index

Quantitative methods in neuroscience

NeuBeh 545/PBIO 545

Tu/Th 10:30-11:50, G328 HSB

Date	Topic and Handouts	Reading and Discussion topics
1/6	Linear Algebra some logistics	linear algebra primer from Eero Simoncelli Linear transformations on Wikipedia Column space demo from class (note: requires some files from linear algebra tutorial - get those first)
1/8	Linear Algebra: Discussion	linear algebra tutorial normrnd PlotVector Plot3DVector statsizechk note: you need all five files; make sure they are all on Matlab's path. You may already have normrnd and statsizechk if you have the statistics toolbox. Markov chain slides (optional part of tutorial)
1/13	Journal club:	Wandell, Foundations of Vision, Chapter 4 Baylor, Nunn and Schnapf (1987) J Physiol 390:145-160.
1/15	Journal club:
1/20	Fourier Analysis, Filters and Convolution	Press et al., Numerical Recipes, pages 496-508 (2nd edition, this is beginning of Ch. 12); Ch. 13 Koch, Biophysics of Computation, Appendix B Wandell, Foundations of Vision, Appendix A (a mix of linear algebra and linear systems stuff).
1/22	Fourier Analysis, Filters and Convolution: Discussion	Fourier analysis tutorial linear systems primer from Eero Simoncelli (note this is not the same as the linear algebra one above - has a lot of Fourier stuff in it). Partha Mitra’s open source Matlab code for spectral analysis, with links to online tutorials: http://chronux.org/home/ spectral analysis notes from Kleinfeld
1/27	Journal club:	Hubel-Wiesel direction selective Hubel-Wiesel RGC Hubel-Wiesel orientation selective papers for discussion: Movshon, 1978a Movshon, 1978b
1/29	Journal club:
2/3	Differential equations and neural dynamics	Howard Berg, Random Walks in Biology, Appendix B Hugh Wilson, Spikes, Decisions and Actions, Chapters 1, 2, 3 Wilson, Chapter 5 (numerical methods)
2/5	Differential equations and neural dynamics: Discussion	tutorial Simulink tutorial (optional)
2/10	Journal club:	Robinson Fuchs, Scudder and Kaneko
2/12	Journal club:	Supplementary material: Villus material part 1 Villus material part 2 Villus material part 3 simulink model (works on Matlab 5)
2/17	Introduction to the Theory of Stochastic Processes	Berg, Apendix A Koch, Chapter 15 Duda, Hart and Stork, Pattern Classification (2nd edition), Appendix 4 probability basics tutorial
2/19	Introduction to the Theory of Stochastic Processes: Discussion	Stochastic Processes Tutorial (note: you need all four files in this folder; make sure they are all on Matlab's path) Moment generating functions tuturial (you need both files in folder) Kemeny and Snell, Finite Markov Chains kemeny_snell_ch1 kemeny_snell_ch2
2/24	Journal club:	Shadlen and Newsome, Current Opinion (primary paper for discussion) Softky and Koch Shadlen and Newsome (longer one) random walk Markov chain demo from class
2/26	Journal club:
3/3	PCA and Dimensional Reduction	PCA tutorial (note: you need all four files in this folder; make sure they are all on Matlab's path)
3/5	PCA and Dimensional Reduction: Discussion	Golomb LGN paper
3/10	Journal club:	Simoncelli chapter (good intro to PCA and friends) Yang Dan complex cell paper
3/12	Journal club: