Note from ModelDB administrator:
    The files you need to run (and examine the code of) the model are 1) newtmaze.ccm and 2) catacomb-2.034.zip,
    both of which are available from links below.  You will likely need java from sun in order to run the model.
    To start the model under linux if you have multiple java's installed you can execute a command like:


/usr/java/jre1.5.0_06/bin/java -jar /home/morse/nrnmodels/newtmaze/catacomb-2.034/ccmb.jar /home/morse/nrnmodels/newtmaze/newtmaze.ccm

or simpler if you use relative paths.

    20170601:
    
    The original source of catacomb web sites are not available at the moment so catacomb is being made available through this copy provided
    by Robert Cannon:

    http://senselab.med.yale.edu/ModelDB/Data/64242/catacomb.tgz
    in addition you will need newtmaze.ccm from here: http://senselab.med.yale.edu/ModelDB/Data/64242/newtmaze.ccm

    The links in the below have been turned off because they (askja.bu.edu site and others) no longer exist however the documentation is still relevant:
    


askja.bu.edu: Computational Neurophysiology at 
the Boston University Center for Memory & Brain



 
Supported by NIDA DA16454 as part of the NSF/NIH
collaborative research in Computational Neuroscience Program, and by
MH60013 and MH61492 and NSF SBE 0354378.








(http://askja.bu.edu/data/models/) BROWSE model files
(http://askja.bu.edu/rak/upload.html) UPLOAD model files
(http://axiope.anc.ed.ac.uk/catacomb/mantis/) Catacomb bug tracker
(http://askja.bu.edu/search.html) search site







A model of the role of hippocampus in spatial navigation









This model addresses the potential role of the hippocampus in goal
directed spatial navigation, the role of theta rhythm oscillations in
reversal learning, and the role of entorhinal cortex as a buffer for
novel information. The model can encode a spatial environment and guide
movement of a virtual rat to find a food reward within this
environment. The structure of the model is constrained by the overall
anatomical connectivity of the hippocampus, and the spread of activity
is constrained by the relative size of place fields in entorhinal
cortex and regions CA3 and CA1 of the hippocampus. The model has a
simple form of theta phase precession. The model avoids interference
from prior retrieval during encoding by implementing separate phases of
encoding and retrieval on each cycle of the theta rhythm. The model
uses sustained spiking activity in entorhinal cortical neurons to allow
slow transitions in sensory input from the environment to cause
synaptic modification dependent upon a very brief temporal window of
spike timing dependent synaptic plasticity.







Prof. Michael E. Hasselmo

Department of Psychology

Center for Memory and Brain,

Program in Neuroscience and

Center for BioDynamics

64 Cummington St.

Boston, MA 02215

Tel: (617) 353-1397


E-mail: (mailto:hasselmo@bu.edu) hasselmo@bu.edu


Overview of research projects:

(http://people.bu.edu/hasselmo/) laboratory web page.


Articles available as PDF files:

(http://people.bu.edu/hasselmo/publications.html) publications page.







Spatial navigation in a T-maze: This integrate-and-fire model
created with Catacomb relates hippocampal physiological data with the
possible functional role of the hippocampus for behavior in a spatial
navigation task.

To test this model:

(1) Download the Catacomb script (http://askja.bu.edu/rak/newtmaze.ccm) newtmaze.ccm.

(Press the right hand mouse button on the link. A "Save As" window
will pop up. At the bottom of the window, make sure to save as "All
files", not as "HTML document".)

(2) Make sure you have Catacomb version 2.034, which the newtmaze model is designed to work with: (http://askja.bu.edu/mike/catacomb-2.034.zip) catacomb-2.034.zip.

Some simple exercises with the newtmaze model are shown (http://askja.bu.edu/mike/exploring-T-maze.html) here.


Obtaining and running Catacomb: The most recent stable release of Catacomb may be obtained at: (http://askja.bu.edu/catacomb/index.html) http://askja.bu.edu/catacomb/.

(The most recent version will not work with the newtmaze model. As
indicated above, that model is designed to work with version 2.034 of
Catacomb.)


To run the Catacomb environment, you need a suitable implementation of JAVA
for your computer and operating system. While Catacomb may run with the
Java provided as a standard installation on your platform, the best way
to insure that Catacomb will run correctly is to install Java from one
of these two sources:

(1) The official Java site at (http://www.java.com/) http://www.java.com.
A box displayed at this site offers automated and manual download of
java software. If you follow the link to the automated download, a page
will appear that immediately attempts an automated installation of the
correct Java for your platform.

If the automated install does not work, or if you wish to manually
select a different platform, such as Linux, Macintosh or Solaris, use
the "Manual Download" link at the front page of (http://www.java.com/) http://www.java.com.

(If your operating system is Windows95, the FAQ link at the official Java site indicates how to install Java properly.)

(2) The Java developers download page at (http://java.sun.com/j2se/1.4/download.html) http://java.sun.com/j2se/1.4/download.html.
Scroll down the page to the section labeled "Download J2SE v 1.4.2_03".
There, download from the column labeled "JRE". Software for all
operating systems is provided.


Project Guidelines for PS530 students: The following guidelines
may be useful for those who would like to learn about Catacomb and the
details of the hippocampal simulation.

    

  • Downloading and Running guidelines for the Catacomb tutorials: (http://askja.bu.edu/rak/catacomb-examples/Exercise1.pdf) Exercise1.pdf.
    
The software page for PS530, (http://askja.bu.edu/mike/index.html) PS530: Neural models of Memory Function.

  • PS530 Students Guidelines for a Final Project using Catacomb: (http://askja.bu.edu/rak/catacomb-examples/CatacombFinalProjectGuidelines2003b.pdf) CatacombFinalProjectGuidelines2003b.pdf
    (or the same document in MS Word (http://askja.bu.edu/rak/catacomb-examples/CatacombFinalProjectGuidelines2003b.doc) .doc format).

  • Assignment 1: (http://askja.bu.edu/rak/catacomb-examples/PS530catacombEx1for2003fPDF.pdf) PS530catacombEx1for2003fPDF.pdf
    (or the same document in MS Word (http://askja.bu.edu/rak/catacomb-examples/PS530catacombEx1for2003f.doc) .doc format).

  • Assignment 2: (http://askja.bu.edu/rak/catacomb-examples/PS530catacombEx2for2003b.pdf) PS530catacombEx2for2003b.pdf
    (or the same document in MS Word (http://askja.bu.edu/rak/catacomb-examples/PS530catacombEx2for2003b.doc) .doc format).


(You will need a PDF reader, such as the free (http://www.adobe.com/products/acrobat/) Acrobat Reader to open the PDF files above.)












Catacomb


Information about the Catacomb simulation environment is available at

(http://askja.bu.edu/catacomb/index.html) http://askja.bu.edu/catacomb/

(a mirror of compneuro.org).


A Catacomb wizard tool that accelerates the construction of standard experiments is in the early stages of development at:

(http://askja.bu.edu/catacomb-wizard/) http://askja.bu.edu/catacomb-wizard/.






The Virtual Rat


A log of ongoing projects and Catacomb simulations collected under the general heading "The Virtual Rat" is maintained at (http://askja.bu.edu/rak/virtual-rat.html) http://askja.bu.edu/rak/virtual-rat.html. The project research described there currently involves models of prefrontal cortical areas and hippocampus in the rat.








(http://askja.bu.edu/) askja.bu.edu -

Tue Apr  5 07:39:26 EST 2005

 - (http://rak.minduploading.org/" target="_top) Randal A. Koene