From 00b209240138660db1ded3ef3870023964ce6e4e Mon Sep 17 00:00:00 2001
From: Jan Huwald <jh@sotun.de>
Date: Mon, 7 May 2012 21:53:27 +0200
Subject: Initial commit


diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..55c9aac
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,46 @@
+.PHONY: all
+all:
+	@echo "All does not exist\nChoose of:\n\tbackup\t- safe code and model definition\n\tclean\n\tcode\t- create code for all simulations\ndata\t- plain data for all models\n\tresults\t- graphs & co (what you expect when typing \"make all\")"
+
+.PHONY: backup
+BAKDIR="BAK/`date '+%Y-%m-%d_%s'`"
+backup: clean
+	mkdir -p ${BAKDIR}
+	cp -a Makefile code model_input ${BAKDIR}
+
+.PHONY: clean
+clean:
+	rm -f *~
+	cd code && make clean
+
+.PHONY: code
+code:
+	cd code && make
+
+.PHONY: input
+input: code
+	cd model_input && make
+
+.PHONY: data
+data: code input data/leakyif_test/timestamp
+
+.PHONY: results
+results: data
+	@echo NOT IMPLEMENTED && false
+
+# HINT: the dataset depends on the executable it is using (simulator might change) as well as on the data sources
+#	It also depends on a timestamp to know if the experiment is outdated
+
+# a test of the leakyif model with some random input (mostly to test the simulator and toolchain)
+INPUTFILES_LEAKYIF_TEST=model_input/neurons/if/1000_nocharge \
+			model_input/topology/if/1000_random \
+			model_input/spikes/1000N_10s_10Hz_random \
+			model_input/global/if/default
+data/leakyif_test/timestamp: code code/core/sim-if $(INPUTFILES_LEAKYIF_TEST) model_input/trace/10s_10ms_all
+	-rm -Rf data/leakyif_test
+	mkdir -p data/leakyif_test
+	./code/glue/sim-wrapper if \
+		$(INPUTFILES_LEAKYIF_TEST) \
+		data/leakyif_test/neuron data/leakyif_test/synapse data/leakyif_test/spikes data/leakyif_test/global \
+		model_input/trace/10s_10ms_all
+	touch data/leakyif_test/timestamp
diff --git a/code/Makefile b/code/Makefile
new file mode 100644
index 0000000..804a0ec
--- /dev/null
+++ b/code/Makefile
@@ -0,0 +1,9 @@
+.PHONY: all clean
+
+SUBDIRS=core trainer matlab 
+
+all:
+	for I in $(SUBDIRS); do cd $$I; make; cd ..; done
+
+clean:
+	for I in $(SUBDIRS); do cd $$I; make clean; cd ..; done
diff --git a/code/anatool/plot_spikes b/code/anatool/plot_spikes
new file mode 100755
index 0000000..58fe722
--- /dev/null
+++ b/code/anatool/plot_spikes
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+(
+    if [ $# -eq 1 ]; then
+	echo "set xrange [0:$1]"
+    fi
+    if [ $# -eq 2 ]; then
+	echo "set xrange [$1:$2]"
+    fi
+    echo "plot 'spikes.out' using 1:2 with dots"
+) | gnuplot -persist
+
diff --git a/code/core/Makefile b/code/core/Makefile
new file mode 100644
index 0000000..df0dd28
--- /dev/null
+++ b/code/core/Makefile
@@ -0,0 +1,57 @@
+# HINT: the paradigma is not to create object files to allow all otpimizations
+#	take place even though the code is scattere across many files
+
+CC=g++
+CCFLAGS=-O3 -ggdb
+LDFLAGS=
+INCLUDE=-I/home/huwald/src/boost
+
+# flags to test
+# -ffast-math -fno-finite-math-only
+
+# debug options
+#   normal program:
+#DEBUGOPTS=
+#   verbose status line for every (!) spike:
+DEBUGOPTS=-DDEBUG_STATUSLINE
+#   enale profiling:
+#DEBUGOPTS=-pg
+
+# list of files every build depends on
+#BASE_SRC_FILES=neuron.cpp simulate.cpp synapse.cpp
+BASE_SRC_FILES=\
+	model_switch.h \
+	reward.h \
+	reward.cpp \
+	event.h \
+	event.cpp \
+	interface.h \
+	interface.cpp \
+	min.h \
+	max.h \
+	neuron.cpp \
+	neuron.h \
+	simulate.cpp \
+	simulate.h \
+	synapse.cpp \
+	synapse.h \
+	tracepoints.h \
+	tracepoints.cpp \
+	fileutils.cpp
+
+.PHONY: all clean wordcount
+
+all: sim print_defaults
+
+clean:
+	rm -f *~ massif.*.* sim print_defaults
+
+
+sim: $(BASE_SRC_FILES) Makefile
+	$(CC) -o $@ $(CCFLAGS) simulate.cpp $(INCLUDE) $(LDFLAGS) $(DEBUGOPTS) -DMODEL_`echo $* | tr '[:lower:]' '[:upper:]'`
+
+print_defaults: $(BASE_SRC_FILES) print_defaults.cpp
+	$(CC) -o $@ $(CCFLAGS) print_defaults.cpp $(LDFLAGS) $(DEBUGOPTS) -DMODEL_`echo $* | tr '[:lower:]' '[:upper:]'`
+
+wordcount:
+	wc *h *cpp Makefile
diff --git a/code/core/bin.cpp b/code/core/bin.cpp
new file mode 100644
index 0000000..e93e4c8
--- /dev/null
+++ b/code/core/bin.cpp
@@ -0,0 +1,6 @@
+#include "bin.h"
+
+void Bin::bin(int neuron) {
+  if (neurons->count(neuron))
+    count++;
+}
diff --git a/code/core/bin.h b/code/core/bin.h
new file mode 100644
index 0000000..302df56
--- /dev/null
+++ b/code/core/bin.h
@@ -0,0 +1,15 @@
+#ifndef BIN_H
+#define BIN_H
+
+#include <set>
+
+class Bin {
+public:
+  Bin(std::set<int> * neurons) : neurons(neurons), count(0) {}
+  void bin(int neuron);
+
+  std::set<int> * neurons;
+  int count;
+};
+
+#endif // BIN_H
diff --git a/code/core/event.cpp b/code/core/event.cpp
new file mode 100644
index 0000000..cb6f5ff
--- /dev/null
+++ b/code/core/event.cpp
@@ -0,0 +1,128 @@
+#include "simulate.h"
+
+#include "event.h"
+
+void Event::execute() {
+  switch (type) {
+  case 0:
+    ((InternalSpike*) this)->execute();
+    break;
+
+  case 1:
+    ((ExternalSpike*) this)->execute();
+    break;
+
+  case 2:
+    ((ExternalNoise*) this)->execute();
+    break;
+
+  case 3:
+    ((IntrinsicNeuron*) this)->execute();
+    break;
+
+  case 4:
+    ((VirtualEvent*) this)->vexecute();
+    break;
+  }
+}
+
+void Event::free() {
+  switch (type) {
+  case 0:
+    delete (InternalSpike*) this;
+    break;
+
+  case 1:
+    delete (ExternalSpike*) this;
+    break;
+
+  case 2:
+    delete (ExternalNoise*) this;
+    break;
+
+  case 3:
+    delete (IntrinsicNeuron*) this;
+    break;
+
+  case 4:
+    delete (VirtualEvent*) this;
+    break;
+  }
+}
+
+// comparison of two events regarding their order in the event list; spike events are processed prior to non-spike events (as spikes are incoming and non-spike are intrinsic and depending on all events up to the present)
+bool Event::operator>(Event &e) {
+  return (time > e.time) || ((time == e.time) && (type > e.type));
+}
+
+void Spike::execute() {
+    double nextEventTime = s.neurons[dst].processCurrent(time, current);
+
+    // check if there is an event to occur
+    if (nextEventTime != INFINITY)
+      s.addEvent(new IntrinsicNeuron(nextEventTime, dst));
+}
+
+void ExternalSpike::execute() {
+  // exec common spike code
+  ((Spike *) this)->execute();
+}
+
+void InternalSpike::execute() {
+  // the spike has to be registered as delieverd in the sending synapse
+  synapse->lastSpike = time;
+  if (synapse->firstSpike == -INFINITY)
+    synapse->firstSpike = time;
+
+  // exec common spike code
+  ((Spike *) this)->execute();
+
+  // synaptic scaling
+  s.neurons[dst].normalizeWeight(g.sumWeight);
+}
+
+void IntrinsicNeuron::execute() {
+  // check if a spike does occur
+  bool spikeDoesOccur;
+  double nextEventTime = s.neurons[dst].generateSpike(time, spikeDoesOccur);
+
+  // check if a spike should be generated
+  if (!spikeDoesOccur)
+    return;
+  
+  // add next intrinsic event
+  if (nextEventTime != INFINITY)
+    s.addEvent(new IntrinsicNeuron(nextEventTime, dst));
+  
+  // create the spike for every neuron where it will be recieved
+  for (SynapseDstList::iterator i = s.neurons[dst].sout.begin(); i != s.neurons[dst].sout.end(); i++) {
+    double ntime = time, ncurrent;
+    i->computePostsynapticPulse(ntime, ncurrent);
+    s.addEvent(new InternalSpike(ntime, i->dst, ncurrent, &(*i)));
+  }
+
+  // check if we should output a spike of this neuron
+  for (s.spikeOIfList.iterator i = s.spikeOIfList.begin(); i != s.spikeOIfList.end(); i++)
+    if (i->isContained(dst)) {
+      SpikeMUX s(dst, time);
+      i->pushObject(s);
+    }
+
+  // bin spikes
+  for (std::set<Bin*>::iterator bin = s.binSets.begin(); bin != s.to.traceBinSets.end(); bin++)
+    (*bin)->bin(dst);
+}
+
+void ExternalNoise::execute() {
+  // pick a random neuron to send noise to (using a temporary event)
