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

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Accession:146949
"... 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."
Reference:
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;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Laminar Connectivity;
Implementer(s): Lytton, William [bill.lytton at downstate.edu]; Neymotin, Sam [Samuel.Neymotin at nki.rfmh.org]; Shepherd, Gordon MG [g-shepherd at northwestern.edu]; Chadderdon, George [gchadder3 at gmail.com]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex M1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
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src
README
infot.mod *
intf6.mod *
intfsw.mod *
matrix.mod
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
boxes.hoc *
col.hoc
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
gcelldata.hoc
gmgs102.nqs
grvec.hoc *
infot.hoc *
init.hoc
intfsw.hoc *
labels.hoc *
load.py
local.hoc *
main.hoc
misc.h *
miscfuncs.py
network.hoc
neuroplot.py *
nload.hoc
nqs.hoc *
nqsnet.hoc
nrnoc.hoc *
params.hoc
run.hoc
samutils.hoc *
saveoutput.hoc
saveweights.hoc
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
wdmaps2.nqs
xgetargs.hoc *
                            
: $Id: misc.mod,v 1.24 2011/10/14 15:00:26 samn Exp $

COMMENT
Misc. routines:
sassign() // assign a string from system
dassign()// assign a double
nokill() // chatch SIGHUP
prtime() // gives date/time
fspitchar(c,file) // sends single char to a file
spitchar(c)       // sends single char to stdout: eg c=1 => ^A
file_exist(file) // returns 1 if filename exists
hocgetc(file) // get single char from a file

  Note that with a SUFFIX equal to "nothing" these functions do not
have a suffix in hoc.  Thus to call sassign() in hoc use simply type
"sassign()" <- without the quotes.

    file_exist(filename)
        - returns 1 if filename exists

    sassign()  (string assign, written by Bill Lytton)
        - This routine is used to set a string in Hoc to something that has
          been returned by a system call.  sassign("name","shell_call ...")
          will produce a file called "sassign" in the cwd that will contain
          a hoc call that sets string 'name' to the result of shell_call 
          which should be a string.
        
    dassign()  (double assign, written and used by Bill Lytton)
        - This routine is used to set a variable in Hoc to something that has
          been returned by a system call.  sassign("name","shell_call ...")
          will produce a file called "dassign" in the cwd that will contain
          a hoc call that sets variable 'name' to the result of shell_call 
          which should be a number.

ENDCOMMENT
                           
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

NEURON {
    SUFFIX nothing
}

VERBATIM
#include <unistd.h>     /* F_OK     */
#include <errno.h>      /* errno    */
#include <signal.h>
#include <sys/types.h>         /* MUST REMEMBER THIS */
#include <time.h>
#include <stdio.h>
#include <limits.h>
extern int hoc_is_tempobj(int narg);
ENDVERBATIM

:* FUNCTION file_exist()
FUNCTION file_exist() {
VERBATIM
    /* Returns TRUE if file exists, if file not exist the need to reset
       errno else will get a nrnoc error.  Seems to be a problem even
       if I don't include <errno.h> */

    char *gargstr(), *filename;

    filename = gargstr(1);

    if (*filename && !access(filename, F_OK)) {
        _lfile_exist = 1;

    } else {
        /* Errno set to 2 when file not found */
        errno = 0;

        _lfile_exist = 0;
    }
ENDVERBATIM
}

FUNCTION istmpobj () {
VERBATIM
  _listmpobj=hoc_is_tempobj_arg(1);
ENDVERBATIM  
}

:* PROCEDURE sassign()
FUNCTION sassign() {
VERBATIM
    FILE *pipein;
    char string[BUFSIZ], **strname, *syscall;
    char** hoc_pgargstr();

    strname = hoc_pgargstr(1);
    syscall = gargstr(2);

    if( !(pipein = popen(syscall, "r"))) {
        fprintf(stderr,"System call failed\n");
        return 0; 
    }
    
    if (fgets(string,BUFSIZ,pipein) == NULL) {
        fprintf(stderr,"System call did not return a string\n");
        pclose(pipein); return 0;
    }

