Studies of stimulus parameters for seizure disruption using NN simulations (Anderson et al. 2007)

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Accession:98902
Architecturally realistic neocortical model using seven classes of excitatory and inhibitory single compartment Hodgkin-Huxley cells. Wiring is adapted to minicolumn hypothesis and incorporates visual and neocortical data. Simulation demonstrates spontaneous bursting onset and cessation, and activity can be altered with external electric field.
Reference:
1 . Anderson WS, Kudela P, Cho J, Bergey GK, Franaszczuk PJ (2007) Studies of stimulus parameters for seizure disruption using neural network simulations. Biol Cybern 97:173-94 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-6 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron;
Channel(s): I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium;
Gap Junctions:
Receptor(s): AMPA; Gaba;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program;
Model Concept(s): Bursting; Epilepsy;
Implementer(s):
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-6 cell; Neocortex V1 interneuron basket PV cell; AMPA; Gaba; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium;
This is the model associated with the paper

Anderson WS, Kudela P, Cho J, Bergey GK, Franaszczuk PJ (2007) Studies
of stimulus parameters for seizure disruption using neural network
simulations. Biol Cybern 97:173-94

To use first type make in the HopkinsModel directory.

Currently I'm (Stan Anderson) running it on a 32-bit 16-node cluster,
also running an older Redhat version. I've been compiling it on a
64-bit machine, but in 32-bit mode, the 64-bit machine is running a
newer Suse version.

As far as the individual c-codes:

mknode.c is the code that sets up the intracolumnar connections and
produces a synapse table that is passed to each node.

mklink.c is the code that sets up the extracolumnar connections, which
produces an unsorted link table that undergoes further
manipulations. This code also calculates which neurons in the
simulation will undergo action potentials during a stimulation pulse.

sublink.c assigns the previously computed extracolumnar links to
specific neurons, and strips away intranodal links, turning that
information into synaptic structures as created in
mknode.c. Extranodal links (i.e. computer to computer) or maintained
as link structures.

link_sort.c sorts the link structures into an order more easily read
by the simulation code.

crl.c actually writes the link information into a file of link
structures that is passed to each node.

netclustwacnmdadiff.c is the main simulation code running on each node
with the integration loop, and accounting of synaptic currents.

clust_cn.c - handles communication via nodes via packet protocols
(very slow in this setting)

the lnet.h and clust_cn.h files are the most important header files,
and most variables can be found here.

mkpar.c enables the user to fill the parameter tables for each cell
class in terms of individual channel kinetic properties.

Version: 20111007 This version contains changes in the sublink.c file.

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