+  s.addEvent(new ExternalSpike(time, rand() % (s.numNeurons * 4 / 5), g.en_current));
+
+  // select the next timepoint from a poisson process
+  s.addEvent(new ExternalNoise(time - (log(1.0 - drand48()) / (g.en_freq * s.numNeurons))));
+}
+
+virtual void GlobalUpdate::vexecute() {
+  static const double td = 0.001;
+  g.evolve(td);
+  s.addEvent(new GlobalUpdate(time + td));
+}
diff --git a/code/core/event.h b/code/core/event.h
new file mode 100644
index 0000000..20d348a
--- /dev/null
+++ b/code/core/event.h
@@ -0,0 +1,74 @@
+#ifndef EVENT_H
+#define EVENT_H
+
+class Event {
+public:
+  double time;
+  int type;
+
+  Event(double ti, int ty) : time(ti), type(ty) {}
+  void execute();
+  void free();
+  bool operator>(Event &e1); // comparison of two events regarding their order in the event list; spike events are processed prior to non-spike events (as spikes are incoming and non-spike are intrinsic and depending on all events up to the present)
+
+private:
+  Event() {};
+};
+
+class Spike : public Event {
+public:
+  int dst;
+  double current;
+
+  Spike(double time, int type, int dst, double current) : Event(time, type), dst(dst), current(current) {}
+  void execute();
+};
+
+
+class ExternalSpike : public Spike {
+public:
+  ExternalSpike(double time, int dst, double current) : Spike(time, 1, dst, current) {}
+  void execute();
+};
+
+class InternalSpike : public Spike {
+public:
+  Synapse *synapse;
+
+  InternalSpike(double time, int dst, double current, Synapse *synapse) : Spike(time, 0, dst, current), synapse(synapse) {}
+  void execute();
+};
+
+class IntrinsicNeuron : public Event {
+public:
+  int dst;
+
+  IntrinsicNeuron(double time, int dst) : Event(time, 3), dst(dst) {}
+  void execute();
+};
+
+class ExternalNoise : public Event {
+public:
+  ExternalNoise(double time) : Event(time, 2) {}
+  void execute();
+};
+
+class VirtualEvent : public Event {
+public:
+  VirtualEvent(double time) : Event(time, 4) {}
+  virtual void vexecute() {}
+  virtual ~VirtualEvent() {}
+};
+
+class GlobalUpdate : public VirtualEvent {
+public:
+  GlobalUpdate(double time) : VirtualEvent(time) {}
+  virtual void vexecute();
+};
+
+class PEventGreater {
+public:
+  bool operator() (Event *e1, Event *e2) { return *e1 > *e2; }
+};
+
+#endif // EVENT_H
diff --git a/code/core/fileutils.cpp b/code/core/fileutils.cpp
new file mode 100644
index 0000000..9d080ce
--- /dev/null
+++ b/code/core/fileutils.cpp
@@ -0,0 +1,37 @@
+#include <string.h>
+#include <stdlib.h>
+
+#include "fileutils.h"
+
+// direction is either false=input or true=output and used to overload parameter '-'
+FILE *fd_magic(char *str, bool direction) {
+  static bool usedDir[2] = { false, false };
+
+  // check if stdin/-out is wanted
+  if (strcmp(str, "-") == 0) {
+    // check if we already used this
+    if (usedDir[direction]) {
+      fprintf(stderr, "stdin/-out cannot be used twice\n");
+      exit(-1);
+    }
+
+    // mark that we used it and return in
+    usedDir[direction] = true;
+    return direction ? stdout : stdin;
+  }
+
+  // check if stdout is wanted
+  if (strcmp(str, "0") == 0) {
+    // replace filename and proceed
+    str = "/dev/null";
+  }
+
+  // open file traditionally
+  FILE *fd = fopen(str, direction ? "w" : "r" );
+  if (fd == NULL) {
+    fprintf(stderr, "Failed to open %s\n", str);
+    exit(-1);
+  }
+
+  return fd;
+}
diff --git a/code/core/fileutils.h b/code/core/fileutils.h
new file mode 100644
index 0000000..324dab7
--- /dev/null
+++ b/code/core/fileutils.h
@@ -0,0 +1,10 @@
+#ifndef FILEUTILS_H
+#define FILEUTILS_H
+
+#include <stdio.h>
+
+// direction is either false=input or true=output and used to overload parameter '-'
+FILE *fd_magic(char *str, bool direction);
+
+
+#endif // FILEUTILS_H
diff --git a/code/core/global.cpp b/code/core/global.cpp
new file mode 100644
index 0000000..83ec666
--- /dev/null
+++ b/code/core/global.cpp
@@ -0,0 +1,115 @@
+#include <math.h>
+
+#include "interface.h"
+
+#include "global.h"
+
+Global::Global() :
+    // neuron related
+  voltage_tau(0.05),  // [s]
+  voltage_base(-0.065), // [V] rest potential 
+  threshold(-0.05),    // [V] above which a spike is emitted
+
+  Wmax(0.004), // [V] 
+  Wmin(0.0),   // [V]
+  sumWeight(0.16),    // [V]
+  absoluteRefractoryTime(0.001), // [V]
+
+  // dopamin
+  dopamin_level(0.0), // [?]
+  dopamin_tau(0.005),   // [s]
+
+  // STDP
+  stdp_tau_plus(0.014),     // [s]
+  stdp_tau_minus(0.034),    // [s]
+  stdp_lambda_plus(0.066),  // [1]
+  stdp_lambda_minus(0.066), // [1]
+  stdp_et_tau(0.1),       // [s] eligibility trace tau
+
+  // IP
+  ip_sliding_avg_tau(), // TODO
+  ip_lambda_R(),
+  ip_lambda_C(),
+  ip_dst_mom1(),
+  ip_dst_mom2(),
+
+  // external noise
+  en_current(0.1) // [V]
+  en_freq(1.0) // [Hz/Neuron]
+
+  // trainer
+  trainer_eval_delay(0.001), // [s]
+  trainer_numSymbols(2),            // [1]
+  trainer_refractoryTime(0.2),     // [s]
+  trainer_rewardAmount(0.1),       // [?]
+  trainer_rd_c1(0.05), // readout delay with
+  trainer_rd_c2(0.0001), //   delay = c1 + t*c2 + r*c3 + t*r'*c4
+  trainer_rd_c3(0.0), // where
+  trainer_rd_c4(0.0001); //   r and r' are two distinct random numbers (equ. dist in [0,1))
+{}
+
+void Global::evolve(double td) {
+  dopamin_level = decay_dopamin(dopamin_level, td);
+}
+
+double decay_dopamin(double level, double td) {
+  return level * exp( - td / dopamin_tau );
+}
+
+template<class Action>
+bool Global::reflect<Action>(Action &a) {
+return
+  // neuron related
+  reflect(voltage_tau, "voltage_tau")
+  && reflect(voltage_base, "voltage_base")
+  && reflect(threshold, "threshold")
+
+  && reflect(Wmin, "Wmin")
+  && reflect(Wmax, "Wmax")
+  && reflect(sumWeight, "sumWeight")
+  && reflect(absoluteRefractoryTime, "absoluteRefractoryTime")
+
+  // dopamin
+  && reflect(dopamin_level, "dopamin_level")
+  && reflect(dopamin_tau, "dopamin_tau")
+
+  // STDP
+  && reflect(stdp_tau_plus, "stdp_tau_plus")
+  && reflect(stdp_tau_minus, "stdp_tau_minus")
+  && reflect(stdp_lambda_plus, "stdp_lambda_plus")
+  && reflect(stdp_lambda_minus, "stdp_lambda_minus")
+  && reflect(stdp_et_tau, "stdp_et_tau")
+
+  // IP
+  && reflect(ip_sliding_avg_tau, "ip_sliding_avg_tau")
+  && reflect(ip_lambda_R, "ip_lambda_R")
+  && reflect(ip_lambda_C, "ip_lambda_C")
+  && reflect(ip_dst_mom1, "ip_dst_mom1")
+  && reflect(ip_dst_mom2, "ip_dst_mom2")
+
+  // external noise
+  && reflect(en_current, "en_current")
+  && reflect(en_freq, "en_freq")
+
+  // trainer
+  && reflect(trainer_eval_delay, "trainer_eval_delay")
+  && reflect(trainer_numSymbols, "trainer_numSymbols")
+  && reflect(trainer_refractoryTime, "trainer_refractoryTime")
+  && reflect(trainer_rewardAmount, "trainer_rewardAmount")
+  && reflect(trainer_rd_c1, "trainer_rd_c1")
+  && reflect(trainer_rd_c1, "trainer_rd_c2")
+  && reflect(trainer_rd_c1, "trainer_rd_c3")
+  && reflect(trainer_rd_c1, "trainer_rd_c4");
+}
+
+static id_type Global::numElements() {
+  return 1;
+}
+
+static Global * singleton(int num) {
+  if (num==0) {
+    return &global;
+  }else{
+    DIE("requested global object with id != 0");
+  }
+}
diff --git a/code/core/global.h b/code/core/global.h
new file mode 100644
index 0000000..8fec3d4
--- /dev/null
+++ b/code/core/global.h
@@ -0,0 +1,63 @@
+#ifndef GLOBAL_H
+#define GLOBAL_H
+
+class Global {
+public:
+  Global();
+
+  // methods
+  void evolve(double td);
+  double decay_dopamin(double level, double td); // return how much the level _would_ have been decayed
+
+  // variables (and quasi constants)
+  //   * neuron related
+  double voltage_tau;  // [s]
+  double voltage_base; // [V] rest potential 
+  double threshold;    // [V] above which a spike is emitted
+
+  double Wmax, Wmin;   // [V]
+  double sumWeight;    // [V]
+  double absoluteRefractoryTime; // [V]
+
+  //   * dopamin
+  double dopamin_level; // [?]
