Thalamocortical augmenting response (Bazhenov et al 1998)

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Accession:37819
In the cortical model, augmenting responses were more powerful in the "input" layer compared with those in the "output" layer. Cortical stimulation of the network model produced augmenting responses in cortical neurons in distant cortical areas through corticothalamocortical loops and low-threshold intrathalamic augmentation. ... The predictions of the model were compared with in vivo recordings from neurons in cortical area 4 and thalamic ventrolateral nucleus of anesthetized cats. The known intrinsic properties of thalamic cells and thalamocortical interconnections can account for the basic properties of cortical augmenting responses. See reference for details. NEURON implementation note: cortical SU cells are getting slightly too little stimulation - reason unknown.
Reference:
1 . Bazhenov M, Timofeev I, Steriade M, Sejnowski TJ (1998) Computational models of thalamocortical augmenting responses. J Neurosci 18:6444-65 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Thalamus;
Cell Type(s): Thalamus geniculate nucleus (lateral) principal neuron; Thalamus reticular nucleus cell; Neocortex V1 pyramidal corticothalamic L6 cell;
Channel(s): I Na,t; I T low threshold; I A; I K,Ca;
Gap Junctions:
Receptor(s): GabaA; GabaB; AMPA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Synchronization; Synaptic Integration;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu];
Search NeuronDB for information about:  Thalamus geniculate nucleus (lateral) principal neuron; Thalamus reticular nucleus cell; Neocortex V1 pyramidal corticothalamic L6 cell; GabaA; GabaB; AMPA; I Na,t; I T low threshold; I A; I K,Ca; Gaba; Glutamate;
: $Id: matrix.mod,v 1.32 2003/09/05 18:52:54 billl Exp $

:* COMMENT
COMMENT
NB: only minimal error checking done
NB: no dynamic allocation - eg m1.transpose(m1) will give a wrong result 
NB: matrix and vec sizes must be correct before using: use .resize()

================            USAGE               ================
objref mat
mat = new Vector(rows*cols)
mat.mprintf(M,N)     // print out as M rows and N columns
mat2.transpose(mat)  // transpose of matrix
y.mmult(mat,x)       // y = mat*x
y.spmult(pre,post,mat,x) // y = mat*x using "sparse matrix"
w.spget(pre,post,row,col) // ie pre,post,post,pre!!
spidget(pre,post,prid,poid ...) // match vals in 4 vecs to 4 vals
wt.mkspcp/chkspcp(pre,post) // copy the indices into integer arrays
mat.outprod(x,y)     // mat = outer product of vectors x and y
mat.mget(i,j,cols)   // i=row#; j=col#
mat.mset(i,j,cols,val)
y.mrow(mat,i,cols)
y.mcol(mat,j,cols)
y.msetrow(mat,i,cols)
y.msetcol(mat,j,cols)
================================================================
ENDCOMMENT

NEURON {
  SUFFIX nothing
}
 
PARAMETER {
  MATRIX_INSTALLED=0
}

:* mat.outprod(x,y) // mat = outer product of vectors x and y
VERBATIM
static double outprod(void* vv) {
  int i, j, nx, ny, nz;
  double *x, *y, *z;
  /* this will be the outer product */
  nx = vector_instance_px(vv, &x);
	
  /* these are the two vectors that make it up */
  ny = vector_arg_px(1, &y); // will be number of columns
  nz = vector_arg_px(2, &z); // will be number of rows
  if (nx != ny*nz) {
    hoc_execerror("Vector size mismatch", 0);
  }
  for (i=0;i<ny;i++) {
    for (j=0;j<nz;j++) {
      x[i*nz+j] = y[i]*z[j];
    }
  }
  return nx;
}
ENDVERBATIM
 
