (12)**

Lecture: Bifurcations and zero eigenvalues.

Lab: More practice with XPPAUT.

If you haven't already done so, download and install an XPPAUT binary from here.

Assignment for this week. The FitzHugh_Nagumo.ode file for XPPAUT (same as last week).

Optional Reading:

- Morris-Lecar model on Scholarpedia.
- Wilson-Cowan model, a brief summary article about this mean-field model.
- .ode examples on Bard Ermentrout's website.
- .ode examples more on Bard Ermentrout's website.

**Week 6 (13)**

Lecture: Three models of gamma.

Lab: ING, PING, and sparse PING. Lab code. Other code we'll need: HH0.m,
ing.m, ping.m, and sparse_ping.m.

Optional Reading:

- A paper on gamma models.
- Much more about modeling rhythms.
- Gamma rhythms and optogenetics.