Computational Modelling in Neuroscience


Administrivia

  • This is the homepage for Neuroscience 9520: Computational Modelling in Neuroscience
  • Class will be Mondays, 2:00pm - 3:30pm, and Thursdays, 11:30am - 1:00pm, in NSC 245A
  • The instructor is Paul Gribble (email: paul [at] gribblelab [dot] org)
  • course syllabus.pdf
  • We will use several chapters from a book on computational motor control: "The Computational Neurobiology of Reaching and Pointing" by Reza Shadmehr and Steven P. Wise, MIT Press, 2005. [ google books link ] [ cover info ]

Code

When there is a python script linked in the notes, you will get a permissions error when clicking on it. I haven't figured out how to avoid this yet. In the meantime, all code can be downloaded here in this tarred gzipped archive: code.tgz


Course Notes

Schedule & Topics


Sep 10: Introductions & course schedule

Sep 13: Getting your computer set up with Python & scientific libraries


Sep 17 : Modelling Dynamical Systems I

Sep 20: Modelling Dynamical Systems II


Sep 24, 27 : no class (Paul away)


Oct 1, 4 : Modelling Action Potentials - Hodgkin-Huxley models


Oct 8, 11 : no class (thanksgiving, SFN)


Oct 15, 18 : no class (SFN)


Oct 22, 25 : Computational Motor Control: Kinematics


Oct 29, Nov 1 : Computational Motor Control: Dynamics

  • assignment4\sol.py
  • course notes: 5: Computational Motor Control: Dynamics
  • read at least two of the papers listed in the course notes
  • read Shadmehr & Wise book, Chapter 20 and Chapter 21 (and Chapter 22 if you are interested in the topic)
  • twojointarm.py utility functions and Python code for doing inverse and forward dynamics of a two-joint arm in a horizontal plane (no gravity) with external driving torques, and animating the resulting arm motion
  • twojointarm\game.py : try your hand at this game in which you have to control a two-joint arm to hit as many targets as you can before time runs out. Use the [d,f,j,k] keys to control [sf,se,ef,ee] joint torques (s=shoulder, e=elbow, f=flexor, e=extensor). Spacebar will "reset" the arm to its home position, handy if your arm starts spinning out of control (though each time you use spacebar your score will be decremented by one). Start the game by typing python twojointarm_game.py at the command line. At the end of the game your score will be printed out on the command line.
  • assignment5.pdf

Nov 5, 8 : Computational Motor Control: Muscle Models


Nov 12, 15 : Computational Models of Learning part 1


Nov 19, 22 : Computational Models of Learning part 2


Nov 26, 29 : Computational Models of Learning part 3


Dec 3 : student presentations

  • each of the 12 students registered in the course will present one paper from the literature in their research area in which a computational modelling approach was used to address a question about how the brain works.
  • presentations are limited to 7 minutes each! Note: this is difficult to pull off, you will have to practice your talk out loud. Also be careful to choose your slides carefully. There will be a timer and a loud gong.
  • Question period will be limited to 1 to 2 minutes per talk.
  • The order of talks will be alphabetical by your last name. A first, Z last. We will need to start at 2pm sharp.
  • Each student giving a talk must also submit a short essay on their chosen paper. Your essay should follow the "Content and Format" style of the "Journal Club" feature in the Journal of Neuroscience. You can choose any paper you want, it doesn't have to be a J. Neurosci. paper and it doesn't have to have been published within the past 2 months.
  • Essays are due Sunday Dec 9th, 2012, no later than 11:59pm EST. Please send your essay to me by email, as a single .pdf file. The filename should be <lastname>_essay.pdf (e.g. gribble\_essay.pdf).

Links

iPython

These notes

These notes can be viewed (and downloaded) in their entirety from a github repository here: CompNeuro


Paul Gribble | Fall 2012
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