:* mmult
VERBATIM
static double mmult(void* vv) {
  int i, j, nx, ny, nz;
  double *x, *y, *z;
  /* x will be the product of matrix y and vec z */
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  nz = vector_arg_px(2, &z);
  if (ny != nx*nz) {
    hoc_execerror("Vector size mismatch", 0);
  }
  for (i=0;i<nx;i++) {
    x[i] = 0.;
    for (j=0;j<nz;j++) {
      x[i] += y[i*nz+j]*z[j];
    }
  }
  return nx;
}
ENDVERBATIM
 
:* ST[PO].spltp(pr,po,wt,ST[PRE])
VERBATIM
static double spltp(void* vv) {
  int ii, jj, nstpr, nstpo, nw, npr, npo, flag, cnt;
  double *stpr, *stpo, *w, *pr, *po;
  extern double hoc_call_func(Symbol*, int narg);

  char func[4] = "ltp";
  Symbol* s = hoc_lookup(func);
  if (! s) { hoc_execerror("Can't find ltp() func", 0); }
  nstpo = vector_instance_px(vv, &stpo);
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  nw = vector_arg_px(3, &w);
  nstpr = vector_arg_px(4, &stpr);
  for (ii=0,jj=0,cnt=0;ii<nstpo;ii++) {
    if (stpo[ii]==1.0) { /* connections to these will be changed */ 
      for (;po[jj]<ii;jj++) ; /* move forward till find a po */
      for (;po[jj]==ii;jj++) { /* move through these po's */
	if (stpr[(int)pr[jj]]==1.) { /*  did the presyn spike? */
	  cnt++; hoc_pushx(1.0);
	} else { 
	  cnt--; hoc_pushx(-1.0);
	}
        hoc_pushx(w[jj]);
        w[jj]=hoc_call_func(s, 2);
      }
    }
  }
  return cnt;
}
ENDVERBATIM
 
VERBATIM
/* Maintain a parallel vector of ints to avoid the slowness of repeated casts in spmult */
static int *pr_int;
static int *po_int;
static int cpfl=0;
ENDVERBATIM

:* wt.mkspcp(pr,po)
VERBATIM
static double mkspcp(void* vv) {
  int j, nw, npr, npo;
  double *w, *pr, *po;
  if (! ifarg(1)) { 
    cpfl=0; 
    if (po_int!=NULL) free(po_int); 
    if (pr_int!=NULL) free(pr_int);
    po_int=(int *)NULL; pr_int=(int *)NULL; 
    return 0;
  }
  nw = vector_instance_px(vv, &w);
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  pr_int=(int *)ecalloc(nw, sizeof(int));
  po_int=(int *)ecalloc(nw, sizeof(int));
  for (j=0;j<nw;j++) {
    po_int[j]=(int)po[j];
    pr_int[j]=(int)pr[j];
  }
  cpfl=nw;
  return cpfl;
}
ENDVERBATIM

:* wt.chkspcp(pr,po)
VERBATIM
static double chkspcp(void* vv) {
  int j, nw, npr, npo, flag;
  double *w, *pr, *po;
  nw = vector_instance_px(vv, &w);
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  flag=1;
  if (po_int==NULL || pr_int==NULL) { cpfl=0; return 0; }
  if (cpfl!=nw) { flag=0;
  } else for (j=0;j<nw;j++) {
    if (po_int[j]!=(int)po[j] || pr_int[j]!=(int)pr[j]) {flag=0; continue;}
  }
  if (flag==0) {
    cpfl=0; free(po_int); free(pr_int); 
    po_int=(int *)NULL; pr_int=(int *)NULL; 
  }
  return flag;
}
ENDVERBATIM

