The virtual slice setup (Lytton et al. 2008)

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Accession:116838
"In an effort to design a simulation environment that is more similar to that of neurophysiology, we introduce a virtual slice setup in the NEURON simulator. The virtual slice setup runs continuously and permits parameter changes, including changes to synaptic weights and time course and to intrinsic cell properties. The virtual slice setup permits shocks to be applied at chosen locations and activity to be sampled intra- or extracellularly from chosen locations. ..."
Reference:
1 . Lytton WW, Neymotin SA, Hines ML (2008) The virtual slice setup. J Neurosci Methods 171:309-15 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Extracellular;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s):
Implementer(s): Lytton, William [bill.lytton at downstate.edu]; Neymotin, Sam [Samuel.Neymotin at nki.rfmh.org];
/
b09jan08
README.html
intf_.mod
misc.mod *
nstim.mod *
stats.mod
vecst.mod
misc.h
mosinit.hoc
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// $Id: misc.h,v 1.11 2009/01/07 21:25:34 billl Exp $

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

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

typedef struct {
  int isz;
  double** pv;
  int* plen;
} ListVec;

#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	SQRT2PI		2.5066282746
#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 */

double *vector_newsize(void* vv, int n);
extern unsigned int scrsz;
extern unsigned int *scr;
extern unsigned int *scrset(int);
extern double BVBASE;
#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 double hoc_epsilon;
extern int stoprun;
extern void set_seed();
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 hoc_is_double_arg(int narg);
extern int hoc_is_tempobj_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*);
int list_vector_px();
extern short *nrn_artcell_qindex_;
extern double nrn_event_queue_stats(double*);
extern void clear_event_queue();
extern Objectdata *hoc_objectdata;
#endif

extern int cmpdfn(double a, double b);
extern unsigned int hashseed2 (int na, double* x);
extern int list_vector_px2(Object *ob, int i, double** px, void** vv);
extern int list_vector_px3 (Object *ob, int i, double** px, void** vv);
extern int list_vector_px4 (Object *ob, int i, double** px, unsigned int n);
extern void mcell_ran4_init(uint32_t idum);
extern int openvec(int, double **);
extern void cvode_fadvance(double);
int list_vector_px(Object *ob, int i, double** px);
double *list_vector_resize(Object *ob, int i, int sz);
int uniq2 (int n, double *x, double *y, double *z);
static void hxe() { hoc_execerror("",0); }
static double sc[6];

ListVec* AllocListVec(Object* p);
ListVec* AllocILV(Object* p, int nx, double *x);
void FillListVec(ListVec* p,double dval);
void FreeListVec(ListVec** pp);


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