+  double dopamin_tau;   // [s]
+
+  //   * STDP
+  double stdp_tau_plus;     // [s]
+  double stdp_tau_minus;    // [s]
+  double stdp_lambda_plus;  // [1]
+  double stdp_lambda_minus; // [1]
+  double stdp_et_tau;       // [s] eligibility trace tau
+
+  //   * IP
+  double ip_sliding_avg_tau;
+  double ip_lambda_R;
+  double ip_lambda_C;
+  double ip_dst_mom1;
+  double ip_dst_mom2;
+
+  //   * external noise
+  double en_current; // [V]
+  double en_freq; // [Hz/Neuron]
+
+  //   * trainer
+  double trainer_eval_delay; // [s]
+  int trainer_numSymbols;            // [1]
+  double trainer_refractoryTime;     // [s]
+  double trainer_rewardAmount;       // [?]
+  double trainer_rd_c1; // readout delay with
+  double trainer_rd_c2; //   delay = c1 + t*c2 + r*c3 + t*r'*c4
+  double trainer_rd_c3; // where
+  double trainer_rd_c4; //   r and r' are two distinct random numbers (equ. dist in [0,1))
+
+  // reflection
+  template<class Action> bool reflect(Action &a);
+  typedef int id_type;
+  static id_type numElements();
+  static Neuron * singleton(int num); // return neuron # num
+} global;
+
+Global &g = global;
+
+#endif //  GLOBAL_H
diff --git a/code/core/interface.cpp b/code/core/interface.cpp
new file mode 100644
index 0000000..c2d3a3b
--- /dev/null
+++ b/code/core/interface.cpp
@@ -0,0 +1,262 @@
+#include <unistd.h>
+#include <asm-generic/errno.h>
+#include <boost/lexical_cast.hpp>
+
+#include "type2name.h"
+#include "log.h"
+#include "min.h"
+
+#include "interface.h"
+
+/* action definitions (the stuff implementing the different reflection primtives) */
+
+// (abstract) action (to implement filtering stuff)
+template<class interface>
+class Action {
+public:
+  Action<interface>(interface *ifc) : ifc(ifc) {}
+
+  bool isFiltered(char *desc) { // true -> don't use this element
+    return ! (ifc->ife.empty() || ifc->ifo.count(desc));
+  }
+
+  interface *ifc;
+};
+
+// count the length of a record assuming binary encoding
+template<class interface>
+class ActionCountRecordSize : public Action<interface> {
+public:
+  ActionCountRecordSize<interface>(interface ifc) : Action<interface>(ifc), result(0) {}
+
+  template<class T>
+  bool operator() (T &val, char *desc) {
+    if (this->isFiltered(desc)) return true;
+    result += sizeof(val);
+    return true;
+  }
+
+  int result;
+};
+
+// put the chosen titles in a string
+template<class interface>
+class ActionWriteTitle : public Action<interface> {
+public:
+  ActionWriteTitle<interface>(interface ifc) : Action<interface>(ifc) {}
+
+  template<class T>
+  bool operator() (T &val, char * desc) {
+    if (this->isFiltered(desc)) return true;
+    this->ifc->bufWrite(desc);
+    this->ifc->bufWrite(" ");
+    return true;
+  }
+};
+
+// put the choosen types in a string
+template<class interface>
+class ActionWriteTypes : public Action<interface> {
+public:
+  ActionWriteTypes<interface>(interface ifc) : Action<interface>(ifc) {}
+
+  template<class T>
+  bool operator() (T &val, char * desc) {
+    if (this->isFiltered(desc)) return true;
+    this->ifc->buf.append(type2name<T>());
+    this->ifc->buf.append(" ");
+    return true;
+  }
+};
+
+// put the serialized values to the string (space-delimited)
+// put the binary values to the string (no delimiter)
+template<class interface>
+class ActionWriteValues : public Action<interface> {
+public:
+  ActionWriteValues<interface>(interface ifc) : Action<interface>(ifc) {}
+
+  template<class T>
+  bool operator() (T &val, char *desc) {
+    if (this->isFiltered(desc)) return true;
+    return this->ifc->bufWrite(val);
+  }
+};
+
+// read serialized values
+template<class interface>
+class ActionRead : public Action<interface> {
+public:
+  ActionRead<interface>(interface ifc) : Action<interface>(ifc) {}
+
+  template<class T>
+  bool operator() (T &val, char * desc) {
+    if (this->isFiltered(desc)) return true;
+    return this->ifc->bufRead(val);
+  }
+};
+
+/* implementation of InputInterface */
+
+template<class T>
+InputInterface<T>::InputInterface(int fd, bool binary, IfObjectFilter *ifo, IfElementFilter *ife)
+  : binary(binary), fd(fd), ifo(ifo), ifo(ife), buf(), rpos(0), npos(0), wpos(0), eof(false) {
+  buf.reserve(buf_size);
+}
+
+template<class T>
+bool InputInterface<T>::garantueeBuf(size_t size) {
+  // no chance?
+  if (eof) return (wpos - rpos >= size);
+  if (size >= buf_size/2) return false;
+
+  // relocate buffer?
+  if (rpos > buf_size/2) {
+    buf = buf.substr(rpos);
+    buf.reserve(buf_size);
+    npos -= rpos;
+    wpos -= rpos;
+    rpos = 0;
+  }
+
+  // read more?
+  do {
+    if (wpos < buf_size) {
+      ssize_t res = read(fd, buf.data(), buf_size - wpos);
+      switch (res) {
+      case 0: // EOF
+	eof = true;
+	break;
+	
+      case EAGAIN:
+	// TO DECIDE: wait?
+	// read again (if neccessary)
+	break;
+	
+      case EIO: case EBADF: case EINVAL: case EINTR: case EFAULT:
+	return false;
+
+      default:
+	// read res bytes
+	wpos += res;
+      }
+    }
+  } while ((wpos - rpos < size) || eof); // loop in case of EAGAIN
+
+  return wpos - rpos >= size;
+}
+
+// make sure that a "\n"-terminated, non-empty string is in the buffer (starting at rpos)
+template<class T>
+bool InputInterface<T>::garantueeLine() {
+  if (npos <= rpos) npos = rpos + 1;
+  while (true) {
+    if ((npos > wpos) && !garantueeBuf(npos - rpos)) return false; // increase amount of data in buffer
+    if (buf[npos] == '\n') return true;
+    npos++;
+  }
+}
+
+template<class T>
+double InputInterface<T>::peekNextTime() {
+  double res;
+  if (!bufRead(res, false)) {
+    if (eof) {
+      return INFINITY;
+    }else{
+      DIE("peeking next time failed");
+    }
+  }
+  return res;
+}
+
+
+template<class Tif> template<class Tval>
+bool InputInterface<Tif>::bufRead(Tval &val, bool proceedRPos=true) {
+  if (binary) {
+    if (!garantueeBuf(sizeof(Tval))) return false;
+    val = *((Tval*) &(buf[npos]));
+    if (proceedRPos) rpos += sizeof(Tval);
+  }else{
+    if (!garantueeLine()) return false;
+
+    // find next delimiter
+    size_t p = buf.find_first_of(" \n", rpos);
+    if (!p || (p == buf.npos)) return false;
+    
+    // parse substring
+    try {
+      val = boost::lexical_cast<Tval>(buf.substr(rpos, p-1));
+    } catch(...) {
+      return false;
+    }
+
+    if (proceedRPos) rpos = p + 1;
+  }
+  return true;
+}
+
+template<class T>
+bool InputInterface<T>::readEntireFile() {
+  return readFileUntil(INFINITY);
+}
+
+template<typename T>
+bool InputInterface<T>::readFileUntil(double time) {
+  // iterate over events
+  while (peekNextTime() <= min(time, INFINITY)) {
+    // read (and forget) time to proceed rpos
+    double _foo; bufRead(_foo);
+
+    // get element id
+    typename T::id_type id;
+    if (!bufRead(id)) return false;
+    // TODO: check if the id refers to a valid object
+
+    // ignore it?
