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 [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
/
b09jan08
README.html
intf_.mod
misc.mod *
nstim.mod *
stats.mod
vecst.mod
misc.h
mosinit.hoc
screenshot.jpg
                            
: $Id: misc.mod,v 1.23 2007/12/07 21:46:51 billl 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()
PROCEDURE 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; 
    }
    
    if (fgets(string,BUFSIZ,pipein) == NULL) {
        fprintf(stderr,"System call did not return a string\n");
        pclose(pipein); return;
    }

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

    pclose(pipein);
    errno = 0;
ENDVERBATIM
}

:* PROCEDURE dassign() 
PROCEDURE 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; 
    }

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

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

    fclose(outfile); pclose(pipein);
    errno = 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
}

:* PROCEDURE sleepfor ()
PROCEDURE sleepfor (sec) {
VERBATIM
  struct timespec ts;
  ts.tv_sec = (time_t)_lsec;
  ts.tv_nsec = (long)0;
  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
}

Lytton WW, Neymotin SA, Hines ML (2008) The virtual slice setup. J Neurosci Methods 171:309-15[PubMed]

References and models cited by this paper

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Carnevale NT, Hines ML (2006) The NEURON Book

Efroni S, Harel D, Cohen IR (2005) Reactive animation: Realistic modeling of complex dynamic systems Computer 38:38-47

Efroni S, Harel D, Cohen IR (2007) Emergent dynamics of thymocyte development and lineage determination. PLoS Comput Biol 3:e13 [PubMed]

Hereld M, Stevens RL, Lee HC, van Drongelen W (2007) Framework for interactive million-neuron simulation. J Clin Neurophysiol 24:189-96 [PubMed]

Hines ML, Carnevale NT (2004) Discrete event simulation in the NEURON environment. Neurocomputing 58-60:1117-1122 [Journal]

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Lytton W, Hines M (2004) Hybrid neural networks - combining abstract and realistic neural units. Conf Proc IEEE Eng Med Biol Soc 6:3996-8 [PubMed]

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

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Lytton WW, Omurtag A, Neymotin SA, Hines ML (2008) Just in time connectivity for large spiking networks Neural Comput 20(11):2745-56 [Journal] [PubMed]

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Lytton WW, Stewart M (2005) A rule-based firing model for neural networks Int J Bioelectromagn 7:47-50

Lytton WW, Stewart M (2006) Rule-based firing for network simulations. Neurocomputing 69:1160-1164

Lytton WW, Stewart M (2007) Data mining through simulation. Methods Mol Biol 401:155-66 [PubMed]

Lytton WW, Stewart M, Hines ML (2008) Simulation of large networks: technique and progress Computational Neuroscience in Epilepsy, Soltesz I:Staley K, ed. pp.3

Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]

   [241 reconstructed morphologies on NeuroMorpho.Org]

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [Journal] [PubMed]

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ModelDB (2007) http:--senselab.med.yale.edu-senselab-ModelDB

Rowat PF, Selverston AI (1993) Modeling the gastric mill central pattern generator of the lobster with a relaxation-oscillator network. J Neurophysiol 70:1030-53 [Journal] [PubMed]

Web_site_neuron (2007) http:--www.neuron.yale.edu

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 [Journal] [PubMed]

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Chadderdon GL, Neymotin SA, Kerr CC, Lytton WW (2012) Reinforcement learning of targeted movement in a spiking neuronal model of motor cortex PLoS ONE 2012 7(10):e47251 [Journal]

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Kerr CC, Van Albada SJ, Neymotin SA, Chadderdon GL, Robinson PA, Lytton WW (2013) Cortical information flow in Parkinson's disease: a composite network-field model. Front Comput Neurosci 7:39:1-14 [Journal] [PubMed]

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(29 refs)