A spatial model of the intermediate superior colliculus (Moren et. al. 2013)

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A spatial model of the intermediate superior colliculus. It reproduces the collicular saccade-generating output profile from NMDA receptor-driven burst neurons, shaped by integrative inhibitory feedback from spreading buildup neuron activity. The model is consistent with the view that collicular activity directly shapes the temporal profile of saccadic eye movements. We use the Adaptive exponential integrate and fire neuron model, augmented with an NMDA-like membrane potential-dependent receptor. In addition, we use a synthetic spike integrator model as a stand-in for a spike-integrator circuit in the reticular formation. NOTE: We use a couple of custom neuron models, so the supplied model file includes an entire version of NEST. I also include a patch that applies to a clean version of the simulator (see the doc/README).
1 . Morén J, Shibata T, Doya K (2013) The mechanism of saccade motor pattern generation investigated by a large-scale spiking neuron model of the superior colliculus. PLoS One 8:e57134 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Connectionist Network;
Brain Region(s)/Organism: Superior colliculus;
Cell Type(s): Abstract integrate-and-fire adaptive exponential (AdEx) neuron;
Gap Junctions:
Receptor(s): NMDA;
Simulation Environment: NEST; Python;
Model Concept(s): Activity Patterns; Bursting; Spatio-temporal Activity Patterns; Action Selection/Decision Making;
Search NeuronDB for information about:  NMDA;
argz.c *
argz_.h *
config-h.in *
configure.ac *
lt__alloc.c *
lt__dirent.c *
lt__strl.c *
lt_dlloader.c *
lt_error.c *
ltdl.c *
ltdl.h *
Makefile.am *
slist.c *
/* argz.c -- argz implementation for non-glibc systems

   Copyright (C) 2004, 2006, 2007, 2008 Free Software Foundation, Inc.
   Written by Gary V. Vaughan, 2004

   NOTE: The canonical source of this file is maintained with the
   GNU Libtool package.  Report bugs to bug-libtool@gnu.org.

GNU Libltdl is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.

As a special exception to the GNU Lesser General Public License,
if you distribute this file as part of a program or library that
is built using GNU Libtool, you may include this file under the
same distribution terms that you use for the rest of that program.

GNU Libltdl is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with GNU Libltdl; see the file COPYING.LIB.  If not, a
copy can be downloaded from  http://www.gnu.org/licenses/lgpl.html,
or obtained by writing to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

#if defined(LTDL) && defined LT_CONFIG_H
#  include LT_CONFIG_H
#  include <config.h>

#include <argz.h>

#include <assert.h>
#include <stddef.h>
#include <stdlib.h>
#include <sys/types.h>
#include <errno.h>
#include <string.h>

#define EOS_CHAR '\0'

argz_append (char **pargz, size_t *pargz_len, const char *buf, size_t buf_len)
  size_t argz_len;
  char  *argz;

  assert (pargz);
  assert (pargz_len);
  assert ((*pargz && *pargz_len) || (!*pargz && !*pargz_len));

  /* If nothing needs to be appended, no more work is required.  */
  if (buf_len == 0)
    return 0;

  /* Ensure there is enough room to append BUF_LEN.  */
  argz_len = *pargz_len + buf_len;
  argz = (char *) realloc (*pargz, argz_len);
  if (!argz)
    return ENOMEM;

  /* Copy characters from BUF after terminating '\0' in ARGZ.  */
  memcpy (argz + *pargz_len, buf, buf_len);

  /* Assign new values.  */
  *pargz = argz;
  *pargz_len = argz_len;

  return 0;

argz_create_sep (const char *str, int delim, char **pargz, size_t *pargz_len)
  size_t argz_len;
  char *argz = 0;

  assert (str);
  assert (pargz);
  assert (pargz_len);

  /* Make a copy of STR, but replacing each occurrence of
     DELIM with '\0'.  */
  argz_len = 1+ strlen (str);
  if (argz_len)
      const char *p;
      char *q;

      argz = (char *) malloc (argz_len);
      if (!argz)
	return ENOMEM;

      for (p = str, q = argz; *p != EOS_CHAR; ++p)
	  if (*p == delim)
	      /* Ignore leading delimiters, and fold consecutive
		 delimiters in STR into a single '\0' in ARGZ.  */
	      if ((q > argz) && (q[-1] != EOS_CHAR))
		*q++ = EOS_CHAR;
	    *q++ = *p;
      /* Copy terminating EOS_CHAR.  */
      *q = *p;

  /* If ARGZ_LEN has shrunk to nothing, release ARGZ's memory.  */
  if (!argz_len)
    argz = (free (argz), (char *) 0);

  /* Assign new values.  */
  *pargz = argz;
  *pargz_len = argz_len;

  return 0;

argz_insert (char **pargz, size_t *pargz_len, char *before, const char *entry)
  assert (pargz);
  assert (pargz_len);
  assert (entry && *entry);

  /* No BEFORE address indicates ENTRY should be inserted after the
     current last element.  */
  if (!before)
    return argz_append (pargz, pargz_len, entry, 1+ strlen (entry));

  /* This probably indicates a programmer error, but to preserve
     semantics, scan back to the start of an entry if BEFORE points
     into the middle of it.  */
  while ((before > *pargz) && (before[-1] != EOS_CHAR))

    size_t entry_len	= 1+ strlen (entry);
    size_t argz_len	= *pargz_len + entry_len;
    size_t offset	= before - *pargz;
    char   *argz	= (char *) realloc (*pargz, argz_len);

    if (!argz)
      return ENOMEM;

    /* Make BEFORE point to the equivalent offset in ARGZ that it
       used to have in *PARGZ incase realloc() moved the block.  */
    before = argz + offset;

    /* Move the ARGZ entries starting at BEFORE up into the new
       space at the end -- making room to copy ENTRY into the
       resulting gap.  */
    memmove (before + entry_len, before, *pargz_len - offset);
    memcpy  (before, entry, entry_len);

    /* Assign new values.  */
    *pargz = argz;
    *pargz_len = argz_len;

  return 0;

char *
argz_next (char *argz, size_t argz_len, const char *entry)
  assert ((argz && argz_len) || (!argz && !argz_len));

  if (entry)
      /* Either ARGZ/ARGZ_LEN is empty, or ENTRY points into an address
	 within the ARGZ vector.  */
      assert ((!argz && !argz_len)
	      || ((argz <= entry) && (entry < (argz + argz_len))));

      /* Move to the char immediately after the terminating
	 '\0' of ENTRY.  */
      entry = 1+ strchr (entry, EOS_CHAR);

      /* Return either the new ENTRY, or else NULL if ARGZ is
	 exhausted.  */
      return (entry >= argz + argz_len) ? 0 : (char *) entry;
      /* This should probably be flagged as a programmer error,
	 since starting an argz_next loop with the iterator set
	 to ARGZ is safer.  To preserve semantics, handle the NULL
	 case by returning the start of ARGZ (if any).  */
      if (argz_len > 0)
	return argz;
	return 0;

argz_stringify (char *argz, size_t argz_len, int sep)
  assert ((argz && argz_len) || (!argz && !argz_len));

  if (sep)
      --argz_len;		/* don't stringify the terminating EOS */
      while (--argz_len > 0)
	  if (argz[argz_len] == EOS_CHAR)
	    argz[argz_len] = sep;