Quantitative methods in neuroscience
Neuro 545/PBIO 545
M/Th 12:301:50, G328 HSB
Date  Topic and Handouts  Reading and Discussion topics 
1/5 
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) 

1/9 
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) ColorSpace HW: script cone spectra monitor spectra 
1/12  Journal club

Wandell, Foundations of Vision, Chapter 4 (good intro) or here: https://foundationsofvision.stanford.edu/chapter4wavelengthencoding/
http://graphics.stanford.edu/courses/cs178/applets/colormatching.html (introduction to color matching) 
1/19  Howard Berg, Random Walks in Biology, Appendix A 

1/23  Introduction to the Theory of Stochastic Processes: Discussion 
accessory files (note: 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 
1/26  Journal club:

Shadlen et al (primary paper for discussion) de la Rocha et al. (supplement re how correlated activity is shaped) 
1/30 
Press et al., Numerical Recipes, pages 496508 (2nd edition, this is beginning of Ch. 12); Ch. 13 

2/2 
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). linear systems primer from David Heeger Partha Mitra’s open source Matlab code for spectral analysis, with links to online tutorials: http://chronux.org/home/ spectral analysis notes from Kleinfeld 

2/6  Journal club:

methods paper (read first): Betzig discussion paper: Dani supplementary: Xu 
2/9  Class Discussion and module wrapup


2/13  Differential equations and neural dynamics 
Howard Berg, Random Walks in Biology, Appendix B 
2/16  
2/23  Journal club:

Robinson (primary paper) Fuchs, Scudder and Kaneko (physiological counterpart to Robinson paper)
Supplementary material: 
2/27  PCA and Dimensional Reduction  
3/2  PCA and Dimensional Reduction: Discussion  
3/6  Journal club:

Rust et al (primary discussion paper) 
3/9  Class Discussion and module wrapup

Instructors and contact info:
Adrienne Fairhall  fairhall@uw.edu 
Fred Rieke  rieke@uw.edu 
Wyeth Bair  wyeth.bair@gmail.com 
Abhishek De  abhisd@uw.edu 

Course project:
Computers, etc:
Computers with MATLAB are available in the PBIO computer room and the Neuroscience office.
Contact one of us if you are having problems finding a machine you can use.
Useful links:
site for Theoretical Neuroscience, Dayan and Abbott (see Exercises)
Mathematical details of Fourier analysis from Wolfram Research