# 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.

# 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.