Mirror Neuron (Antunes et al 2017)

 Download zip file 
Help downloading and running models
Accession:229276
Modeling Mirror Neurons Through Spike-Timing Dependent Plasticity. This script reproduces Figure 3B.
Reference:
1 . Antunes G, Faria da Silva SF, Simoes de Souza FM (2018) Mirror Neurons Modeled Through Spike-Timing-Dependent Plasticity are Affected by Channelopathies Associated with Autism Spectrum Disorder. Int J Neural Syst 28:1750058 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s):
Channel(s): I Calcium; I M; I h; I Potassium; I Sodium;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s): Cav1.2 CACNA1C; Cav1.3 CACNA1D;
Transmitter(s): Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Detailed Neuronal Models; STDP;
Implementer(s): Simoes-de-Souza, Fabio [fabio.souza at ufabc.edu.br];
Search NeuronDB for information about:  AMPA; NMDA; I M; I h; I Sodium; I Calcium; I Potassium; Glutamate;
/
Final
mechanisms
Ca_HVA.mod *
Ca_LVAst.mod *
CaDynamics_E2.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
ProbAMPANMDA_EMS.mod *
ProbGABAAB_EMS.mod *
SK_E2.mod *
SKv3_1.mod *
STDP_triplet.mod
Ca_HVA.c
Ca_HVA.o
Ca_LVAst.c
Ca_LVAst.o
CaDynamics_E2.c
CaDynamics_E2.o
Ih.c
Ih.o
Im.c
Im.o
K_Pst.c
K_Pst.o
K_Tst.c
K_Tst.o
mod_func.c
mod_func.o
Nap_Et2.c
Nap_Et2.o
NaTa_t.c
NaTa_t.o
NaTs2_t.c
NaTs2_t.o
nrnmech.dll
ProbAMPANMDA_EMS.c
ProbAMPANMDA_EMS.o
ProbGABAAB_EMS.c
ProbGABAAB_EMS.o
SK_E2.c
SK_E2.o
SKv3_1.c
SKv3_1.o
STDP_triplet.c
STDP_triplet.o
                            
/* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
 
#if METHOD3
extern int _method3;
#endif

#if !NRNGPU
#undef exp
#define exp hoc_Exp
extern double hoc_Exp(double);
#endif
 
#define _threadargscomma_ _p, _ppvar, _thread, _nt,
#define _threadargs_ _p, _ppvar, _thread, _nt
 
#define _threadargsprotocomma_ double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt,
#define _threadargsproto_ double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt
 	/*SUPPRESS 761*/
	/*SUPPRESS 762*/
	/*SUPPRESS 763*/
	/*SUPPRESS 765*/
	 extern double *getarg();
 /* Thread safe. No static _p or _ppvar. */
 
#define t _nt->_t
#define dt _nt->_dt
#define gamma _p[0]
#define decay _p[1]
#define depth _p[2]
#define minCai _p[3]
#define ica _p[4]
#define cai _p[5]
#define Dcai _p[6]
#define v _p[7]
#define _g _p[8]
#define _ion_ica	*_ppvar[0]._pval
#define _ion_cai	*_ppvar[1]._pval
#define _style_ca	*((int*)_ppvar[2]._pvoid)
 
#if MAC
#if !defined(v)
#define v _mlhv
#endif
#if !defined(h)
#define h _mlhh
#endif
#endif
 
