NEURON interfaces to MySQL and the SPUD feature extraction algorithm (Neymotin et al. 2008)

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See the readme.txt for information on setting up this interface to a MySQL server from the NEURON simulator. Note the SPUD feature extraction algorithm includes its own readme in the spud directory.
1 . Neymotin S, Uhlrich DJ, Manning KA, Lytton WW (2008) Data mining of time-domain features from neural extracellular field data Applic. of Comput. Intel. in Bioinf. and Biomed.: Current Trends and Open Problems 151:119-140
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism:
Cell Type(s):
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Lytton, William [billl at]; Neymotin, Sam [samn at];
Files displayed below are from the implementation
// $Id: misc.h,v 1.29 2009/09/04 19:05:27 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

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]; \

//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 *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 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 int 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);

Neymotin S, Uhlrich DJ, Manning KA, Lytton WW (2008) Data mining of time-domain features from neural extracellular field data Applic. of Comput. Intel. in Bioinf. and Biomed.: Current Trends and Open Problems 151:119-140

References and models cited by this paper

References and models that cite this paper

Adeli H, Zhou Z, Dadmehr N (2003) Analysis of EEG records in an epileptic patient using wavelet transform. J Neurosci Methods 123:69-87 [PubMed]

Ascoli GA, De Schutter E, Kennedy DN (2003) An information science infrastructure for neuroscience. Neuroinformatics 1:1-2 [Journal] [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

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Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2000) Expanding NEURON's repertoire of mechanisms with NMODL. Neural Comput 12:995-1007 [PubMed]

Johnson SG,Frigo M (2007) A modified split-radix FFT with fewer arithmetic operations IEEE Transactions on Signal Processing 55:111-119

Lytton WW (2006) Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics 4:163-76 [Journal] [PubMed]

   Neural Query System NQS Data-Mining From Within the NEURON Simulator (Lytton 2006) [Model]

Lytton WW, Omurtag A (2007) Tonic-clonic transitions in computer simulation. J Clin Neurophysiol 24:175-81 [PubMed]

   Tonic-clonic transitions in a seizure simulation (Lytton and Omurtag 2007) [Model]

Macqueen JB (1967) Some methods for classification and analysis of multivariate observations Proceedings Of 5th Berkeley Symposium On Mathematical Statistics And Probability 1:281-297

Sweldens W (1997) The lifting scheme: A construction of second generation wavelets SIAM Journal on Mathematical Analysis 29:511-546

Uhlrich DJ, Manning KA, O'Laughlin ML, Lytton WW (2005) Photic-induced sensitization: acquisition of an augmenting spike-wave response in the adult rat through repeated strobe exposure. J Neurophysiol 94:3925-37 [PubMed]

Neymotin SA, Hilscher MM, Moulin TC, Skolnick Y, Lazarewicz MT, Lytton WW (2013) Ih Tunes Theta/Gamma Oscillations and Cross-Frequency Coupling In an In Silico CA3 Model PLoS ONE 8(10):e76285 [Journal] [PubMed]

   Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013) [Model]

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [Journal] [PubMed]

   Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]

(18 refs)