ModelDB: KInNeSS : a modular framework for computational neuroscience (Versace et al. 2008)

KInNeSS : a modular framework for computational neuroscience (Versace et al. 2008)

Accession: 113939

The xml files provided here implement a network of excitatory and inhibitory spiking neurons, governed by either Hodgkin-Huxley or quadratic integrate-and-fire dynamical equations. The code is used to demonstrate the capabilities of the KInNeSS software package for simulation of networks of spiking neurons. The simulation protocol used here is meant to facilitate the comparison of KInNeSS with other simulators reviewed in Brette et al. (2007). See the associated paper "Versace et al. (2008) KInNeSS : a modular framework for computational neuroscience." for an extensive description of KInNeSS .
Reference: Versace M, Ames H, Leveille J, Fortenberry B, Gorchetchnikov A (2008) Kinness: a modular framework for computational neuroscience. Neuroinformatics 6(4):291-309 [PubMed]

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Model Information (Click on a link to find other models with that property)

Model Type:	Network;
Brain Region(s)/Organism:
Cell Type(s):	Neocortical pyramidal neuron: deep; Neocortical pyramidal neuron: superficial;
Channel(s):	I Chloride; I Na,t; I K;
Gap Junctions:
Receptor(s):	GabaA; AMPA;
Gene(s):
Transmitter(s):	Gaba; Glutamate;
Simulation Environment:	KInNeSS;
Model Concept(s):	Activity Patterns; Methods;
Implementer(s):	Gorchetchnikov, Anatoli [anatoli at cns.bu.edu];

Search NeuronDB for information about: Neocortical pyramidal neuron: deep; Neocortical pyramidal neuron: superficial; GabaA; AMPA; I Chloride; I Na,t; I K; Gaba; Glutamate;

Model files

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Description of benchmark test implementations for the paper
by Versace et al. (2008). KInNeSS: A modular framework for 
computational neuroscience, Submitted to Neuroinformatics. 

Specifically, this code can be used to simulate in Kinness 
either of the following two networks:

1. A network of spiking Hodgkin-Huxley neurons whose topology 
follows that used in the 'cobahh' model presented in: Brette 
et al. (2007). Simulation of networks of spiking neurons: a 
review of tools and strategies. J Comp Neurosci 23:349-98.

2. A network of quadratic Integrate & Fire neurons with the 
same network topology as in (1).

Simulation notes:
The input pattern is stored in 'paperTest0.png'. From the Kinness 
GUI, open file 'paperTest.xml' to load this pattern. This can be 
done by clicking File/Open...

The network of Hodgkin-Huxley cells is defined in 'paperTestHH.nml'. 
The network of quadratic Integrate and Fire cells is defined in 
'paperTestQIAF.nml'. Load either network from the Kinness GUI 
by clicking Network/Load... The structure of the loaded network is 
then easily accessed by clicking Network/Edit...

After loading both input and network files, the simulation can be run 
by clicking Simulation/Run...

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