An electrophysiological model of GABAergic double bouquet cells (Chrysanthidis et al. 2019)

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Accession:257610
We present an electrophysiological model of double bouquet cells (DBCs) and integrate them into an established cortical columnar microcircuit model that implements a BCPNN (Bayesian Confidence Propagation Neural Network) learning rule. The proposed architecture effectively solves the problem of duplexed learning of inhibition and excitation by replacing recurrent inhibition between pyramidal cells in functional columns of different stimulus selectivity with a plastic disynaptic pathway. The introduction of DBCs improves the biological plausibility of our model, without affecting the model's spiking activity, basic operation, and learning abilities.
Reference:
1 . Chrysanthidis N, Fiebig F, Lansner A (2019) Introducing double bouquet cells into a modular cortical associative memory model Journal of Computational Neuroscience
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 interneuron basket PV GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Abstract integrate-and-fire adaptive exponential (AdEx) neuron; Neocortex layer 2-3 interneuron; Neocortex bitufted interneuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEST;
Model Concept(s): Learning;
Implementer(s): Chrysanthidis, Nikolaos [nchr at kth.se]; Fiebig, Florian [fiebig at kth.se]; Lansner, Anders [ala at kth.se];
Search NeuronDB for information about:  Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 interneuron basket PV GABA cell;
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ChrysanthidisEtAl2019
BCPNN_NEST_Module
module-100725
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loaders
m4
README *
aclocal.m4 *
argz.c *
argz_.h *
config-h.in *
configure *
configure.ac *
COPYING.LIB *
lt__alloc.c *
lt__dirent.c *
lt__strl.c *
lt_dlloader.c *
lt_error.c *
ltdl.c *
ltdl.h *
Makefile.am *
Makefile.in *
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
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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
#else
#  include <config.h>
#endif

#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'

error_t
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;
}


error_t
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;
	      else
		--argz_len;
	    }
	  else
	    *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;
}


error_t
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))
    --before;

  {
    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;
    }
  else
    {
      /* 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;
      else
	return 0;
    }
}


void
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;
	}
    }
}