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|
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
E-mail: (mailto:email@example.com) firstname.lastname@example.org
Overview of research projects:
Articles available as PDF files:
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
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/.
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:
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.
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/.
(http://askja.bu.edu/) askja.bu.edu - Tue Apr 5 07:39:26 EST 2005 - (http://rak.minduploading.org/" target="_top) Randal A. Koene