A Rice/UTHSC-H joint effort to build a biophysically and anatomically accurate computational model of the rat hippocampal formation with which to evaluate existing, and construct novel, cognitive theories of spatial navigation.
Senior Personnel: Steve Cox, Jim Knierim, Harel Shouval, Paul Smolen, and Danny Sorensen.
Funding: We are pleased to acknowledge the generous support of the Sheafor/Lindsay Fund via the ERIT program at Rice's Computer and Information Technology Institute CITI .
Courses:
Intro at Rice/Baylor .
Advanced at
UTHSC-H
Activities:
Fall 08 Seminar: VIGRE, CAAM 499 Sec 1.
Tues. 4-5:30 in BROWN 146
Summer 08 Work
Spring 08 Seminar: VIGRE, CAAM 499 Sec 1.
Tuesday 4-6pm in HZ 119
Fall 07 Seminar: VIGRE, CAAM 499 Sec 1.
Wednesday 10-11am in DH 3110
Summer 07 Work
Spring 07 Seminar: VIGRE, CAAM 499 Sec 1.
Wednesday 5-6pm in KH 101
Fall 06 Seminar: VIGRE, CAAM 499 Sec 1.
Wednesday 5-6pm in KH 105
Summer 06 Work
Spring 06 Seminar: VIGRE, CAAM 499 Sec 1.
Summer 06 Work Groups:
Network: Computation and Visualization
Knierim Lab, UTH: Data recording and analysis
Neuronal Calcium Signaling
Spring 06 Seminar Participants: Paul Anzel, Sha'kia Boggan,
Andy Bost, Jesse Chan, Sam Feng, Toby Isaac,
Neel Kishan,
Brad Peercy, Jay Raol, Francesco Savelli, Nick Stepankiw, Nan Xiao
Code:
+ Single Cell Solver and Viewer by Nan Xiao
Background Reading
gzipped tar ball of matlab code
To unpack type tar -xvvf nxball.tar.gz from Unix prompt.
To run type cellscript_act from matlab prompt.
+ Parallel Integrate and Fire Code by Tony Kellems
PIAF
+ The Cell Assembly Network of Lansner and Fransen as reconstructed by Derrick Roos.
See Derrick's connexions module for details and demo.
Resources:
+ Cray XD1
(2C) Toby Isaac, Richard Hall
(IaF) Nick Stepankiw, Tony Kellems
(Pop) Jay Raol
Chris Conner
With Cox and Saggau at BCM: Sam Feng, Nan Xiao, Ray Hwong,
Resources: Saggau ,
Parker 1
Parker 2
Parker 3
Summer poster ,
Summer Sam and Ray report
With Peercy at Rice: Lucca Sabbatini
+ January 11: Cox. Specify project goals and introduce
Samsanovich and Ascoli
Assignment Due 1/19. One page summary of introductory chapter on
The Neurobiology of Spatial Behavior.
+ January 19: Cox. The Pathfinding Algorithm of S&A. Review
theta rhythm and phase precession. Discuss their
code. This is a very high level representation -
for there don't appear to be any neurons in sight. One challenge is to build
neuronal nets that in fact exhibit theta waves and phase precession.
Chapter 7 in Traub and Miles is a great place to start. Beyond that,
for theta I recommend this paper of Wang
and for phase precession this paper of
Magee. These notions are brought together in an Integrate & Fire paper
of Tsodyks et. al that exploits the
experimental findings of Skaggs et. al.
Assignment Due 1/26. Build a bigger (at least 10-by-10) maze and
suppress the
interactive aspect of samasc.m
and wrap it in a driver that produces a histogram like S&A figure 3C. Submit
hard copies of code and histogram. You might like the hist command in matlab.
At this early phase you may not work together. Ask Cox and/or Peercy for
help.
+ January 26: Brad Peercy. Putting neurons into the maze. A careful
look at theta waves and phase precession as discussed in the above papers
of Skaggs et. al and Tsodyks et. al.
+ February 2: Andy & Jesse. Mechanisms that lead to asymmetry in
Tsodyks may come from Head Direction
and or Grid cells.
+ February 9: Neel & Sha'Kia. Integrate and Fire nets in C and MPI
on the Rice Terascale cluster.
Assignment Due 2/16. Two page summary of
Wang .
+ February 16: Toby will lead discussion of rythmogenesis in the
CA3 model of Pinsky and Rinzel.
+ February 23: Sam will lead discussion of rythmogenesis in the
CA3 model of Traub and Miles. Here are notes on the
prologue and
chapter 5 and
chapter 6 .
+ March 2: Moser speaks at UTH (MSB 3.001) on Grid Cells.
Meet at the (Non-Magregor) stop light on the jogging path between
Sid & Lovett at
3:40 pm.
+ March 9: Jay will lead discussion of
An effective kinetic representation of
fluctuation driven neuronal netwoks.
+ March 16: Spring Break and, more importantly,
Brain
Awareness Week.
+ March 23: Sam will discuss chapters 6 and 7 of Traub and Miles.
Raol and Cox will counter with a population model of
Nykamp and Tranchina
+ March 30: Cox and Raol continue the disection of Nykamp and Tranchina.
+ April 6: Spring recess, poster prep.
+ April 13: Cox and Raol continue the disection of Nykamp and Tranchina.
The CA3 population model of the Budapest group is comprised of
Part 1 and
Part 2.
+ The Pinsky & Rinzel CA3 network of
Chan & Isaac
+ The MEC/CA3 simulator of Katie Ward.
See her Master's Thesis for background,
and her Connexions Module for details on the grid cell model.
+ Rice Terascale Cluster Home
+
The Hippocampus as a Cognitive Map by O'keefe and Nadel.
+
GCC for Theoretical & Computational Neuroscience
+ Duke Southampton Archive of Neuronal Morphology
+ Rice Baylor Archive of Neuronal Morphology
+ Computational
Neuroanatomy of the Hippocampus
+ Levy Lab at UVa.
+ Budapest Computational Neuroscience Group
+ NeuroJet