BioNB 441

Computing for Neurobiology
Cornell University
BioNB 441
Fall 2006

This page is no longer maintained.
Last modified Dec 2006.

This is the home page for BioNB 441 which deals with computing aspects of biological research. This year the course will feature programming in Matlab, with applications including graphics, signal analysis and virtual instrument design.The course is currently taught by Bruce Land, who is a staff member in Neurobiology and Behavior and Electrical Engineering.

Contents

Reading

Week of Aug 24 and Aug28:
- Class overview
- Spend an hour browsing the main Matlab Technical doc page,
  but notice that the last link in the left-hand frame takes you to the PDF versions.
- Getting Started with Matlab parts 1-4
- Matlab tutorials (UMich, Utah, UFL)
Week of Sept 4:
- Spend an hour brousing the links at the bottom of this page
- Using Graphics
Week of Sept 11
- Spectrogram tutorial
Week of Sept 18
- GUI programming
Week of Sept 25
- Filter design
Week of Oct 2
- 3D Modeling
Week of October 9 and Oct 16
- 3D reconstruction from images
Week of October 23
- DAQ design

Laboratory assignments

1. Introduction to Matlab.

2. 2D graphs

3. More graphs

4. GUI design

5. Signals and Filters

6. 3D modeling and animation

7. 3D reconstruction

8. Data acquisition

9. Final project

Old lab assignments

Old homework assignments

Course Schedule

Lectures:: Tues/Thurs 8:40- 9:55 am, Corson/Mudd Atrium A409
Lab:: Wednesday afternoon 1:25-4:25 pm, 1124 Comstock

Staff

Bruce Land,
246 Mudd Hall, 4-4346, BRL4@cornell.edu

Useful links:

Class
Matlab
- A Matlab Tutorial (Cornell EE215)
- Matlab hypertext reference (Portland State)
- Matlab (mathtools.net)
- Matlab Tutorial (RIT)
- Building GUIs with MATLAB
- References (Indiana)
- Intro. Computational Programming (SDSU)
- Educational Sites (Maine)
- Matlab (Yahoo.com)
- Matlab techniques (dmoz open directory project)
- Data visualization toolbox
- Cellular Automata (Tomoaki SUZUDO)
- Evolutionary Algorithms (geatbx.com)
- Matlab functions for computer vision and image analysis (Pete Kovesi)
- Econometrics Toolbox (James P. LeSage)
- Bayes Net Toolbox (Kevin Murphy)
- Camera Calibration Toolbox for Matlab (Jean-Yves Bouguet)
- VOICEBOX: Speech Processing Toolbox (Mike Brookes)
- Scientific Image Processing (Prof. dr. ir. L.J. van Vliet)
- EEG Lab
- Auditory Toolbox (Malcolm Slaney)
Instrumentation
- DAQ Toolbox doc (Mathworks)
- Intro to DAQ toolbox
Neurobiology
- Methods in Computational Neurobiology (UIUC)
- Robotics toolbox (CSIRO)
- Neural Simulations in Java
- Computational Neuroscience list
- Hodgkin-Huxley Model (upenn)
- HH model (caltech)
- HH simulator (rice)
- Neuroexplorer software
- DataMunch analysis software
- Spike-sorting toolbox
Math
- Quantitative Curriculum for Live Science (UTK)
- Mathematical Models in Biology (UTK)
- Fourier synthesis (Gustavus Adolphus College)
- Fourier series analysis (Johns Hopkins)
- Fourier series approximation (Johns Hopkins)
- Signals, Systems and Control (Johns Hopkins)
- Gibbs Phenomenon (SOS Math)
- SOS Math
- MATLAB Functions for Computer Vision and Image Analysis
Cellular Automata and Alife
- CA links
- CAfun
- Windows Alife programs (evoweb)
- Evoweb
- Complex Systems VL -- Cellular automata
- Complexity ONline
- Primordial Soup Kitchen
- Graphics Applications of Cellular Automata
- Short CA tutorial
- Cellular Automata Laboratory (Rudy Rucker and John Walker)
- Applets for Neural Networks and Artificial Life
L-Systems

July 2006 Copyright Cornell University