:* y.spmult(pr,po,wt,x[,flag])
: y=W*x, y will be the product of matrix w with pre/post indices and vec x
: optional flag (5th arg present) - do not clear dest vector initially
VERBATIM
static double spmult(void* vv) {
  int i, j, nx, ny, nw, npr, npo, flag;
  double *x, *y, *w, *pr, *po, xx;
  ny = vector_instance_px(vv, &y);
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  nw = vector_arg_px(3, &w);
  nx = vector_arg_px(4, &x);
  if (ifarg(5)) {flag=1;} else {flag=0;}
  if (nw!=npr || nw!=npo) {
    hoc_execerror("Sparse mat must have 3 identical size vecs for pre/post/wt", 0); 
  }
  if (flag==0) for (i=0;i<ny;i++) y[i] = 0.; // clear dest vec
  if (cpfl==0) {
    for (j=0;j<nw;j++) y[(int)po[j]] += (x[(int)pr[j]]*w[j]);
  } else if (cpfl!=nw) { hoc_execerror("cpfl!=nw in spmult", 0); } else {
    for (j=0;j<nw;j++) if (x[pr_int[j]]!=0) { y[po_int[j]] += ((x[pr_int[j]])*w[j]); }
  }
  return nx;
}
ENDVERBATIM
 

:* wt.spget(pr,po,row,col) returns weight value
VERBATIM
static double spget(void* vv) {
  int j, nw, npr, npo;
  double *w, *pr, *po, row, col;
  nw = vector_instance_px(vv, &w);
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  row = *getarg(3);
  col = *getarg(4);
  for (j=0;j<nw;j++) if (row==po[j]&&col==pr[j]) break;
  if (j==nw) return 0.; else return w[j];
}
ENDVERBATIM

:* spidget(prv,pov,pridv,poidv,pr,po,prid,poid) returns an index
FUNCTION spidget() { : gaussian distribution around 0
VERBATIM
{
  int j, npr, npo, nprid, npoid;
  double *pr, *po, *prid, *poid, pri, poi, pridi, poidi;
  npr = vector_arg_px(1, &pr);
  npo = vector_arg_px(2, &po);
  nprid = vector_arg_px(3, &prid);
  npoid = vector_arg_px(4, &poid);
  pri= *getarg(5);
  poi= *getarg(6);
  pridi= *getarg(7);
  poidi= *getarg(8);
  for (j=0;j<npr;j++) { 
    if (poi==po[j]&&pri==pr[j]&&pridi==prid[j]&&poidi==poid[j]) break;
  }
  if (j==npr) _lspidget=-1.0; else _lspidget=(double)j;
}
ENDVERBATIM
}

:* transpose
VERBATIM
static double transpose(void* vv) {
  int i, j, nx, ny, rows, cols;
  double *x, *y;
  /* x will be the transpose of matrix y */
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  rows = (int)*getarg(2);
  cols = (int)*getarg(3);
  if (ny != nx) {
    hoc_execerror("Vector size mismatch", 0);
  }
  for (i=0;i<rows;i++) {
    for (j=0;j<cols;j++) {
      x[j*rows+i] = y[i*cols+j];
    }
  }
  return nx;
}
ENDVERBATIM
 
:* mprintf
VERBATIM
static double mprintf(void* vv) {
  int i, j, nx, rows, cols;
  double *x;
  /* x will be printed out */
  nx = vector_instance_px(vv, &x);
  rows = (int)*getarg(1);
  cols = (int)*getarg(2);
  if (nx != rows*cols) {
    hoc_execerror("Vector size mismatch", 0);
  }
  for (i=0;i<rows;i++) {
    for (j=0;j<cols;j++) {
      printf("%g\t",x[i*cols+j]);
    }
    printf("\n");
  }
  return nx;
}
ENDVERBATIM
 
:* mget(i,j,cols)
VERBATIM
static double mget(void* vv) {
  int i, j, nx, rows, cols;
  double *x;
  nx = vector_instance_px(vv, &x);
  i = (int)*getarg(1);
  j = (int)*getarg(2);
  cols = (int)*getarg(3);
  if (i*cols+j >= nx) {
    hoc_execerror("Indices out of bounds", 0);
  }
  return x[i*cols+j];
}
ENDVERBATIM
 