#if defined(__cplusplus)
extern "C" {
#endif
 static int hoc_nrnpointerindex =  -1;
 static Datum* _extcall_thread;
 static Prop* _extcall_prop;
 /* external NEURON variables */
 /* declaration of user functions */
 static int _mechtype;
extern void _nrn_cacheloop_reg(int, int);
extern void hoc_register_prop_size(int, int, int);
extern void hoc_register_limits(int, HocParmLimits*);
extern void hoc_register_units(int, HocParmUnits*);
extern void nrn_promote(Prop*, int, int);
extern Memb_func* memb_func;
 extern void _nrn_setdata_reg(int, void(*)(Prop*));
 static void _setdata(Prop* _prop) {
 _extcall_prop = _prop;
 }
 static void _hoc_setdata() {
 Prop *_prop, *hoc_getdata_range(int);
 _prop = hoc_getdata_range(_mechtype);
   _setdata(_prop);
 hoc_retpushx(1.);
}
 /* connect user functions to hoc names */
 static VoidFunc hoc_intfunc[] = {
 "setdata_CaDynamics_E2", _hoc_setdata,
 0, 0
};
 /* declare global and static user variables */
 /* some parameters have upper and lower limits */
 static HocParmLimits _hoc_parm_limits[] = {
 0,0,0
};
 static HocParmUnits _hoc_parm_units[] = {
 "decay_CaDynamics_E2", "ms",
 "depth_CaDynamics_E2", "um",
 "minCai_CaDynamics_E2", "mM",
 0,0
};
 static double cai0 = 0;
 static double delta_t = 0.01;
 /* connect global user variables to hoc */
 static DoubScal hoc_scdoub[] = {
 0,0
};
 static DoubVec hoc_vdoub[] = {
 0,0,0
};
 static double _sav_indep;
 static void nrn_alloc(Prop*);
static void  nrn_init(_NrnThread*, _Memb_list*, int);
static void nrn_state(_NrnThread*, _Memb_list*, int);
 static void nrn_cur(_NrnThread*, _Memb_list*, int);
static void  nrn_jacob(_NrnThread*, _Memb_list*, int);
 
static int _ode_count(int);
static void _ode_map(int, double**, double**, double*, Datum*, double*, int);
static void _ode_spec(_NrnThread*, _Memb_list*, int);
static void _ode_matsol(_NrnThread*, _Memb_list*, int);
 
#define _cvode_ieq _ppvar[3]._i
 /* connect range variables in _p that hoc is supposed to know about */
 static const char *_mechanism[] = {
 "6.2.0",
"CaDynamics_E2",
 "gamma_CaDynamics_E2",
 "decay_CaDynamics_E2",
 "depth_CaDynamics_E2",
 "minCai_CaDynamics_E2",
 0,
 0,
 0,
 0};
 static Symbol* _ca_sym;
 
extern Prop* need_memb(Symbol*);

static void nrn_alloc(Prop* _prop) {
	Prop *prop_ion;
	double *_p; Datum *_ppvar;
 	_p = nrn_prop_data_alloc(_mechtype, 9, _prop);
 	/*initialize range parameters*/
 	gamma = 0.05;
 	decay = 80;
 	depth = 0.1;
 	minCai = 0.0001;
 	_prop->param = _p;
 	_prop->param_size = 9;
 	_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
 	_prop->dparam = _ppvar;
 	/*connect ionic variables to this model*/
 prop_ion = need_memb(_ca_sym);
 nrn_check_conc_write(_prop, prop_ion, 1);
 nrn_promote(prop_ion, 3, 0);
 	_ppvar[0]._pval = &prop_ion->param[3]; /* ica */
 	_ppvar[1]._pval = &prop_ion->param[1]; /* cai */
 	_ppvar[2]._pvoid = (void*)(&(prop_ion->dparam[0]._i)); /* iontype for ca */
 
}
 static void _initlists();
  /* some states have an absolute tolerance */
 static Symbol** _atollist;
 static HocStateTolerance _hoc_state_tol[] = {
 0,0
};
 static void _update_ion_pointer(Datum*);
 extern Symbol* hoc_lookup(const char*);
extern void _nrn_thread_reg(int, int, void(*f)(Datum*));
extern void _nrn_thread_table_reg(int, void(*)(double*, Datum*, Datum*, _NrnThread*, int));
extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
extern void _cvode_abstol( Symbol**, double*, int);

 void _CaDynamics_E2_reg() {
	int _vectorized = 1;
  _initlists();
 	ion_reg("ca", -10000.);
 	_ca_sym = hoc_lookup("ca_ion");
 	register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
 _mechtype = nrn_get_mechtype(_mechanism[1]);
     _nrn_setdata_reg(_mechtype, _setdata);
     _nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
  hoc_register_prop_size(_mechtype, 9, 4);
 	nrn_writes_conc(_mechtype, 0);
 	hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
 	hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
 	hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
 	ivoc_help("help ?1 CaDynamics_E2 C:/Users/Fabio/Desktop/NEURON_Book/Markram/hoc_combos_syn.1_0_10.allzips/Neurons/Fabio_L5_TTPC1_cADpyr232_5/mechanisms/CaDynamics_E2.mod\n");
 hoc_register_limits(_mechtype, _hoc_parm_limits);
 hoc_register_units(_mechtype, _hoc_parm_units);
 }
 static double FARADAY = 96485.3;
static int _reset;
static char *modelname = "";

static int error;
static int _ninits = 0;
static int _match_recurse=1;
static void _modl_cleanup(){ _match_recurse=1;}
 
static int _ode_spec1(_threadargsproto_);
/*static int _ode_matsol1(_threadargsproto_);*/
 static int _slist1[1], _dlist1[1];
 static int states(_threadargsproto_);
 
