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Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014)

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"... We developed a computational model based primarily on a unified set of brain activity mapping studies of mouse M1. The simulation consisted of 775 spiking neurons of 10 cell types with detailed population-to-population connectivity. Static analysis of connectivity with graph-theoretic tools revealed that the corticostriatal population showed strong centrality, suggesting that would provide a network hub. ... By demonstrating the effectiveness of combined static and dynamic analysis, our results show how static brain maps can be related to the results of brain activity mapping."
1 . Chadderdon GL, Mohan A, Suter BA, Neymotin SA, Kerr CC, Francis JT, Shepherd GM, Lytton WW (2014) Motor cortex microcircuit simulation based on brain activity mapping. Neural Comput 26:1239-62 [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 L5/6 pyramidal GLU cell; Neocortex M1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Laminar Connectivity;
Implementer(s): Lytton, William [bill.lytton at]; Neymotin, Sam [Samuel.Neymotin at]; Shepherd, Gordon MG [g-shepherd at]; Chadderdon, George [gchadder3 at]; Kerr, Cliff [cliffk at];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex M1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
infot.mod *
intf6.mod *
intfsw.mod *
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
boxes.hoc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
grvec.hoc *
infot.hoc *
intfsw.hoc *
labels.hoc *
local.hoc *
misc.h *
network.hoc *
nqs.hoc *
nrnoc.hoc *
samutils.hoc *
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
xgetargs.hoc *
// $Id: misc.h,v 1.38 2011/11/02 15:26:48 billl Exp $

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

#if !defined(t)
  #define _pval pval

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]; \
#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)
#define dmaxuint 4294967295. // for 32 bits

// 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 *vector_newsize (IvocVect* vv, int n);
#ifndef NRN_VERSION_GTEQ_8_2_0
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 void mcell_ran4_init(uint32_t idum);
extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);
extern int nrn_mlh_gsort(double* vec, int* base_ptr, int total_elems, int (*cmp)(double, double));
extern int ivoc_list_count(Object*);
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 double nrn_event_queue_stats(double*);
extern void clear_event_queue();
extern void cvode_fadvance(double);
extern int hoc_is_tempobj_arg(int narg);
extern Object* ivoc_list_item(Object*, int);
extern double hoc_epsilon;
extern int stoprun;
extern void set_seed();
extern unsigned int hashseed2 (int na, double* x);
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 void dshuffle(double* x,int nx);
extern void ishuffle(int* x,int nx);
extern unsigned int valseed;
extern int list_vector_px2 (Object *ob, int i, double** px, IvocVect** vv);
extern int list_vector_px3 (Object *ob, int i, double** px, IvocVect** vv);
extern int list_vector_px4 (Object *ob, int i, double** px, unsigned int n);
extern int cmpdfn(double a, double b);
extern int openvec(int, double **);
int list_vector_px(Object *ob, int i, double** px);
double *list_vector_resize(Object *ob, int i, int sz);
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 int IsList (Object* p);
extern int uniq2 (int n, double *x, double *y, double *z);
static void vprpr (double x, int base);

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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