networks

This is the large scale model of turtle visual cortex (the "NGU model")
described in:

Nenadic, Z., Ghosh, B.K. and Ulinski. P. (2003)
Propagating Waves in Visual Cortex: A Large Scale Model of Turtle Visual
Cortex", J. Computational Neuroscience 14:161-184.

and

Nenadic, Z., Ghosh, B.K. and Ulinski. P. (2002) Modeling and Estimation
Problems in the Turtle Visual Cortex, IEEE Trans. Bio-Med. Eng., 49:753-762

It is also described in considerable detail in the file
TurtleVisCortex-descrip.pdf, which is included in this archive.

This simulation was developed by Dieter Jaeger as
as an exercise in script programming of networks, using a synfire
chain network as an example.

A synfire chain network is a feedforward network consisting of several
parallel chains of cells. Each cell has excitatory connections to cells on
the next chain, with no connections within the chain, or to the previous
chain. This network has the interesting property that desynchronized spike
trains at the input chain can become synchronized at the final chain.

The main script is netsim.g. It creates 10 columns, with 10 cells in each

The archive hippo2_data.tar.gz contains supplementary files that were
originally included with the "hippo2" hippocampal network model
contributed by Kerstin Menne, and that were removed to save space.

When unpacked, the 38 MB gzipped tar file will produce a hippo2_data/
directory that is about 137 MB in size.

The directory DATA contains examplary network output. Please refer to
the README (DATA/README.txt) file for an explanation.

The .avi files are movies (pans and zooms of cell visualizations) for
illustrative purposes.

This is a small hippocampal network model consisting of 72 pyramidal cells
(Traub 1994 model) and 18 interneurons (Traub 1995 model), developed and
submitted to BABEL, the GENESIS Users Group, by Kerstin Menne, and
published in

Menne, K.M.L., Folkers, A., Malina, T., Maex, R. and Hofmann, U. G. (2002)
Test of spike sorting algorithms on the basis of simulated network data.
Neurocomputing 44-46:1119-1126.

The contents of her README file are appended below. To save space, the
video files (pans and zooms of cell visualizations) and the large data

Contains the GENESIS implementations of the Vogels and Abbott (2005) model using single compartment neurons with Hodgkin-Huxley dynamics. This was used as a benchmark for neural simulators in the review by Brette et al. (2007). The README file gives gives further details.

Everything you have to know about my biologically realistic simulation
of a part of hippocampal CA3.

Paper and diplomathesis (Menne_*.pdf) contain detailed information
about the why and how of the simulation.

The directory SIMULATION contains the simulation scripts
themselves. Pleas have a look at the README file.

The directory DATA contains examplary network output. Please refer to
the README file for an explanation.

And finally, the movies are for illustrative purposes.

Enjoy!

Contact:menne@isip.mu-luebeck.de
Kerstin Menne

The simulation, which is based on the MultiCell program by Matt Wilson,
closely follows the three neuron model of the tritonia CPG described in
Chapter 6 (by Peter Getting) of Methods in Neuronal Modeling, edited by
Koch and Segev.

The cells are all single-compartment models of a soma with synaptically
activated channels. (The one exception to this is the vsi neuron, which
also has a Hodgkin-Huxley K channel.) The channels are created with a
modification of the MultiCell "makechannel" function which has been changed