+    if (!ifo->empty() && !ifo->count(id)) return false;
+
+    // construct interface action and apply it
+    ActionRead<InputInterface<T> > ia(this);
+    if (!(T::singleton(id)->interface(ia))) return false;
+  }
+  return true;
+}
+
+template<class T>
+OutputInterface<T>::OutputInterface(int fd, bool binary, IfObjectFilter *ifo, IfElementFilter *ife)
+  : fd(fd), binary(binary), ifo(ifo), ife(ife), buf() {}
+
+template<class T>
+bool OutputInterface<T>::pushObject(T *o) {
+  ActionWriteValues<OutputInterface<T> > ia(this);
+  return o->interface(ia);
+}
+
+template<class T>
+bool OutputInterface<T>::pushClass() {
+  if (ifo->empty()) {
+    // for every object of the class
+    for (int i=0; i<T::numElements(); i++)
+      if (!pushObject(T::singleton(i))) return false;
+  }else{
+    // for all objects specified by ifo
+    for (IfObjectFilter::iterator i = ifo->begin(); i != ifo->end(); i++)
+      if (!pushObject(T::singleton(*i))) return false;
+  }
+}
+
+template<class T>
+bool OutputInterface<T>::isContained(typename T::id_type id) {
+  return ifo->empty() || ifo->count(id);
+}
+
+template<class Tif> template<class Tval>
+bool OutputInterface<Tif>::bufWrite(Tval &val) {
+  try {
+    buf.append(boost::lexical_cast<std::string>(val));
+  }catch (...) {
+    return false;
+  }
+  return true;
+}
diff --git a/code/core/interface.h b/code/core/interface.h
new file mode 100644
index 0000000..b53b741
--- /dev/null
+++ b/code/core/interface.h
@@ -0,0 +1,62 @@
+#ifndef INTERFACE_H
+#define INTERFACE_H
+
+#include <string>
+#include <set>
+#include <boost/lexical_cast.hpp>
+
+#include "math.h"
+
+// filters to select which objects/variables (not) to select
+typedef std::set<int> IfObjectFilter;
+typedef std::set<std::string> IfElementFilter;
+
+// interface-class .. holds long-time stuff for reflecting on a per class (template), per file (instance) and per direction (class) basis 
+template<class T>
+class InputInterface {
+public:
+  // A. the methods you want to call
+  // creation
+  InputInterface<T>(int fd, bool binary, IfObjectFilter ifo, IfElementFilter ife);
+  bool readEntireFile();
+  bool readFileUntil(double time);
+  double peekNextTime(); // read a line ahead (if possible) and check at what time it occurs
+
+  // B. internal state
+  bool binary;  
+  int fd;
+  std::string buf;
+  size_t rpos, npos, wpos;
+  static const size_t buf_size = 32768;
+  bool eof;
+  IfObjectFilter ifo;
+  IfElementFilter ife;
+
+  // C. internal functions
+  bool garantueeBuf(size_t size); // returns only after wpos - rpos >= size, but reads as much as possible without blocking
+  bool garantueeLine();
+
+  template<class Tval> bool bufRead(Tval &val, bool proccedRPos);
+};
+
+template<class T>
+class OutputInterface {
+public:
+  OutputInterface<T>(int fd, bool binary, IfObjectFilter *ifo, IfElementFilter *ife);
+
+  bool pushObject(T *o); // serialize one object
+  bool pushClass(); // serialize the entire class (selective by filter)
+  bool isContained(typename T::id_type id);
+
+  // internal state
+  int fd;
+  std::string buf;
+  bool binary;
+  IfObjectFilter *ifo;
+  IfElementFilter *ife;
+
+  // internal functions
+  template<class Tval> bool bufWrite(Tval &val);
+};
+
+#endif // INTERFACE_H
diff --git a/code/core/log.h b/code/core/log.h
new file mode 100644
index 0000000..57fb21b
--- /dev/null
+++ b/code/core/log.h
@@ -0,0 +1,7 @@
+#ifndef LOG_H
+#define LOG_H
+
+#define WARN(str) fprintf(stderr, "WARN at " __FILE__ ":%d: " str "\n", __LINE__, str);
+#define DIE(str) { fprintf(stderr, "FATAL at " __FILE__ ":%d: " str "\n", __LINE__, str); exit(-1); }
+
+#endif
diff --git a/code/core/max.h b/code/core/max.h
new file mode 100644
index 0000000..490b338
--- /dev/null
+++ b/code/core/max.h
@@ -0,0 +1,13 @@
+#ifndef MAX_H
+#define MAX_H
+
+template<class L, class R>
+inline L max(L l, R r) {
+  if (l > r) {
+    return l;
+  }else{
+    return r;
+  }
+}
+
+#endif // MAX_H
diff --git a/code/core/min.h b/code/core/min.h
new file mode 100644
index 0000000..78472ab
--- /dev/null
+++ b/code/core/min.h
@@ -0,0 +1,13 @@
+#ifndef MIN_H
+#define MIN_H
+
+template<class L, class R>
+inline L min(L l, R r) {
+  if (l < r) {
+    return l;
+  }else{
+    return r;
+  }
+}
+
+#endif // MIN_H
diff --git a/code/core/neuron.cpp b/code/core/neuron.cpp
new file mode 100644
index 0000000..c35afcc
--- /dev/null
+++ b/code/core/neuron.cpp
@@ -0,0 +1,164 @@
+//#include "model_switch.h"
+
+#include <stdio.h>
+
+#include "neuron.h"
+
+Neuron::Neuron() {
+  // neurons are initialized before the Global objects is; therefore this call to init() is preliminary
+  // and has to be repeated after the Global object has been loaded
+  init();
+}
+
+Neuron::init() {
+  // general neuron params
+  voltage = global.base_voltage;
+  refractoryTime = 0.0;
+
+  // IP
+  fac_voltage_tau = 1.0;
+  fax_current = 1.0;
+
+  ip_R = 1.0;
+  ip_C = 1.0;
+
+  ip_est_mom1 = global.ip_dst_mom1;
+  ip_est_mom2 = global.ip_dst_mom2;
+  ip_dst_mom1 = global.ip_dst_mom1;
+  ip_dst_mom2 = global.ip_dst_mom2;
+
+  // clock
+  lastEvent = 0.0;
+  lastSpike = - INFINITY;
+ 
+  // WARN: synapse lists not initialized (!) (well .. they have a constructor)
+}
+
+// evolve the neuron's state time [seconds]
+//   RETURN: the time difference between the this and the last update
+double Neuron::evolve(double time) {
+  // update internal clock
+  double dt = time - lastEvent;
+  lastEvent = time;
+
+  // voltage decay
+  voltage -= (voltage - global.voltage_base) * (1.0 - exp( - td / (global.voltage_tau * fac_voltage_tau)));
+  
+  return dt;
+}
+
+// apply an incoming spike of current to this neurons state giving it the current time [s] of the simulation; returns the time of the next spike to occur
+double Neuron::processCurrent(double time, double current) {
+  // process the model until the current time
+  evolve(time);
+
+  // add spike
+  if (time > refractoryTime)
+    voltage += fac_current * current;
+
+  // return when the neuron should fire the next time (0.0 is an option, too)
+  return predictSpike(time);
+}
+
+// generate a spike wich has been predicted earlier to occur at time [s]
+// RETURN when the next spike is expected to occur and the current of the spike
+double Neuron::generateSpike(double time, bool &doesOccur) {
+  // update the model (to the after-firing-state)
+  evolve(time);
+
+  // check if a spike occurs (the spike date might be outdated)
+  doesOccur = (voltage >= global.fire_threshold) && (time >= refractoryTime);
+
+  if (doesOccur) {
+    // 0. update internal state (instantaneously)
+    voltage = global.voltage_base;
+    refractoryTime = time + global.absoluteRefractoryTime;
+
+    // 1. do intrinsic plasticity
+    intrinsicPlasticity(time - lastSpike);
+
+    // 2. do stdp related accounting in the incoming synapses
+    //    (check each synapse for event(s))
+    for (SynapseSrcList::iterator i = sin.begin(); i != sin.end(); i++) {
+      // do not touch constant synapses (calc'ing the values below is a waste of time)
+      if (i->constant)
+	continue;
+
+      // check if pre-neuron has fired since we have fired the last time
+      // this info is stored in the synapse between pre- and this neuron
+      if ((lastSpike != -INFINITY) && (i->firstSpike != -INFINITY)) {
+	// depression
+	i->evolve(i->firstSpike);
+	i->stdp(lastSpike - i->firstSpike);
+
+	// facilitation
+	i->evolve(time);
+	i->stdp(time - i->lastSpike);
+
+	// reset firstFired to allow the next max calculation
+	i->firstSpike = -INFINITY;
+      }
+    }
+
+    // 3. update the last time this neuron has fired
+    lastSpike = time;
+  }
+  
+  return predictSpike(time);
+}
+
+void Neuron::predictSpike(double time) {
+  if (voltage >= global.voltage_threshold) {
+    return fmax(time, refractoryTime);
+  }else{
+    return INFINITY;
+  }
+}
+
+void Neuron::intrinsicPlasticity(double td) {
+  if (!ip)
+    return;
+
+  // update rate estimation
+  double edt = exp( td / g.ip_sliding_avg_tau );
+  double freq = 1.0 / td; // HINT: td=0 is not possible (because of an absolute refractory period)
+  ip_est_mom1 = edt * ip_est_mom1 + (1 - edt) * freq;
+  ip_est_mom2 = edt * ip_est_mom2 + (1 - edt) * freq * freq;
+
+  // modify internal representation
+  ip_R += g.ip_lambda_R * (ip_est_mom1 - ip_dst_mom1) * td;
+
+  double m2d = g.ip_lambda_C * (ip_est_mom2 - ip_dst_mom2);
+  ip_C += pow(ip_C, 2) * m2d * td
+        / ( 1.0 + ip_C * m2d * td );
+
+  // update coefficients
+  fac_voltage_tau = ip_R * ip_C;
+  fac_current = ip_R;
+}
+
+template<class Action>
+bool Neuron::reflect<Action>(Action &a) {
+  return 
+       a(voltage, "voltage")
+    && a(refractoryTime, "refractoryTime")
+    && a(ip, "ip")
+    && a(ip_est_mom1, "ip_est_mom1")
+    && a(ip_est_mom2, "ip_est_mom2")
+    && a(ip_dst_mom1, "ip_dst_mom1")
+    && a(ip_dst_mom2, "ip_dst_mom2")
+    && a(ip_R, "ip_R")
+    && a(ip_C, "ip_C")
