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This directory contains the documented GENESIS network model simulations:
RSnet/ - RSnet is a demonstration of a simple network, consisting of a grid of simplified neocortical regular spiking pyramidal cells, each one coupled with excitory synaptic connections to its four nearest neighbors. It is described and analyzed in the GENESIS Modeling Tutorial section "Creating large networks with GENESIS".
par-RSnet/ - par-RSnet is the version of RSNet for parallel GENESIS, and can be run with PGENESIS on PCs with multicore processors. It is described and analyzed in the GENESIS Modeling Tutorial section "Converting large network simulations to PGENESIS" .
synfirenet/ - Contains an example of a more abstract type of network connectivity, the synfire chain. These scripts were developed by Dieter Jaeger as as an exercise in script programming of networks, and the scripts were designed to be easily modified. The network model also allows Hebbian learning. The main script is netsim.g. The GUI lets you experiment with the model, and the HELP menu offers suggestions on ways to modify the model. The README file explains about synfire chains and the details of this model.
Vogels-Abbott_net/ - 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).
VAnet2 model - An efficient hsolved GENESIS version of the Vogels and Abbott (2005) model. It serves as a tutorial on the use of hsolve to achieve at least a factor of 10 speedup, in the context of a very simple model. The 'VAnet2-batch.g' script is intended to be extended for testing GENESIS spike timing dependent plasticity (STDP) implementations with hsolve. This script would be a good starting point for models that use more realistic cells and connections.
ACnet2 is an auditory cortex model that also serves as a tutorial and template for creating neocortical network models.
The fMRInet model, which is available at http://genesis-sim.org/GENESIS/fMRInet illusrates how to provide unusual stimuli, such as the effects of electromagnetic fields, by using a 'script_out' object to provide the stimulus at clocked intervals.
hippo2/ - 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 (Menne et al., 2002) It contains papers and a thesis with detailed documentation of the model.
TurtleVisCortex/ - This is the Nenadic et al. (2003) large scale model of turtle visual cortex. It contains 368 lateral neurons, 311 medial neurons, 20 horizontal, 45 stellate neurons, and 44 subpial neurons in a simulated 1.6 x 1.6 mm piece of cortex. There are also 201 LGN input neurons.
Brette R, Rudolph M, Carnevale T, Hines M, Beeman D, Bower JM, Diesmann M, Morrison A, Goodman PH, Harris Jr FC, Zirpe M, Natschlager T, Pecevski D, Ermentrout B, Djurfeldt M, Lansner A, Rochel O, Vieville T, Muller E, Davison AP, El Boustani S, and Destexhe A (2007) Simulation of networks of spiking neurons: a review of tools and strategies. J. Comput. Neurosci. 23: 349-398.
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.
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.
Vogels TP, Abbott LF. (2005) Signal propagation and logic gating in networks of integrate-and-fire neurons. J. Neurosci. 25: 10786-10795.
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