Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010)

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Accession:136095
"... We sought to measure how the activity of the network alters information flow from inputs to output patterns. Information handling by the network reflected the degree of internal connectivity. ... With greater connectivity strength, the recurrent network translated activity and information due to contribution of activity from intrinsic network dynamics. ... At still higher internal synaptic strength, the network corrupted the external information, producing a state where little external information came through. The association of increased information retrieved from the network with increased gamma power supports the notion of gamma oscillations playing a role in information processing."
Reference:
1 . Neymotin SA, Jacobs KM, Fenton AA, Lytton WW (2011) Synaptic information transfer in computer models of neocortical columns. J Comput Neurosci. 30(1):69-84 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,t; I A; I K;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Information transfer;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; I Na,t; I A; I K;
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ncdemo
readme.txt
A.mod
AMPA.mod *
AMPAr.mod
clampex.mod *
cp.mod *
cp2.mod *
field.mod
GABAa.mod
GABAar.mod
GABAb.mod
GABAbr.mod
H.mod
Iahp.mod *
Ican.mod *
IL.mod
IL3.mod *
infot.mod *
intf_.mod
intfsw.mod *
kdr2.mod *
kmbg.mod
misc.mod *
naf2.mod *
nap.mod *
NMDA.mod *
NMDAr.mod
nthh.mod *
ntIh.mod *
ntt.mod *
OFThpo.mod
OFThresh.mod
pregencv.mod
stats.mod
updown.mod *
vecst.mod
bg_cvode.inc
misc.h *
mosinit.hoc
netcon.inc *
netrand.inc
ofc.inc
                            
// $Id: misc.h,v 1.33 2010/06/05 15:32:28 billl Exp $

#include <stdlib.h>
#include <math.h>
#include <limits.h> /* contains LONG_MAX */
#include <time.h>
#include <sys/time.h> 
#include <values.h>
#include <pthread.h>

#if !defined(t)
  #define _pval pval
#endif

typedef struct LISTVEC {
  int isz;
  Object* pL;
  double** pv;
  unsigned int* plen;
  unsigned int* pbuflen;
} ListVec;

typedef struct BVEC {
 int size;
 int bufsize;
 short *x;
 Object* o;
} bvec;

#define BYTEHEADER int _II__;  char *_IN__; char _OUT__[16]; int BYTESWAP_FLAG=0;
#define BYTESWAP(_X__,_TYPE__) \
    if (BYTESWAP_FLAG == 1) { \
	_IN__ = (char *) &(_X__); \
	for (_II__=0;_II__<sizeof(_TYPE__);_II__++) { \
		_OUT__[_II__] = _IN__[sizeof(_TYPE__)-_II__-1]; } \
	(_X__) = *((_TYPE__ *) &_OUT__); \
    }

#define UNCODE(_X_,_J_,_Y_) {(_Y_)=floor((_X_)/sc[(_J_)])/sc[4]; \
                             (_Y_)=floor(sc[4]*((_Y_)-floor(_Y_))+0.5);}
#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
#define MAX(X,Y) ((X) > (Y) ? (X) : (Y))

//square root of 2 * PI
#define SQRT2PI 2.5066282746310002416
//ln(2), base e log of 2
#define LG2 0.69314718055994530941723212145818
#define VRRY 200
#define ISVEC(_OB__) (strncmp(hoc_object_name(_OB__),"Vector",6)==0)

// Andre Fentons cast designations
typedef	unsigned char	ui1;	/* one byte unsigned integer */
typedef	char		si1;	/* one byte signed integer */
typedef unsigned short	ui2;	/* two byte unsigned integer */
typedef short		si2;	/* two byte signed integer */
typedef unsigned int	ui4;	/* four byte unsigned integer */ 
typedef int		si4;	/* four byte signed integer */ 
typedef float		sf4;	/* four byte signed floating point number */ 
typedef double		sf8;	/* eight byte signed floating point number */ 

extern double ERR,GET,SET,OK,NOP,ALL,NEG,POS,CHK,NOZ,GTH,GTE,LTH,LTE,EQU;
extern double EQV,EQW,EQX,NEQ,SEQ,RXP,IBE,EBI,IBI,EBE;

extern double *vector_newsize();
extern unsigned int  dcrsz;
extern double       *dcr;
extern double       *dcrset(int);
extern unsigned int  scrsz;
extern unsigned int *scr;
extern unsigned int *scrset(int);
extern unsigned int  iscrsz;
extern int *iscr;
extern int *iscrset(int);
extern double BVBASE;
extern double* hoc_pgetarg();
extern void hoc_notify_iv();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern Object** hoc_objgetarg();
char *gargstr();
char** hoc_pgargstr();
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double* vector_vec();
extern int vector_buffer_size(void*);
extern double hoc_epsilon;
extern int stoprun;
extern void set_seed();
extern void dshuffle(double* x,int nx);
extern unsigned int valseed;
extern void mcell_ran4_init(unsigned int *idum);
extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);
extern int nrn_mlh_gsort();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
extern int list_vector_px2();
extern int hoc_is_double_arg(int narg);
extern int hoc_is_str_arg(int narg);
extern int hoc_is_object_arg(int narg);
extern int hoc_is_pdouble_arg(int narg);
extern Symbol *hoc_get_symbol(char *);
extern Symbol *hoc_lookup(const char*);
extern Point_process* ob2pntproc(Object*);

extern char* hoc_object_name(Object*);
extern int cmpdfn();
extern int openvec(int, double **);
int list_vector_px();
double *list_vector_resize();
static void hxe() { hoc_execerror("",0); }
extern void FreeListVec(ListVec** pp);
extern ListVec* AllocListVec(Object* p);
extern ListVec* AllocILV(Object*, int, double *);
void FillListVec(ListVec* p,double dval);
void ListVecResize(ListVec* p,int newsz);
extern short *nrn_artcell_qindex_;
extern double nrn_event_queue_stats(double*);
extern void clear_event_queue();

static double sc[6];
static FILE*  testout;

//* in vecst.mod
extern int** getint2D(int rows,int cols);
extern void freeint2D(int*** ppp,int rows);
extern double** getdouble2D(int rows,int cols);
extern void freedouble2D(double*** ppp,int rows);
extern double ismono1 (double *x, int n, int flag);

//* in stats.mod
double kcorfast(double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);
double Rktau (double* x, double* y, int n); // R version
double kcorfast (double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);

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