+    && a(fac_voltage_tau, "fac_voltage_tau")
+    && a(fac_current, "fac_current")
+    && a(lastEvent, "lastEvent")
+    && a(lastSpike, "lastSpike");
+}
+
+static id_type Neuron::numElements() {
+  return s.numNeurons;
+}
+
+static Neuron * Neuron::singleton(id_type id) {
+  return &(s.neurons[id]);
+}
diff --git a/code/core/neuron.h b/code/core/neuron.h
new file mode 100644
index 0000000..03c0dbb
--- /dev/null
+++ b/code/core/neuron.h
@@ -0,0 +1,64 @@
+/*************************************************************
+neuron.h
+  implementation the axon hillock
+
+  STORES
+  * current tuning of neuron body (parameters)
+  * list of synapses (-> connections to other neurons)
+**************************************************************/
+
+#ifndef NEURON_H
+#define NEURON_H
+
+#include <boost/intrusive/slist.hpp>
+
+#include "synapse.h"
+
+using namespace boost::intrusive;
+
+typedef slist<Synapse, member_hook<Synapse, slist_member_hook<>, &Synapse::hook_dst> > SynapseDstList;
+typedef slist<Synapse, member_hook<Synapse, slist_member_hook<>, &Synapse::hook_src> > SynapseSrcList;
+
+class Neuron {
+public:
+  Neuron();
+  void init();
+
+  // functions operating on neuronal state
+  double evolve(double time);
+  double processCurrent(double time, double current);
+  double generateSpike(double time, bool &doesOccur);
+  double predictSpike(double time);
+  void intrinsicPlasticity(double td);
+
+  // reflection
+  template<class Action> bool reflect(Action &a);
+  typedef int id_type;
+  static id_type numElements();
+  static Neuron * singleton(int num); // return neuron # num
+
+  // list of outgoing and incoming synapses
+  SynapseSrcList sin;
+  SynapseDstList sout;
+  //Synapse **sin, *sout;// list of _in_coming and _out_going _s_ynapses; HINT: sin is a list of pointers to synapses in the corresponding outgoing neuron
+
+  // basic neuron properties
+  double voltage; // [V]
+  double refractoryTime; // [s]
+
+  // IP related
+  bool ip; // if this neuron has IP at all
+  double ip_est_mom1, ip_est_mom2; // estimated moments (using exponential sliding average (exact integration))
+  double ip_dst_mom1, ip_dst_mom2; // targeted moments
+  double ip_R, ip_C; // internal correspondences to christinas model
+  double fac_voltage_tau, fac_current; // resulting coefficients for neuron behaviour
+
+  // local clocks
+  double lastEvent; // timepoint when the last event occured
+  double lastSpike;
+};
+
+const int numNeurons = 1000;
+Neuron n[numNeurons];
+
+#endif // NEURON_H
diff --git a/code/core/print_defaults.cpp b/code/core/print_defaults.cpp
new file mode 100644
index 0000000..7fbc7c2
--- /dev/null
+++ b/code/core/print_defaults.cpp
@@ -0,0 +1,10 @@
+#include <stdio.h>
+
+
+
+int main () {
+  TO BE IMPLEMENTED AGAIN
+  using the relflection interface
+
+  return 0;
+}
diff --git a/code/core/regex.cpp b/code/core/regex.cpp
new file mode 100644
index 0000000..ef98209
--- /dev/null
+++ b/code/core/regex.cpp
@@ -0,0 +1,134 @@
+// file access
+#include <fcntl.h>
+#include <errno.h>
+#include <list>
+#include <boost/xpressive/xpressive_static.hpp>
+#include <boost/xpressive/regex_actions.hpp>
+#include <boost/type_traits/is_same.hpp>
+#include <boost/foreach.hpp>
+
+#include "interface.h"
+
+#include "log.h"
+#include "simulate.h"
+#include "tracepoints.h"
+#include "global.h"
+#include "neuron.h"
+#include "synapse.h"
+#include "spike.h"
+
+#include "regex.h"
+
+// pollute seperate namespace with regex expressions
+namespace tracepoints {
+
+  using namespace boost::xpressive;
+
+  /* parser result variables */
+  std::set<int> intSet;
+  std::set<std::string> stringSet;
+  double targetTimeOffset = 0.0;
+  std::string filename;
+  bool ioDirection; // tue -> write; false -> read
+  bool ioBinary;
+
+  /* parser callback implementations */
+  struct push_impl
+  {
+    typedef void result_type;     // Result type, needed for tr1::result_of
+    
+    template<typename Set, class Value>
+    void operator()(Set &s, Value const &val) const { s.insert(val); }
+  };
+  function<push_impl>::type const push = {{}};
+
+  /* I/O interface launcher */
+  template<class T>
+  struct start_interface_impl
+  {
+    typedef void result_type;     // Result type, needed for tr1::result_of
+    
+    void operator() () const {
+      // open src/dst file
+      int fd = open(filename.c_str, write ? (O_WRONLY | O_APPEND | O_CREAT) : (O_RDONLY | O_NONBLOCK));
+      if (fd == -1) DIE("could not open file");
+
+      // execute task
+      if (ioDirection) { // write
+	if (boost::is_same<T, SpikeMUX>::value) {
+	  // create a persistent interface to write out spikes as they occur
+	  s.spikeOIfList.push_back(new OutputInterface<SpikeMUX>(fd, ioBinary, stringSet, intSet));
+	}else{
+	  // create a temporary interface to write out any state
+	  OutputInterface<T> oif(fd, ioBinary, stringSet, intSet);
+	  oif.pushClass();
+	  close(fd);
+	}
+      }else{ // read
+	// create long living input interface (terminates itself when EOF is discovered)
+	FileInputEvent<T>::createInputStream(new InputInterface<T>(fd, ioBinary, stringSet, intSet));
+      }
+      
+      // clean up vars for next command
+      ioBinary = false;
+      stringSet.empty();
+      intSet.empty();
+    }
+  };
+
+  function<start_interface_impl<Global> >::type const start_interface_global = {{}};
+  function<start_interface_impl<Neuron> >::type const start_interface_neuron = {{}};
+  function<start_interface_impl<Synapse> >::type const start_interface_synapse = {{}};
+  function<start_interface_impl<Spike> >::type const start_interface_spike = {{}};
+
+  /* regex pattern definitions */
+
+  // character sets
+  cregex Delim = as_xpr(';');
+  cregex VarNameChar = alnum | as_xpr('_');
+
+  // basic elements
+  cregex Time = (+_d >> !('.' >> +_d))[ ref(targetOffseTime)=as<double>(_) ];
+
+  cregex Index = (+_d)[ push(as<int>(_)) ];
+
+  cregex Element = (+varnamechar)[ push(as<std::string>(_)) ];
+
+  cregex Filename = (+varnamechar)[ ref(filename)=<std::string>(_) ];
+
+  cregex IODirWrite = as_xpr('>') [ ref(ioDirection)=true ];
+  cregex IODirRead = as_xpr('>') [ ref(ioDirection)=false ];
+  cregex IODirection = IODirWrite | IODirRead;
+
+  cregex IOBinaryTrue = as_xpr('#') [ ref(ioBinary)=true ];
+  cregex IOBinary = !IOBinaryTrue;
+
+  cregex IOCmd = IOBinary >> IODirection >> Filename;
+
+  // lists
+  cregex ObjectListInner = *space >> (s1= index) >> *space;
+  cregex ObjectList = *space >> '(' >> object_list_inner >> *( delim >> object_list_inner ) >> ')';
+
+  cregex ElementListInner = *space >> (s1= element) >> *space;
+  cregex ElementList = *space >> '{' >> element_list_inner >> *( delim >> element_list_inner ) >> '}';
+
+  // trace commands
+  cregex TraceCmdTail = *space >> !ElementList >> *space >> !ObjectList >> *space >> IOCmd;
+
+  cregex TraceGlobal  = (icase( "global" )  >> TraceCmdTail [ start_interface_global() ];
+  cregex TraceNeuron  = (icase( "neuron" )  >> TraceCmdTail [ start_interface_neuron() ];
+  cregex TraceSynapse = (icase( "synapse" ) >> TraceCmdTail [ start_interface_synapse() ];
+  cregex TraceSpike   = (icase( "spike" )   >> TraceCmdTail [ start_interface_spike() ];
+
+  // whole line
+  // target format  what
+  //  cregex channel = *space >> +delim >> *space >> ( neuron | synapse | global | spikes );
+  //  cregex traceline = time  >> *channel >> *( delim | space );
+  cregex traceLine = !icase("proceed") >> +space >> time;
+  cregex line = *space >> *(inputElem | outputElem | traceElem) >> *( delim | space ));
+
+  bool parseRequest(char *str) {
+    return regex_match(str, line);
+  }
+  
+};
diff --git a/code/core/regex.h b/code/core/regex.h
new file mode 100644
index 0000000..0d1f3d3
--- /dev/null
+++ b/code/core/regex.h
@@ -0,0 +1,8 @@
+#ifndef REGEX_H
+#define REGEX_H
+
+namespace regex {
+  bool parseRequest(char *str);
+};
+
+#endif // REGEX_H
diff --git a/code/core/reward.cpp b/code/core/reward.cpp
new file mode 100644
index 0000000..0738c19
--- /dev/null
+++ b/code/core/reward.cpp
@@ -0,0 +1,105 @@
+#include <vector>
+
+#include "simulate.h"
+#include "bin.h"
+
+#include "reward.h"
+
+// only called once to init the da-reward system; later the more specific events are called
+void Reward::vexecute() {
+  // for ease of viewing ascendingly select 50 neurons per symbol
+  inputNeurons  = new IOPop(g.trainer_numSymbols);
+  outputNeurons = new IOPop(g.trainer_numSymbols);
+  for (int i = 0; i<g.trainer_numSymbols; i++)
+    for (int j=i*50; j<(i+1)*50; j++) {
+      (*inputNeurons)[i].insert(j);
+      (*outputNeurons)[i].insert(799 - j);
+    }
+
+
+  // present the first symbol after 0.5 second
+  s.addEvent(new Reward_Input(time + 10, inputNeurons, outputNeurons));
+}
+
+// choose and present a random input, then wait a random time
+void Reward_Input::vexecute() {
+  int symbol = rand() % g.trainer_numSymbols;