/*CVODE*/
 static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {int _reset = 0; {
   Dcai = - ( 10000.0 ) * ( ica * gamma / ( 2.0 * FARADAY * depth ) ) - ( cai - minCai ) / decay ;
   }
 return _reset;
}
 static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
 Dcai = Dcai  / (1. - dt*( ( - ( ( 1.0 ) ) / decay ) )) ;
 return 0;
}
 /*END CVODE*/
 static int states (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) { {
    cai = cai + (1. - exp(dt*(( - ( ( 1.0 ) ) / decay ))))*(- ( (- ( 10000.0 ))*(( ( (ica)*(gamma) ) / ( 2.0 * FARADAY * depth ) )) - ( ( ( - minCai ) ) ) / decay ) / ( ( - ( ( 1.0 ) ) / decay) ) - cai) ;
   }
  return 0;
}
 
static int _ode_count(int _type){ return 1;}
 
static void _ode_spec(_NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
  ica = _ion_ica;
  cai = _ion_cai;
     _ode_spec1 (_p, _ppvar, _thread, _nt);
  _ion_cai = cai;
 }}
 
static void _ode_map(int _ieq, double** _pv, double** _pvdot, double* _pp, Datum* _ppd, double* _atol, int _type) { 
	double* _p; Datum* _ppvar;
 	int _i; _p = _pp; _ppvar = _ppd;
	_cvode_ieq = _ieq;
	for (_i=0; _i < 1; ++_i) {
		_pv[_i] = _pp + _slist1[_i];  _pvdot[_i] = _pp + _dlist1[_i];
		_cvode_abstol(_atollist, _atol, _i);
	}
 	_pv[0] = &(_ion_cai);
 }
 
static void _ode_matsol(_NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
  ica = _ion_ica;
  cai = _ion_cai;
 _ode_matsol1 (_p, _ppvar, _thread, _nt);
 }}
 extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
 static void _update_ion_pointer(Datum* _ppvar) {
   nrn_update_ion_pointer(_ca_sym, _ppvar, 0, 3);
   nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 1);
 }

static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
  int _i; double _save;{
 
}
}

static void nrn_init(_NrnThread* _nt, _Memb_list* _ml, int _type){
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 v = _v;
  ica = _ion_ica;
  cai = _ion_cai;
 initmodel(_p, _ppvar, _thread, _nt);
  _ion_cai = cai;
  nrn_wrote_conc(_ca_sym, (&(_ion_cai)) - 1, _style_ca);
}}

static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _v){double _current=0.;v=_v;{
} return _current;
}

static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 
}}

static void nrn_jacob(_NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml];
#if CACHEVEC
  if (use_cachevec) {
	VEC_D(_ni[_iml]) += _g;
  }else
#endif
  {
     _nd = _ml->_nodelist[_iml];
	NODED(_nd) += _g;
  }
 
}}

static void nrn_state(_NrnThread* _nt, _Memb_list* _ml, int _type) {
 double _break, _save;
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
 _nd = _ml->_nodelist[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 _break = t + .5*dt; _save = t;
 v=_v;
{
  ica = _ion_ica;
  cai = _ion_cai;
 { {
 for (; t < _break; t += dt) {
   states(_p, _ppvar, _thread, _nt);
  
}}
 t = _save;
 } {
   }
  _ion_cai = cai;
}}

}

static void terminal(){}

static void _initlists(){
 double _x; double* _p = &_x;
 int _i; static int _first = 1;
  if (!_first) return;
 _slist1[0] = &(cai) - _p;  _dlist1[0] = &(Dcai) - _p;
_first = 0;
}

#if defined(__cplusplus)
} /* extern "C" */
#endif

Loading data, please wait...