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

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Accession:168866
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).
Reference:
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]
Citations  Citation Browser
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;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEST; Python;
Model Concept(s): Activity Patterns; Bursting; Spatio-temporal Activity Patterns; Action Selection/Decision Making;
Implementer(s):
Search NeuronDB for information about:  NMDA;
/
NEST-SCModel
nest-2.2.2
libltdl
loaders
dld_link.c *
dlopen.c *
dyld.c *
load_add_on.c *
loadlibrary.c *
preopen.c *
shl_load.c *
                            
/* loader-preopen.c -- emulate dynamic linking using preloaded_symbols

   Copyright (C) 1998, 1999, 2000, 2004, 2006,
                 2007, 2008 Free Software Foundation, Inc.
   Written by Thomas Tanner, 1998

   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.
*/

#include "lt__private.h"
#include "lt_dlloader.h"

/* Use the preprocessor to rename non-static symbols to avoid namespace
   collisions when the loader code is statically linked into libltdl.
   Use the "<module_name>_LTX_" prefix so that the symbol addresses can
   be fetched from the preloaded symbol list by lt_dlsym():  */
#define get_vtable	preopen_LTX_get_vtable

LT_BEGIN_C_DECLS
LT_SCOPE lt_dlvtable *get_vtable (lt_user_data loader_data);
LT_END_C_DECLS


/* Boilerplate code to set up the vtable for hooking this loader into
   libltdl's loader list:  */
static int	 vl_init  (lt_user_data loader_data);
static int	 vl_exit  (lt_user_data loader_data);
static lt_module vm_open  (lt_user_data loader_data, const char *filename,
                           lt_dladvise advise);
static int	 vm_close (lt_user_data loader_data, lt_module module);
static void *	 vm_sym   (lt_user_data loader_data, lt_module module,
			  const char *symbolname);

static lt_dlvtable *vtable = 0;

/* Return the vtable for this loader, only the name and sym_prefix
   attributes (plus the virtual function implementations, obviously)
   change between loaders.  */
lt_dlvtable *
get_vtable (lt_user_data loader_data)
{
  if (!vtable)
    {
      vtable = (lt_dlvtable *) lt__zalloc (sizeof *vtable);
    }

  if (vtable && !vtable->name)
    {
      vtable->name		= "lt_preopen";
      vtable->sym_prefix	= 0;
      vtable->module_open	= vm_open;
      vtable->module_close	= vm_close;
      vtable->find_sym		= vm_sym;
      vtable->dlloader_init	= vl_init;
      vtable->dlloader_exit	= vl_exit;
      vtable->dlloader_data	= loader_data;
      vtable->priority		= LT_DLLOADER_PREPEND;
    }

  if (vtable && (vtable->dlloader_data != loader_data))
    {
      LT__SETERROR (INIT_LOADER);
      return 0;
    }

  return vtable;
}



/* --- IMPLEMENTATION --- */


/* Wrapper type to chain together symbol lists of various origins.  */
typedef struct symlist_chain
{
  struct symlist_chain *next;
  const lt_dlsymlist   *symlist;
} symlist_chain;


static int add_symlist   (const lt_dlsymlist *symlist);
static int free_symlists (void);

/* The start of the symbol lists chain.  */
static symlist_chain	       *preloaded_symlists		= 0;

/* A symbol list preloaded before lt_init() was called.  */
static const	lt_dlsymlist   *default_preloaded_symbols	= 0;


/* A function called through the vtable to initialise this loader.  */
static int
vl_init (lt_user_data LT__UNUSED loader_data)
{
  int errors = 0;

  preloaded_symlists = 0;
  if (default_preloaded_symbols)
    {
      errors = lt_dlpreload (default_preloaded_symbols);
    }

  return errors;
}


/* A function called through the vtable when this loader is no
   longer needed by the application.  */
static int
vl_exit (lt_user_data LT__UNUSED loader_data)
{
  vtable = NULL;
  free_symlists ();
  return 0;
}


/* A function called through the vtable to open a module with this
   loader.  Returns an opaque representation of the newly opened
   module for processing with this loader's other vtable functions.  */
static lt_module
vm_open (lt_user_data LT__UNUSED loader_data, const char *filename,
         lt_dladvise LT__UNUSED advise)
{
  symlist_chain *lists;
  lt_module	 module = 0;

  if (!preloaded_symlists)
    {
      LT__SETERROR (NO_SYMBOLS);
      goto done;
    }