+  fprintf(stderr, "Pin: %d                              \n", symbol);
+
+  // excite symbol specific input neurons with 0.1 V
+  for (std::set<int>::iterator i = (*inputNeurons)[symbol].begin(); i != (*inputNeurons)[symbol].end(); i++)
+    s.addEvent(new ExternalSpike(time + drand48() * 0.001, *i, 0.15));
+
+  // wait a (not yet) random time until evaluation
+  s.addEvent(new Reward_EnableBinning(time + g.trainer_eval_delay, inputNeurons, outputNeurons, symbol));
+}
+
+// start the binning of relevant neurons
+void Reward_EnableBinning::vexecute() {
+  // add bins
+  vector<Bin*> *bins = new vector<Bin*>(g.trainer_numSymbols);
+  for (int i=0; i < (*outputNeurons).size(); i++) {
+    Bin *b = new Bin(&((*outputNeurons)[i]));
+    s.to.traceBinSets.insert(b);
+    (*bins)[i] = b;
+  }
+
+  // wait a small amount until reading the result of this binning
+  double delay = g.trainer_rd_c1
+               + g.trainer_rd_c2 * time
+               + g.trainer_rd_c3 * drand48()
+               + g.trainer_rd_c4 * time * drand48();
+  s.addEvent(new Reward_Readout(time + delay, symbol, inputNeurons, outputNeurons, bins));
+}
+
+// read the output frequencies and give reward
+void Reward_Readout::vexecute() {
+  if (estimatePerformance() > 1.0) {
+    deployReward(g.trainer_rewardAmount);
+  }else{
+    deployReward(-g.trainer_rewardAmount);
+  }
+
+  // delete bin trace commands
+  for (int i=0; i<bins->size(); i++) {
+    s.to.traceBinSets.erase((*bins)[i]);
+    delete (*bins)[i];
+  }
+  delete bins;
+
+  // wait a refractory time
+  s.addEvent(new Reward_Input(time + g.trainer_refractoryTime, inputNeurons, outputNeurons));
+}
+
+double Reward_Readout::estimatePerformance() {
+  int max_freq = 0, // max. freq of all populations _except_ target population
+    target_freq;
+
+  for (int i=0; i<bins->size(); i++) {
+    fprintf(stderr, "Pout: %d -> %d              \n", i, (*bins)[i]->count);
+    if (i == symbol) {
+      target_freq = (*bins)[i]->count;
+    }else{
+      max_freq = max(max_freq, (*bins)[i]->count);
+    }
+  }
+
+  double res;
+  if (max_freq == 0) {
+    if (target_freq == 0) {
+      res = 0.0;
+    }else{
+      res = ((double) target_freq) * INFINITY;
+    }
+  }else{
+    res = ((double) target_freq) / max_freq;
+  }
+
+  fprintf(stderr, "PERF: %f\n", res);
+  return res;
+}
+
+void Reward_Readout::deployReward(double reward) {
+  g.dopamin_level += reward;
+  s.da_history.push_front(pair<double,double>(time, g.dopamin_level));
+}
diff --git a/code/core/reward.h b/code/core/reward.h
new file mode 100644
index 0000000..1bc13f4
--- /dev/null
+++ b/code/core/reward.h
@@ -0,0 +1,53 @@
+#ifndef REWARD_H
+#define REWARD_H
+
+#include <vector>
+#include <set>
+
+#include <queue>
+
+#include "event.h"
+#include "bin.h"
+
+using namespace std;
+
+class Reward : public VirtualEvent {
+public:
+  typedef vector< std::set<int> > IOPop;
+
+  Reward(double time) : VirtualEvent(time) {}
+  Reward(double time, IOPop *inputNeurons, IOPop *outputNeurons) : VirtualEvent(time), inputNeurons(inputNeurons), outputNeurons(outputNeurons) {}
+  virtual void vexecute();
+
+  // state
+  IOPop *inputNeurons, *outputNeurons;
+};
+
+class Reward_Input : public Reward {
+public:
+  Reward_Input(double time, IOPop *inputNeurons, IOPop *outputNeurons) : Reward(time, inputNeurons, outputNeurons) {}
+  virtual void vexecute();  
+};
+
+class Reward_EnableBinning : public Reward {
+public:
+  Reward_EnableBinning(double time, IOPop *inputNeurons, IOPop *outputNeurons, int symbol) : Reward(time, inputNeurons,  outputNeurons), symbol(symbol) {}
+  virtual void vexecute();
+
+  int symbol;
+};
+
+class Reward_Readout : public Reward {
+public:
+  Reward_Readout(double time, int symbol, IOPop *inputNeurons, IOPop *outputNeurons, vector<Bin*> *bins) : Reward(time, inputNeurons, outputNeurons), symbol(symbol), bins(bins) {}
+  virtual void vexecute();
+
+  double estimatePerformance();
+  void deployReward(double reward);
+
+  int symbol;
+  vector<Bin*> * bins;
+};
+
+
+#endif // REWARD_H
diff --git a/code/core/simulate.cpp b/code/core/simulate.cpp
new file mode 100644
index 0000000..69252bb
--- /dev/null
+++ b/code/core/simulate.cpp
@@ -0,0 +1,134 @@
+#include <utility>
+#include <map>
+#include <signal.h>
+
+#include "model_switch.h"
+#include "synapse.h"
+#include "neuron.h"
+#include "topology.h"
+#include "reward.h"
+#include "tracepoints.h"
+#include "fileutils.h"
+#include "log.h"
+
+#include "simulate.h"
+
+// include cpp files to allow all otpimizations to take place across all files
+#include "synapse.cpp"
+#include "neuron.cpp"
+#include "topology.cpp"
+#include "fileutils.cpp"
+#include "event.cpp"
+#include "reward.cpp"
+#include "bin.cpp"
+#include "tracepoints.cpp" // should be excluded to speed up compilation
+
+
+Simulation::Simulation() :
+  // debug related stuff
+#ifdef DEBUG_STATUSLINE
+  numSpikes(0),
+  charCount(0),
+#endif
+
+  // init globals
+  currentTime(0.0),
+{
+  // set the initial dopamin level
+  da_history.push_front(pair<double, double>(0.0, g.dopamin_level));
+}
+
+bool Simulation::Step() {
+  // check if there are pending events
+  if (pendingSpikes.empty())
+    return false;
+
+  // retrieve and check next event
+  Event *e = pendingSpikes.top();
+  pendingSpikes.pop();
+
+  // proceed to the new time
+  if (currentTime > e->time)
+    DIE("tried to execute event of the past");
+  currentTime = e->time;
+
+#ifdef DEBUG_STATUSLINE
+  if (numSpikes % 16384 == 0) {
+    // remove old line
+    while (charCount-- > 0)
+      fprintf(stderr, " ");
+    fprintf(stderr, "\r");
+
+    // print new line
+    charCount += fprintf(stderr, "%f s, %d, %lld events (%d\tpending:", e->type, currentTime, numSpikes, pendingSpikes.size());
+    for (map<int, int>::iterator i = eventCount.begin(); i != eventCount.end(); i++) {
+      charCount += fprintf(stderr, "\t%d: %d", i->first, i->second);
+      charCount += 7; // tab
+    }
+    charCount += fprintf(stderr, ")\r");
+    charCount += 7; // tab
+  }
+  fflush(stderr);
+
+  numSpikes++;
+  eventCount[e->type]--;
+#endif
+
+  // execute event
+  e->execute();
+  e->free();
+
+  return true;
+}
+
+bool Simulation::proceedTime(double targetTime) {
+  // insert an intrinsic event for each neuron to have it computed up to exactly targetTime
+  for (int i=0; i < numNeurons; i++) {
+    addEvent(new IntrinsicNeuron(targetTime, i));
+  }
+
+  // proceed until no event is left before the time-point to be reached
+  // then also currentTime == targetTime holds
+  while (!pendingSpikes.empty() && (pendingSpikes.top()-> time <= targetTime)) {
+    Step();
+  }
+
+  // check if there are events left ... with the new event system this should always be the case
+  // and does not anymore indicate that the network is alive
+  return !pendingSpikes.empty();
+}
+
+void Simulation::addEvent(Event *e) {
+  pendingSpikes.push(e);
+#ifdef DEBUG_STATUSLINE
+  eventCount[e->type]++;
+#endif
+}
+
+void initStaticVars() {
+  Synapse::numSynapses = 0;
+}
+
+int main(int argc, char **argv) {
+  // ignore broken pipe signals (they should be handled by stdio file handlers and our usual error functions)
+  signal(SIGPIPE, SIG_IGN);
+
+  initStaticVars();
+
+  // load the network
+  // tp_load(s.fd_isynapse);
+  // neuron_load(s.fd_ineuron);
+
+  // init services implemented via events by adding one of them to the event population
+  s.addEvent(new ExternalNoise(0.0));
+  s.addEvent(new Reward(0.0));
+
+  // check for autoexciting events (and init neurons btw)
+  s.proceedTime(0.0);
+
+  // pass control to the tracepoint parser
+  // this allows to run the simulation interactively
+  executeTracepoints(s.fd_trace, s.fd_ispike, s.fd_iglobal);
+
+  return 0;
+}
diff --git a/code/core/simulate.h b/code/core/simulate.h
new file mode 100644
index 0000000..3d84b6e
--- /dev/null
+++ b/code/core/simulate.h
@@ -0,0 +1,70 @@
+#ifndef SIMULATE_H
+#define SIMULATE_H
+
+#include <queue>
+#include <list>
+
+#include "neuron.h"
+#include "synapse.h"
+#include "tracepoints.h"
+#include "event.h"
+#include "interface.h"
+#include "spike.h"
+
+using namespace std;
+ 
+class Simulation {
+public:
+  Simulation();
+
+  // ----- FUNCTIONS -----
+
+  // controlling functions
+  bool Step(); // do a single step (fire one neuron); return if the net is dead
+  bool proceedTime(double td);
+  bool proceedSpikes(long count);
+
+  void addEvent(Event*);
+
+  // ----- SIMULATION STATE -----
+
+  // simulation global variables
+  double currentTime;
+
+  // list of spikes and events
+  priority_queue<Event, vector<Event*>, PEventGreater> pendingSpikes;
+
+  // list of discontinous dopamin changes (time, amount), sorted by time (newest is front)
+  std::list<pair<double, double> > da_history;
+
+  // ----- HELPER VARS -----
+
+  // reflection & traces
+  std::list<OutputInterface<SpikeMUX> *> spikeOIfList;
+
+  std::set<Bin*> binSets;
+