    /*  assign_hoc_str(strname, string, 0); */
    hoc_assign_str(strname, string);

    pclose(pipein);
    errno = 0;
    return 0;
ENDVERBATIM
}

:* PROCEDURE dassign() 
FUNCTION dassign() {
VERBATIM
    FILE *pipein, *outfile;
    char *strname, *syscall;
    double num;

    strname = gargstr(1);
    syscall = gargstr(2);

    if ( !(outfile = fopen("dassign","w"))) {
        fprintf(stderr,"Can't open output file dassign\n");
        return 0; 
    }

    if( !(pipein = popen(syscall, "r"))) {
        fprintf(stderr,"System call failed\n");
        fclose(outfile); return 0; 
    }
    
    if (fscanf(pipein,"%lf",&num) != 1) {
        fprintf(stderr,"System call did not return a number\n");
        fclose(outfile); pclose(pipein); return 0; 
    }

    fprintf(outfile,"%s=%g\n",strname,num);
    fprintf(outfile,"system(\"rm dassign\")\n");

    fclose(outfile); pclose(pipein);
    errno = 0;
    return 0;
ENDVERBATIM
}

:* PROCEDURE nokill() 
: nohup
PROCEDURE nokill() {
VERBATIM
  signal(SIGHUP, SIG_IGN);
ENDVERBATIM
}

:* FUNCTION prtime()
FUNCTION prtime () {
VERBATIM
_lprtime = clock();
ENDVERBATIM
}

:* FUNCTION now ()
FUNCTION now () {
VERBATIM
  _lnow = time((time_t*)0);
  _lnow -= (12784) * 24*60*60; // time from the Epoch to 01/01/05
ENDVERBATIM
}

:* FUNCTION sleepfor (seconds[,nanoseconds])
: returns 0 on success, -1 on failure, nanosecond arg should be < 1 second
FUNCTION sleepfor (sec) {
VERBATIM
  struct timespec ts;
  ts.tv_sec = (time_t)_lsec;
  ts.tv_nsec = ifarg(2)?(long)*getarg(2):(long)0;
  return (double) nanosleep(&ts,(struct timespec*)0);
ENDVERBATIM
}

:* PROCEDURE spitchar
PROCEDURE spitchar(c) {
VERBATIM
{	
  printf("%c", (int)_lc);
}
ENDVERBATIM
}

:* PROCEDURE spitchar
VERBATIM
static char *pmlc;
ENDVERBATIM

PROCEDURE mymalloc(sz) {
VERBATIM
{ 
  size_t x,y;
  x=(size_t)_lsz;
  pmlc=(char *)malloc(x);
  printf("Did %ld: %x\n",x,pmlc);
  y=(unsigned int)_lsz-1;
  pmlc[y]=(char)97;
  printf("WRITE/READ 'a': "); 
  printf("%c\n",pmlc[y]);
  if (ifarg(2)) free(pmlc); else printf("Use unmalloc() to free memory\n");
}
ENDVERBATIM
}

PROCEDURE unmalloc() {
VERBATIM
  free(pmlc);
ENDVERBATIM
}

:* FUNCTION hocgetc
FUNCTION hocgetc() {
VERBATIM
{	
  FILE* f, *hoc_obj_file_arg();
  f = hoc_obj_file_arg(1);
  _lhocgetc = (double)getc(f);
}
ENDVERBATIM
}

PROCEDURE pwd() {
  VERBATIM
  {char cwd[1000],cmd[1200];
  getcwd(cwd, 1000);
  sprintf(cmd, "execute1(\"strdef cwd\")\n");         hoc_oc(cmd);
  sprintf(cmd, "execute1(\"cwd=\\\"%s\\\"\")\n",cwd); hoc_oc(cmd);
  }
  ENDVERBATIM
}







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