:* mrow(mat,i,cols)
VERBATIM
static double mrow(void* vv) {
  int i, j, nx, ny, rows, cols;
  double *x, *y;
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  i = (int)*getarg(2);
  cols = (int)*getarg(3); rows=ny/cols;
  if (cols!=nx) { 
    nx=vector_buffer_size(vv);
    if (cols<=nx) {
      vector_resize(vv, cols); nx=cols; 
    } else {
      printf("%d > %d :: \n",cols,nx);
      hoc_execerror("Vector max capacity too small in mrow", 0);
    }
  }
  if (i>=rows) { hoc_execerror("Indices out of bounds", 0); }
  for (j=0;j<nx;j++) { x[j] = y[i*cols+j]; }
  return nx;
}
ENDVERBATIM
 
:* mcol(mat,j,cols)
VERBATIM
static double mcol(void* vv) {
  int i, j, nx, ny, rows, cols;
  double *x, *y;
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  j = (int)*getarg(2);
  cols = (int)*getarg(3); rows=ny/cols;
  if (rows!=nx) { 
    nx=vector_buffer_size(vv);
    if (rows<=nx) {
      vector_resize(vv, rows); nx=rows; 
    } else {
      printf("%d > %d :: ",rows,nx);
      hoc_execerror("Vector max capacity too small in mcol ", 0);
    }
  }
  if (j>=cols) { hoc_execerror("Indices out of bounds", 0); }
  for (i=0;i<nx;i++) { x[i] = y[i*cols+j]; }
  return nx;
}
ENDVERBATIM
 
:* msetrow(mat,i,cols)
VERBATIM
static double msetrow(void* vv) {
  int i, j, nx, ny, rows, cols;
  double *x, *y;
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  i = (int)*getarg(2);
  cols = (int)*getarg(3);
  if (cols!=nx || i>=ny/cols) {
    hoc_execerror("Indices out of bounds", 0);
  }
  for (j=0;j<nx;j++) { y[i*cols+j] = x[j]; }
  return nx;
}
ENDVERBATIM

:* msetcol(mat,j,cols)
VERBATIM
static double msetcol(void* vv) {
  int i, j, nx, ny, rows, cols;
  double *x, *y;
  nx = vector_instance_px(vv, &x);
  ny = vector_arg_px(1, &y);
  j = (int)*getarg(2);
  cols = (int)*getarg(3);
  if (cols!=ny/nx || j>=cols) {
    hoc_execerror("Indices out of bounds", 0);
  }
  for (i=0;i<nx;i++) { y[i*cols+j] = x[i]; }
  return nx;
}
ENDVERBATIM
 
:* mset(i,j,cols,val)
VERBATIM
static double mset(void* vv) {
  int i, j, nx, rows, cols;
  double *x, val;
  nx = vector_instance_px(vv, &x);
  i = (int)*getarg(1);
  j = (int)*getarg(2);
  cols = (int)*getarg(3);
  val = *getarg(4);
  if (i*cols+j >= nx) {
    hoc_execerror("Indices out of bounds", 0);
  }
  return (x[i*cols+j]=val);
}
ENDVERBATIM
 
:* PROCEDURE install_matrix()
PROCEDURE install_matrix() {
  MATRIX_INSTALLED=1
VERBATIM
  /* the list of additional methods */
  install_vector_method("outprod", outprod);
  install_vector_method("mmult", mmult);
  install_vector_method("spmult", spmult);
  install_vector_method("spget", spget);
  install_vector_method("mkspcp", mkspcp);
  install_vector_method("chkspcp", chkspcp);
  install_vector_method("spltp", spltp);
  install_vector_method("transpose", transpose);
  install_vector_method("mprintf", mprintf);
  install_vector_method("mget", mget);
  install_vector_method("mset", mset);
  install_vector_method("mrow", mrow);
  install_vector_method("mcol", mcol);
  install_vector_method("msetrow", msetrow);
  install_vector_method("msetcol", msetcol);
ENDVERBATIM
}

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