  /* Can't use NULL as the reflective symbol header, as NULL is
     used to mark the end of the entire symbol list.  Self-dlpreopened
     symbols follow this magic number, chosen to be an unlikely
     clash with a real module name.  */
  if (!filename)
    {
      filename = "@PROGRAM@";
    }

  for (lists = preloaded_symlists; lists; lists = lists->next)
    {
      const lt_dlsymlist *symbol;
      for (symbol= lists->symlist; symbol->name; ++symbol)
	{
	  if (!symbol->address && streq (symbol->name, filename))
	    {
	      /* If the next symbol's name and address is 0, it means
		 the module just contains the originator and no symbols.
		 In this case we pretend that we never saw the module and
	         hope that some other loader will be able to load the module
	         and have access to its symbols */
	      const lt_dlsymlist *next_symbol = symbol +1;
	      if (next_symbol->address && next_symbol->name)
		{
	          module = (lt_module) lists->symlist;
	          goto done;
		}
	    }
	}
    }

  LT__SETERROR (FILE_NOT_FOUND);

 done:
  return module;
}


/* A function called through the vtable when a particular module
   should be unloaded.  */
static int
vm_close (lt_user_data LT__UNUSED loader_data, lt_module LT__UNUSED module)
{
  /* Just to silence gcc -Wall */
  module = 0;
  return 0;
}


/* A function called through the vtable to get the address of
   a symbol loaded from a particular module.  */
static void *
vm_sym (lt_user_data LT__UNUSED loader_data, lt_module module, const char *name)
{
  lt_dlsymlist	       *symbol = (lt_dlsymlist*) module;

  symbol +=2;			/* Skip header (originator then libname). */

  while (symbol->name)
    {
      if (streq (symbol->name, name))
	{
	  return symbol->address;
	}

    ++symbol;
  }

  LT__SETERROR (SYMBOL_NOT_FOUND);

  return 0;
}



/* --- HELPER FUNCTIONS --- */


/* The symbol lists themselves are not allocated from the heap, but
   we can unhook them and free up the chain of links between them.  */
static int
free_symlists (void)
{
  symlist_chain *lists;

  lists = preloaded_symlists;
  while (lists)
    {
      symlist_chain *next = lists->next;
      FREE (lists);
      lists = next;
    }
  preloaded_symlists = 0;

  return 0;
}

/* Add a new symbol list to the global chain.  */
static int
add_symlist (const lt_dlsymlist *symlist)
{
  symlist_chain *lists;
  int		 errors   = 0;

  /* Search for duplicate entries:  */
  for (lists = preloaded_symlists;
       lists && lists->symlist != symlist; lists = lists->next)
    /*NOWORK*/;

  /* Don't add the same list twice:  */
  if (!lists)
    {
      symlist_chain *tmp = (symlist_chain *) lt__zalloc (sizeof *tmp);

      if (tmp)
	{
	  tmp->symlist = symlist;
	  tmp->next = preloaded_symlists;
	  preloaded_symlists = tmp;
	}
      else
	{
	  ++errors;
	}
    }

  return errors;
}



/* --- PRELOADING API CALL IMPLEMENTATIONS --- */


/* Save a default symbol list for later.  */
int
lt_dlpreload_default (const lt_dlsymlist *preloaded)
{
  default_preloaded_symbols = preloaded;
  return 0;
}


/* Add a symbol list to the global chain, or with a NULL argument,
   revert to just the default list.  */
int
lt_dlpreload (const lt_dlsymlist *preloaded)
{
  int errors = 0;

  if (preloaded)
    {
      errors = add_symlist (preloaded);
    }
  else
    {
      free_symlists();

      if (default_preloaded_symbols)
	{
	  errors = lt_dlpreload (default_preloaded_symbols);
	}
    }

  return errors;
}


/* Open all the preloaded modules from the named originator, executing
   a callback for each one.  If ORIGINATOR is NULL, then call FUNC for
   each preloaded module from the program itself.  */
int
lt_dlpreload_open (const char *originator, lt_dlpreload_callback_func *func)
{
  symlist_chain *list;
  int		 errors = 0;
  int		 found  = 0;

  /* For each symlist in the chain...  */
  for (list = preloaded_symlists; list; list = list->next)
    {
      /* ...that was preloaded by the requesting ORIGINATOR... */
      if ((originator && streq (list->symlist->name, originator))
          || (!originator && streq (list->symlist->name, "@PROGRAM@")))
	{
	  const lt_dlsymlist *symbol;
	  unsigned int idx = 0;

	  ++found;

	  /* ...load the symbols per source compilation unit:
	     (we preincrement the index to skip over the originator entry)  */
	  while ((symbol = &list->symlist[++idx])->name != 0)
	    {
	      if ((symbol->address == 0)
		  && (strneq (symbol->name, "@PROGRAM@")))
		{
		  lt_dlhandle handle = lt_dlopen (symbol->name);
		  if (handle == 0)
		    {
		      ++errors;
		    }
		  else
		    {
		      errors += (*func) (handle);
		    }
		}
	    }
	}
    }

  if (!found)
    {
      LT__SETERROR(CANNOT_OPEN);
      ++errors;
    }

  return errors;
}