V80.0302001/G80.3042001 -- Spring, 2009

Special Topics in Neural Science:
Introduction to Computer Modeling of Neuronal Systems

Instructor: John Rinzel
Time: Monday 4:00 - 6:00 pm
Location: Center for Neural Science, Rm 815
Prerequisites: Calculus I - II.

Brief Description:

We will use neural modeling software (and pre-written Matlab codes) to understand how neurons, synapses, and networks/systems work. We will simulate cellular neurophysiology experiments to explore resting and action potentials, firing properties, synaptic conductances and integration. Idealized models (firing rate and probability-based functional descriptions) will be used for system-level and network properties including receptive fields, perceptual and cognitive dynamics including decision-making, perceptual grouping and multistability. The software will include dynamic visualization and animation tools. The course will involve classroom lectures and interactive computing lab sessions, homework and a simulation project. No programming experience is necessary.

Syllabus
Project report and presentation

Schedule:

Date Presenter Topic Materials Homework
26 Jan John Rinzel Intro to computl neuro, to sims; NEURON anims.
Intro to Neurons in Action (NIA), first tutorial 		Lecture slides
Lecture slides 		 
2 Feb John Rinzel NIA: The Membrane Tutorial.
NIA: Equilbrium Potentials 		Tut sum: JR

 HW 1
9 Feb John Rinzel
Josh Lucan
 NIA: The Na Action Potential
NIA: Threshold: To Fire or Not to Fire

Tut sum: JL
JR comments 		 
16 Feb   Presidents Day -- No Class    
23 Feb DimitriVassilev
Jaya Tiwari
Phi Pham 		NIA: Voltage Clamping a Patch
NIA: The Neuromuscular Junction
NIA: Postsynaptic Inhibition 		Tut sum:DV
Tut sum: JT
Tut sum: PP 		Chattering Ion Channels
The Ca Action Potential
HW 2
2 March David Hunt
Mark Mikhly
Bingxing Huo
Jon Grinstein 		NIA: Interactions of Synaptic Potentials
NIA: The Passive Axon
NIA: The Unmyelinated Axon
NIA: Axon Diameter Change 		Tut sum:DH
Tut sum:MM
Tut sum:BH
Tut sum:JG 		 
9 March Kyoko Kamishima
Aaron Bornstein
Dawei Wu
NIA: Na and K Channel Kinetics
NIA: Synaptic Integration
NIA: Coincidence Detection


Tut sum:DW 		The Myelinated Axon
Partial Demyelination
HW 3
16 March   NYU Spring Break -- No Class    
23 March Anne Takesian
Michiel Remme 		NIA: Site of Impulse Initiation
NEURON: implementing a model 		Tut sum:AT
NEURON Demo 		 
30 March John Rinzel
Tutorial on dynamical systems
Dissecting the HH model
Morris-Lecar model, phase plane.
XPP demo 		Borisyuk/Rinzel chapt
JR lecture
Ermentrout: XPP stuff 		HW 4
6 April John Rinzel
SDA: Firing rate models for
short term memory 		  SDA: 6.4,6.5,7.4
13 April John Rinzel
SDA: Competition models:
decision making
perceptual bistability/alternations 		  SDA: 6.7, 8.6
20 April  
SDA: E-I network oscillations
Thalamic rhythms 		  SDA: 8.2, 8.4, 12.5
27 April  
SDA: CPGs & swimming
  SDA: 12.2, 12.3

Books:

  • Neurons in Action 2 , by JW Moore and AE Stuart. Sinauer 2007.
  • Spikes, Decisions, and Actions: The Dynamical Foundations of Neuroscience , by HR Wilson. Oxford University Press 1999.
    e-copy SDA book, corrections, Matlab codes

    XPP stuff (Ermentrout):

    Downloads
    Tutorial
    JR/GBE Chapt