Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

 Download zip file 
Help downloading and running models
Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
data
distributionPlot
exportfig
fig
figs
mtrand
README
.exrc *
an_m_to.m
an_to.m
barwitherr.m *
btagstats.m *
CImg.h *
constructs. *
constructs.cpp *
constructs.h
csvgraph.m
defaults.m
dir2.m *
gconstructs.cpp *
getspikedata.m *
getsynstate.m *
getsynstate2.m *
graphs.m *
hist_percents.m *
hist_with_errs.m *
interact.m *
kurtos.m *
lamodel
lamodel.cpp
LICENSE *
make_graphs.m *
Makefile *
matlab.mat *
mtrand.cpp *
mtrand.h *
multistats.m *
nextplot.m *
pairstrong.m *
repeated.m *
rotateXLabels.m *
run_to.sh
S2sparse.m *
savefig.m *
scratch.m *
sensitivity.m *
stats.m *
stats.py *
stderr.m *
strong2.m *
strongstrong.m *
submit_lamodel.sh *
three.m *
to.cpp
trevrolls.m *
vis.py *
weastrong.m *
wxglmodel *
wxglmodel.cpp *
wxglmodel.h *
wxmodel.cpp *
wxmodel.h *
                            
// mtrand.h
// C++ include file for MT19937, with initialization improved 2002/1/26.
// Coded by Takuji Nishimura and Makoto Matsumoto.
// Ported to C++ by Jasper Bedaux 2003/1/1 (see http://www.bedaux.net/mtrand/).
// The generators returning floating point numbers are based on
// a version by Isaku Wada, 2002/01/09
//
// Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
//
// 1. Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//
// 3. The names of its contributors may not be used to endorse or promote
//    products derived from this software without specific prior written
//    permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Any feedback is very welcome.
// http://www.math.keio.ac.jp/matumoto/emt.html
// email: matumoto@math.keio.ac.jp
//
// Feedback about the C++ port should be sent to Jasper Bedaux,
// see http://www.bedaux.net/mtrand/ for e-mail address and info.

#ifndef MTRAND_H
#define MTRAND_H

class MTRand_int32 { // Mersenne Twister random number generator
public:
// default constructor: uses default seed only if this is the first instance
  MTRand_int32() { if (!init) seed(5489UL); init = true; }
// constructor with 32 bit int as seed
  MTRand_int32(unsigned long s) { seed(s); init = true; }
// constructor with array of size 32 bit ints as seed
  MTRand_int32(const unsigned long* array, int size) { seed(array, size); init = true; }
// the two seed functions
  void seed(unsigned long); // seed with 32 bit integer
  void seed(const unsigned long*, int size); // seed with array
// overload operator() to make this a generator (functor)
  unsigned long operator()() { return rand_int32(); }
// 2007-02-11: made the destructor virtual; thanks "double more" for pointing this out
  virtual ~MTRand_int32() {} // destructor
protected: // used by derived classes, otherwise not accessible; use the ()-operator
  unsigned long rand_int32(); // generate 32 bit random integer
private:
  static const int n = 624, m = 397; // compile time constants
// the variables below are static (no duplicates can exist)
  static unsigned long state[n]; // state vector array
  static int p; // position in state array
  static bool init; // true if init function is called
// private functions used to generate the pseudo random numbers
  unsigned long twiddle(unsigned long, unsigned long); // used by gen_state()
  void gen_state(); // generate new state
// make copy constructor and assignment operator unavailable, they don't make sense
  MTRand_int32(const MTRand_int32&); // copy constructor not defined
  void operator=(const MTRand_int32&); // assignment operator not defined
};

// inline for speed, must therefore reside in header file
inline unsigned long MTRand_int32::twiddle(unsigned long u, unsigned long v) {
  return (((u & 0x80000000UL) | (v & 0x7FFFFFFFUL)) >> 1)
    ^ ((v & 1UL) ? 0x9908B0DFUL : 0x0UL);
}

inline unsigned long MTRand_int32::rand_int32() { // generate 32 bit random int
  if (p == n) gen_state(); // new state vector needed
// gen_state() is split off to be non-inline, because it is only called once
// in every 624 calls and otherwise irand() would become too big to get inlined
  unsigned long x = state[p++];
  x ^= (x >> 11);
  x ^= (x << 7) & 0x9D2C5680UL;
  x ^= (x << 15) & 0xEFC60000UL;
  return x ^ (x >> 18);
}

// generates double floating point numbers in the half-open interval [0, 1)
class MTRand : public MTRand_int32 {
public:
  MTRand() : MTRand_int32() {}
  MTRand(unsigned long seed) : MTRand_int32(seed) {}
  MTRand(const unsigned long* seed, int size) : MTRand_int32(seed, size) {}
  ~MTRand() {}
  double operator()() {
    return static_cast<double>(rand_int32()) * (1. / 4294967296.); } // divided by 2^32
private:
  MTRand(const MTRand&); // copy constructor not defined
  void operator=(const MTRand&); // assignment operator not defined
};

// generates double floating point numbers in the closed interval [0, 1]
class MTRand_closed : public MTRand_int32 {
public:
  MTRand_closed() : MTRand_int32() {}
  MTRand_closed(unsigned long seed) : MTRand_int32(seed) {}
  MTRand_closed(const unsigned long* seed, int size) : MTRand_int32(seed, size) {}
  ~MTRand_closed() {}
  double operator()() {
    return static_cast<double>(rand_int32()) * (1. / 4294967295.); } // divided by 2^32 - 1
private:
  MTRand_closed(const MTRand_closed&); // copy constructor not defined
  void operator=(const MTRand_closed&); // assignment operator not defined
};

// generates double floating point numbers in the open interval (0, 1)
class MTRand_open : public MTRand_int32 {
public:
  MTRand_open() : MTRand_int32() {}
  MTRand_open(unsigned long seed) : MTRand_int32(seed) {}
  MTRand_open(const unsigned long* seed, int size) : MTRand_int32(seed, size) {}
  ~MTRand_open() {}
  double operator()() {
    return (static_cast<double>(rand_int32()) + .5) * (1. / 4294967296.); } // divided by 2^32
private:
  MTRand_open(const MTRand_open&); // copy constructor not defined
  void operator=(const MTRand_open&); // assignment operator not defined
};

// generates 53 bit resolution doubles in the half-open interval [0, 1)
class MTRand53 : public MTRand_int32 {
public:
  MTRand53() : MTRand_int32() {}
  MTRand53(unsigned long seed) : MTRand_int32(seed) {}
  MTRand53(const unsigned long* seed, int size) : MTRand_int32(seed, size) {}
  ~MTRand53() {}
  double operator()() {
    return (static_cast<double>(rand_int32() >> 5) * 67108864. + 
      static_cast<double>(rand_int32() >> 6)) * (1. / 9007199254740992.); }
private:
  MTRand53(const MTRand53&); // copy constructor not defined
  void operator=(const MTRand53&); // assignment operator not defined
};

#endif // MTRAND_H

Loading data, please wait...