+  // file descriptors
+  FILE *fd_ineuron,
+    *fd_isynapse,
+    *fd_ispike,
+    *fd_iglobal,
+    *fd_oneuron,
+    *fd_osynapse,
+    *fd_ospike,
+    *fd_oglobal,
+    *fd_trace; // command file
+
+  // debug vars
+#ifdef DEBUG_STATUSLINE
+  long long numSpikes; // number of spikes (counted after axon hillock) processed so far
+  map<int, int> eventCount;
+  int charCount;
+#endif
+};
+
+// init neural network
+Simulation s;
+
+
+#endif // SIMULATE_H
diff --git a/code/core/spike.cpp b/code/core/spike.cpp
new file mode 100644
index 0000000..7b12c18
--- /dev/null
+++ b/code/core/spike.cpp
@@ -0,0 +1,28 @@
+#include "spike.h"
+
+static SpikeMUX * SpikeMUX::singleton(id_type num) {
+  staticSpikeMUX.dst = num;
+  return &staticSpikeMUX;  
+}
+
+// special case for reading a spike from a file
+template<>
+bool SpikeMUX::reflect<ActionRead>(ActionRead &a) {
+  bool res = reflect(dst, "dst")
+    && reflect(time, "time")
+    && reflect(current, "current")
+    && (time > s.currentTime);
+
+  if (res)
+    s.addEvent(new ExternalSpike(time, dst, current));
+
+  return res;
+}
+
+// general reflection case
+template<class Action>
+bool SpikeMUX::reflect<Action>(Action &a) {
+  return reflect(dst, "dst")
+    && reflect(time, "time")
+    && reflect(current, "current");
+}
diff --git a/code/core/spike.h b/code/core/spike.h
new file mode 100644
index 0000000..2b2e4da
--- /dev/null
+++ b/code/core/spike.h
@@ -0,0 +1,28 @@
+#ifndef SPIKE_H
+#define SPIKE_H
+
+#include <math.h>
+
+#include "neuron.h"
+#include "log.h"
+
+class SpikeMUX {
+public:
+  typedef Neuron::id_type id_type; // WARN: this id refers to the spiking neuron, not the spike itself wich can not be addressed directly
+  SpikeMUX(id_type dst) : dst(dst), time(-INFINITY), current(0.0) {}
+  SpikeMUX(id_type dst, double time) : dst(dst), time(time), current(0.0) {}
+
+  // reflection
+  template<class Action> bool reflect(Action &a);
+  static id_type numElements() { DIE("Spike::numElements() called"); }
+  static SpikeMUX * singleton(id_type num); // do some reflection magic to multiplex between IntrinsicNeuron and ExternalNoise
+
+  // properties
+  id_type dst;
+  double time;
+  double current;
+};
+
+SpikeMUX staticSpikeMUX(-1); // single copy to use for reading spikes
+
+#endif // SPIKE_H
diff --git a/code/core/synapse.cpp b/code/core/synapse.cpp
new file mode 100644
index 0000000..cc7399a
--- /dev/null
+++ b/code/core/synapse.cpp
@@ -0,0 +1,118 @@
+#include <math.h>
+
+#include "synapse.h"
+
+Synapse::Synapse() :
+  src(-1), dst(-1), // seeing this value indicates an unused synapse
+  weight(0.0),
+  eligibility(0.0),
+  delay(0.0),
+  constant(false),
+  firstSpike(- INFINITY),
+  lastSpike(- INFINITY),
+  evolvedUntil(0.0)
+{}
+
+// given an input time and current calculate their output values
+void Synapse::computePostsynapticPulse(double &time, double &current) {
+  time += delay;
+  current = weight;
+}
+
+void Synapse::evolve(double time) {
+  if (time < evolvedUntil)
+    return;
+
+  // get the dopamin history starting from a dopamin event earlier than the synpase's last event
+  std::list<pair<double, double> >::iterator i = s.da_history.begin();
+  while (i->first > evolvedUntil)
+    i++;
+
+  // evolve synapse state for each interval given by the dopamin history
+  while (evolvedUntil < time) {
+    double da_level = i->second;
+    if (i->first < evolvedUntil) // the first dopamin event partially lies outside our time window
+      da_level = g.decay_dopamin(da_level, evolvedUntil - i->first);
+
+    double td = - evolvedUntil;
+    if (i == s.da_history.begin()) {
+      // this is the last (=newest) element of the history
+      td += time;
+      evolvedUntil = time;
+    }else{
+      i--;
+      if (i->first > time) {
+	// dopamin history goes furher (in time) than we have to simulate
+	td += time;
+	evolvedUntil = time;
+      }else{
+	td += i->first;
+	evolvedUntil += td;
+      }
+    }
+
+    /* below is the exact solution of the equation system
+         dc/dt = -Cc          c - eligibility trace, C - cf. tau
+         dd/dt = -Dd          d - dopamin level, D - cf. tau
+         dw/dt = cd           w - weight
+    */
+    
+    if (!constant) {
+      double tau = g.dopamin_tau * g.stdp_et_tau / (g.dopamin_tau + g.stdp_et_tau);
+      double dw = da_level * eligibility * tau * (1 - exp( -td / tau ));
+      weight += dw;
+      weight = fmax( msg.Wmin, fmin( msg.Wmax, weight ));
+    }
+    eligibility *= exp( -td / g.stdp_et_tau );
+  }
+}
+
+// modify eligibility trace according to a single STDP event given by
+// a pre-post time difference (= t_post - t_pre)
+void Synapse::stdp(double td) {
+  if (td >= 0.0) {// WARN: this doesn't work with negative zero
+    eligibility = g.stdp_lambda_plus * exp( - td / g.stdp_tau_plus );
+  }else{
+    eligibility = - g.stdp_lambda_minus * exp( td / g.stdp_tau_minus );
+  }
+}
+
+static void Synapse::updateTopology() {
+  // clear the sin/sout lists of all neurons
+  for (int i=0; i<numNeurons; i++) {
+    n[i].sout.clear();
+    n[i].sin.clear();
+  }
+
+  // iterate over all synapses wich have a valid source and destination (neuron) and add them to sin/sout lists
+  int i;
+  for (i=0; (i<maxSynapses) && (syn[i].src != -1) && (syn[i].dst != -1); i++) {
+    n[syn[i].src].sout.push_front(syn[i]);
+    n[syn[i].dst].sin.push_front(syn[i]);
+  }
+
+  // store number of (used) synapses
+  numSynapses = i;
+}
+
+template<class Action>
+bool Synapse::reflect<Action>(Action &a) {
+  return
+    a(src, "src")
+    && a(dst, "dst")
+    && a(weight, "weight")
+    && a(eligibility, "eligibility")
+    && a(delay, "delay")
+    && a(constant, "constant")
+    && a(firstSpike, "firstSpike")
+    && a(lastSpike, "lastSpike")
+    && a(evolvedUntil, "evolvedUntil");
+}
+
+static id_type Synapse::numElements() {
+  return numSynapsesDec;
+}
+
+static Synapse * Synapse::singleton(id_type id) {
+  return &(synapses[id]);
+}
diff --git a/code/core/synapse.h b/code/core/synapse.h
new file mode 100644
index 0000000..3eef12d
--- /dev/null
+++ b/code/core/synapse.h
@@ -0,0 +1,48 @@
+#ifndef SYNAPSE_H
+#define SYNAPSE_H
+
+#include <boost/intrusive/slist.hpp>
+
+using namespace boost::intrusive;
+
+class Neuron;
+
+class Synapse {
+public:
+  Synapse();
+
+  // functions
+  void computePostsynapticPulse(double &time, double &current); // given an input time and current calculate their output value
+  void evolve(double time);
+  void stdp(double dt);
+  static void updateTopology(); // recreate all sin/sout lists in the neurons
+
+  // reflection
+  template<class Action> bool reflect(Action &a);
+  typedef int id_type;
+  static id_type numElements();
+  static Synapse * singleton(id_type num); // return neuron # num
+  static id_type numSynapses;
+
+  // model specifics
+  int src, dst;       // pre- and postsynaptic neuron
+  double weight;      // [V]
+  double eligibility; // [?]
+  double delay;       // total delay from presynaptic axon hillock to postsynaptic axon hillock
+  bool constant;      // if the weight can change (HINT: weight < 0 implies constness, too)
+
+  // sim helper vars
+  double firstSpike,   // time the first/last spike arrived at it's dst neuron in a given interval
+         lastSpike;    // HINT: firstSpike is set to -INFINITY every time after it is processed
+                       // by the STDP rule
+  double evolvedUntil; // up to wich time has the model been evolved
+
+  // hock to use intrusive lists (defined in neuron.h)
+  slist_member_hook<> hook_src, hook_dst;  
+};
+
+const int maxSynapses = 200000;
+Synapse syn[maxSynapses];
+
+
+#endif // SYNAPSE_H
diff --git a/code/core/tracepoints.cpp b/code/core/tracepoints.cpp
new file mode 100644
index 0000000..7243f1c
--- /dev/null
+++ b/code/core/tracepoints.cpp
@@ -0,0 +1,57 @@
+#include "event.h"
+#include "regex.h"
+
+#include "simulate.h"
+
+/* input event streams */
+
+template<class T>
+static void FileInputEvent<T>::CreateInputStream(InputInterface<T> *iface) {
+  double time = iface->peekNextTime();
+  if (time == INFINITY) {
+    delete iface;
+    return;
+  }
+  if (time < s.currentTime) {
+    DIE("tried to include a file with events of the past");
+  }
+  s.addEvent(new FileInputEvent(iface, time));
+}
+
+template<class T>
+void FileInputEvent<T>::vexecute() {
+  iface->readFileUntil(time);
+  CreateInputStream(iface);
+}
+
+/* command loop */
+
+bool executeTracepoints() {
+  // the main loop of the program
+  char *str = NULL;
+  size_t _foo;
+
+  // loop over trace commands
+  while (getline(&str, &_foo, stdin) > 0) {
+    // parse request
+    if (!regex::parseRequest(str))
+      DIE("Invalid tracepoint format");
+
+    // proceed time if a run command was given
+    if (regex::targetTimeOffset != 0.0) {
+      if (!s.proceedTime(s.currentTime + tracepoints::targetTimeOffset))
+	fprintf(stderr, "Warning: network is dead\n");
