BENG 260 / BGGN 260 / PHYS 279 | Fall 2016

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Computational Lab and Assignments

All computational labs and homeworks should be completed in Python or Matlab. We recommend using one programming language the entire course. Assignments are due by 3pm on the specified due date. See individual assignment files for submission guidelines.
Both computational labs and homeworks are graded!

Week Date Instructions and Background Material Assignment
0 9/23
1 9/30
2 10/7
3 10/14
4 10/21
  • Functions to calculate inter-spike interval and spike phase in Python and Matlab
5 10/28
  • Homework 1-3 review and homework 4 open hours
6 11/4
  • Computational Lab 5: NEURON simulator (no homework, lab is just going to be fun)
    • NEURON neuron simulator homepage
    • Installation of NEURON for use with IPython Notebook:
      • Windows - Python(x,y) v2.7: download and unzip a special version. You will need to run or install.bat as administrator (right-click and choose "Run as administrator"). You can then delete the unzipped files.
      • ACMS computer: download the Windows version, unzip to your home directory, and run the "enable-this-folder-on-ACMS" script
      • Mac / Linux - For full Python and IPython Notebook integration you will probably have to build from source (see instructions here), but for today just use ACMS computers
  • ModelDB: a database of published models, most in NEURON, BRIAN, or MATLAB
  • Neuroscience Gateway (NSG) Portal: HPC resources and infrastructure for computational neuroscience include XSEDE shared parallel computing simulation environment
  • Computational Lab 6: Large neural networks, STDP, and BRIAN (no homework, lab is just going to be fun)
  • See the projects page about the project description due on Wed, 11/9
  • Computational Lab 6
  • (Comp. lab won't be graded, and there is no homework)
  • Neurodynamics projects. See the projects page for the schedule and information