# Hodkin Huxley Models for Cellular Neuroscience

Spiking neuron model.
Voltage clamp mode steps voltages.
Anode break code.
Propagating spike.
All variables as a function of V.
Current ramped up slowly.
# Computational Neuroscience NBIO 136b Spring 2007

# THIS IS LAST YEAR'S COURSE! --- MAY STILL BE USEFUL THOUGH

## Matlab Primer

If you are thinking of taking this class, it is worth working through
this Matlab primer ahead of time if you can --- that way, you'll have less
to learn when class starts.

Introductory tutorial for Matlab
Matlab Quick Reference sheet.
Matlab checklist PDF file.
## Matlab Tutorial files

Basic Matlab tutorial.
or Word file of tutorial is better than web page
Basic Matlab exercises.
or Word document of exercises is better.
## Links to some neuroscience teaching animations

North Harris College
Blackwell Publishing
Georgia Southwestern
Daniel Simons Visual Attention
## Lecture 1, Jan 17th 2007: Matlab files

Exponential growth
Exponential decay
Integration of a cosine to give a sine then adding noise
## Lecture 3, Jan 24th 2007

PDF file of Leaky-integrate-and-fire neuron
## Lecture 4, Jan 26th 2007: Matlab files

### Files that produce spike trains (comments to follow soon)

Regular spikes with a rate that has two values
Homogeneous Poisson train
Several trials of Poisson with ramping rate
Poisson with oscillating rate
### Codes that analyze spike trains

Calculates ISI distribution, then CV and CV_2 (1 trial)
Calculates Fano factor, F(t) needs many trials (ntrials)
Calculates autocorrelation function (1 trial)
## Lecture 5, Jan 30th 2007: Matlab file

Connors-Stevens conductance-based model
## Lecture 6, Feb 2nd 2007: Matlab files

Response to voltage steps of
Connors-Stevens model
Plots of voltage-dependence of conductances for Ca_T and Connors-Stevens model
Leaky integrate-and-fire model with
spike-rate adaptation and a conductance-based refractory period
## Lecture 7, Feb 6th 2007 Matlab files and handout

Handout on bursting and pacemaker circuits
Post-inhibitory rebound (thalamic relay) model
Two-compartment alternative to Pinsky-Rinzel model
Two-compartment Pinsky-Rinzel model
## Lecture 9, Feb 13th 2007 Matlab file

Phase response curve calculation with the Connors-Stevens model
## Lecture 10, Feb 16th 2007 Matlab files

Pair of post-inhibitory rebound neurons coupled
by inhibition to oscillate in out of phase bursts.
Regular train of spikes through
depressing and facilitating synapses
Poisson spike trains with steps in rate through
depressing and facilitating synapses
## Lecture 11, Feb 27th 2007

Encoding and spike-triggered average
Papers on WebCT
## Lecture 13, March 6th 2007

Decoding and ROC analysis
Matlab code to show kernel integration for HW4
## Lecture 14, March 9th 2007

Noisy spike trains and Hidden Markov Models
Matlab code to show trial-averaging of Poisson spikes from a
ramping rate
Matlab code to show trial-averaging of Poisson spikes from a
randomly jumping rate
## Lecture 15, March 13th 2007

Firing Rate Models
Matlab code to generate f-I curve of a noisy LIF neuron
(comments to follow)
Matlab code to look at average synaptic input from
a group of cells with Poisson spiking (comments to follow)
## Lecture 16, March 16th 2007

Uncommented orientation tuning Matlab code
for use with homework 5
Papers on orientation tuning can be found in WebCT
## Lecture 17, March 20th 2007

Commented discrete memory code
Commented spatial memory code, could be useful for HW5
Power point presentation from class on memory
## Lecture 18, March 23rd 2007

Winner-takes-all decision-making code.
Noisy decision-making code.
## Lecture 19, March 27th 2007

Simple recurrent feedback continuous memory/integrator rate code.
Many bistable units with a readout cell (rate model).
Handout on attractors and integrators.
## Lecture 20, March 30th 2007

Code for memory-based decisions needed for HW6.
Powerpoint presentation.
## Lecture 21, April 13th 2007

Code for spike-timing dependent plasticity
between rate-model cells that undergo sequential, overlapping input
Code that segregates inputs from two groups
of correlated cells via STDP on an LIF neuron.
Handout on Hebbian plasticity.
## Lecture 22, April 17th 2007

Powerpoint presentation on
the CaMKII/PP1 model of LTP.
Class Handout on CaMKII and stochastic modeling.
## Lecture 23, April 20th 2007

Papers on WebCT.
Code that demonstrates the
effects of heterogeneity on spatial memory.
## Lecture 25, April 27th 2007

Code to implement eyeblink conditioning.
## Lecture 26, May 1st 2007

Code to implement the weather prediction task by reward-based plasticity.
Code to implement the matching task.

Last modified April 30th, 2007
Paul Miller, pmiller@brandeis.edu

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