+      // reset target time
+      targetTimeOffset = 0.0;
+      // reset spike output list
+      BOOST_FOREARCH(SpikeMUX *i, s.spikeOIfList) { delete i; }
+      s.spikeOIfList.empty();
+    }
+
+
+    free(str);
+    str = NULL;
+  }
+  
+  return true;
+}
diff --git a/code/core/tracepoints.h b/code/core/tracepoints.h
new file mode 100644
index 0000000..d0ea9fe
--- /dev/null
+++ b/code/core/tracepoints.h
@@ -0,0 +1,25 @@
+#ifndef TRACEPOINTS_H
+#define TRACEPOINTS_H
+
+#include <list>
+#include <set>
+
+#include "interface.h"
+#include "bin.h"
+#include "event.h"
+
+// read tracepoints from fd and execute them
+bool executeTracepoints(FILE *fd_trace, FILE *fd_spike, FILE *fd_global);
+
+template<class T>
+class FileInputEvent : public VirtualEvent {
+public:
+  FileInputEvent<T>(InputInterface<T> *iface, double time) : VirtualEvent(time), iface(iface) {}
+  static void createInputStream(InputInterface<T> *iface);
+  void vexecute();
+
+  InputInterface<T> *iface;
+};
+
+
+#endif // TRACEPOINTS_H
diff --git a/code/core/type2name.h b/code/core/type2name.h
new file mode 100644
index 0000000..1917a6a
--- /dev/null
+++ b/code/core/type2name.h
@@ -0,0 +1,20 @@
+#ifndef TYPE2NAME_H
+#define TYPE2NAME_H
+
+// if the type is not known
+template<class T>
+char * type2name() { return "type_not_stringified"; }
+
+template<>
+char * type2name<bool>() { return "bool"; }
+
+template<>
+char * type2name<char>() { return "char"; }
+
+template<>
+char * type2name<int>() { return "int"; }
+
+template<>
+char * type2name<double>() { return "double"; }
+
+#endif // TYPE2NAME_H
diff --git a/code/glue/Makefile b/code/glue/Makefile
new file mode 100644
index 0000000..35bd16b
--- /dev/null
+++ b/code/glue/Makefile
@@ -0,0 +1,8 @@
+.PHONY: all clean
+all: repeat-trace-cmd
+
+clean:
+	rm *~ repeat-trace-cmd
+
+repeat-trace-cmd: repeat-trace-cmd.c
+	gcc repeat-trace-cmd.c -o repeat-trace-cmd -O23
\ No newline at end of file
diff --git a/code/glue/da-controlled-sim-wrapper b/code/glue/da-controlled-sim-wrapper
new file mode 100755
index 0000000..918de4a
--- /dev/null
+++ b/code/glue/da-controlled-sim-wrapper
@@ -0,0 +1,62 @@
+#!/bin/sh
+
+# check param count
+if [ ! $# -eq 7 ]; then
+    echo 'wrong parameter count (see the source for parameter order)' >&2
+    # 1. model name (e.g. the "if" from "sim-if")
+    # 2. controller name (relative to trainer-dir)
+    # 3. input_neuron_file
+    # 4. input_synapse_file
+    # 5. output_neuron_file
+    # 6. output_synapse_file
+    # 7. performance output
+    exit 1
+fi
+
+# determine the path of the simulaton program
+SIM=`dirname $0`/../core/sim-$1
+if [ ! -x $SIM ]; then
+    echo "executable ($SIM) does not exist" >&2
+    exit 1
+fi
+
+# determine the path of the controller programm
+CTL=`dirname $0`/../trainer/$2-$1
+if [ ! -x $CTL ]; then
+    echo "executable ($CTL) does not exist" >&2
+    exit 1
+fi
+
+
+# create tmp dir
+FIFODIR=`mktemp -td fasimu.XXXXXXXXXX`
+
+# create fifos
+mkfifo $FIFODIR/spike_in
+mkfifo $FIFODIR/spike_out
+mkfifo $FIFODIR/trace_in
+mkfifo $FIFODIR/global_in
+mkfifo $FIFODIR/global_out
+
+# TODO: check if an additional i/o file is an executable
+
+# launch controller and simulator
+#echo $CTL - $FIFODIR/trace_in $FIFODIR/global_in $FIFODIR/global_out $FIFODIR/spike_in $FIFODIR/spike_out "2> trainer.err &"
+$CTL $7 $FIFODIR/trace_in $FIFODIR/global_in $FIFODIR/global_out $FIFODIR/spike_in $FIFODIR/spike_out 2> trainer.err &
+
+#echo $SIM "2> sim.err" $3 $4 $FIFODIR/spike_in $FIFODIR/global_in $5 $6 $FIFODIR/spike_out $FIFODIR/global_out $FIFODIR/trace_in
+$SIM 2> sim.err $3 $4 $FIFODIR/spike_in $FIFODIR/global_in $5 $6 $FIFODIR/spike_out $FIFODIR/global_out $FIFODIR/trace_in
+
+# hint: simulator params are
+    # input_neuron_file
+    # input_synapse_file
+    # input_spike_file
+    # input_global_file
+    # output_neuron_file
+    # output_synapse_file
+    # output_spike_file
+    # output_global_file
+    # trace_commando_file
+
+# delete tmp dir
+rm -R $FIFODIR
diff --git a/code/glue/distill-performance b/code/glue/distill-performance
new file mode 100755
index 0000000..af90f2f
--- /dev/null
+++ b/code/glue/distill-performance
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+if [ -f performance.out.raw ]; then
+   cat performance.out.raw | tr "\r" "\n" | grep ^PERF | cut -d" " -f2 > performance.out
+fi
diff --git a/code/glue/exec-matlab b/code/glue/exec-matlab
new file mode 100755
index 0000000..ccb0d23
--- /dev/null
+++ b/code/glue/exec-matlab
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+if [ -f $0.m ]; then
+    env - bash -c "(echo \"$1\"; cat $0.m) | matlab -nodesktop"
+#    env - bash -c "cat $0.m | octave"
+else
+    echo file $0.m not found
+fi
diff --git a/code/glue/extract-matlab-matrix b/code/glue/extract-matlab-matrix
new file mode 100755
index 0000000..b5021a4
--- /dev/null
+++ b/code/glue/extract-matlab-matrix
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# TODO: use tail instead of cat where only the top of the file is needed
+
+# extract the multiplier of the matrix
+MUL=`cat $1 \
+| egrep -o 'e\+[0-9]* \*' \
+| tr -d 'e+ *'`
+
+if [ -z "$MUL" ]; then
+    MUL=1
+fi
+
+# get the number of cols
+COLS=`cat $1 \
+| egrep '([:space:]*([01](\.[0-9]*){0,1})[:space:]*)+$' \
+| tail -n1 \
+| wc -w`
+
+# read the matrix, multiply to correct value and put it out
+cat $1 \
+| egrep '([:space:]*([01](\.[0-9]*){0,1})[:space:]*)+$' \
+| tr " " "\n" \
+| egrep -v '^$' \
+| while read; do 
+    echo $MUL '*' $REPLY
+done  \
+| bc \
+| sed 's/\([0-9]\+\)\.0*/\1/' \
+| ( I=1
+    while read; do
+	if [ $I -eq $COLS ]; then
+	    echo "$REPLY"
+	    I=1
+	else
+	    echo -n "$REPLY,"
+	    I=$(( $I + 1 ))
+	fi
+    done )
+
+
+# old debug stuff
+#echo $MUL $COLS
\ No newline at end of file
diff --git a/code/glue/plot_sliding_perf b/code/glue/plot_sliding_perf
new file mode 100755
index 0000000..c71d42b
--- /dev/null
+++ b/code/glue/plot_sliding_perf
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+if [ -f "performance.out" ]; then
+  echo "x=load('performance.out');
+        x=(x > 1);
+	y=length(x);
+	p=zeros(y-100,1);
+	for i=1:(y-100)
+	  p(i)=mean(x(i:(i+100),1));
+	end
+	p" \
+  | octave -q \
+  | tr -dc "0123456789.\n" \
+  |grep -v "^$" \
+  > performance.out.sliding-avg
+
+  PWD=`pwd`
+
+  echo "set title 'performance (sliding avg, window size 100) $PWD'
+        set terminal postscript
+	set output 'performance.out.ps'
+	plot 'performance.out.sliding-avg' using 1 with lines, 0.5" \
+  | gnuplot
+fi
diff --git a/code/glue/plot_spike_time_hist b/code/glue/plot_spike_time_hist
new file mode 100755
index 0000000..ad45305
--- /dev/null
+++ b/code/glue/plot_spike_time_hist
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+if [ -f "spikes.out" ]; then
+    cat spikes.out | cut -d, -f1 > spikes.out.timing
+
+    echo "x = load('spikes.out.timing');
+          y = hist(x, ceil(max(x)/10));
+          y'" \
+    | octave -q \
+    | tr -dc "0123456789.\n" \
+    | grep -v "^$" \
+    > spikes.out.binned-timing
+
+    echo "set title 'population frequency $PWD'
+          set terminal postscript
+	  set output 'spikes.out.binned-timing.ps'
+	  plot 'spikes.out.binned-timing' using 1 with lines" \
+    | gnuplot
+fi
\ No newline at end of file
diff --git a/code/glue/print-params b/code/glue/print-params
new file mode 100755
index 0000000..3df1e19
--- /dev/null
+++ b/code/glue/print-params
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+echo $@
diff --git a/code/glue/repeat-trace-cmd b/code/glue/repeat-trace-cmd
new file mode 100755
index 0000000..b889e0b
Binary files /dev/null and b/code/glue/repeat-trace-cmd differ
diff --git a/code/glue/repeat-trace-cmd.c b/code/glue/repeat-trace-cmd.c
new file mode 100644
index 0000000..ac35733
--- /dev/null
+++ b/code/glue/repeat-trace-cmd.c
@@ -0,0 +1,27 @@
+#include <stdio.h>
+
+int main(int argc, char **argv) {
+  double t, dt;
+  long n;
+
+  if (argc != 4) {
+    fprintf(stderr, "ERROR: wrong argument count\nUse %s total_time time_per_trace \"trace command(s) \"\n", argv[0]);
+    return -1;
+  }
+
+  if ((sscanf(argv[1], "%lf", &t) != 1) ||
+      (sscanf(argv[2], "%lf", &dt) != 1)) {
+    fprintf(stderr, "failed to read arg 1/2\n");
+    return -1;
+  }
+  printf("%f, %f\n", t, dt);
+  // print the full command once
+
+  // now print enough newline (= command repetitions)
+  // TODO: be faster than lame-duck-speed
+  n = (long) (t / dt); // on step already passed because of above printf statement
+  while (n>1) {
+    printf("\n");
+    n--;
+  }
+}
diff --git a/code/glue/sim-wrapper b/code/glue/sim-wrapper
new file mode 100755
index 0000000..9825409
--- /dev/null
+++ b/code/glue/sim-wrapper
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+if [ ! $# -eq 10 ]; then
+    echo 'wrong parameter count (see ./sim-current for parameter order and add the model (current/if/...) as the first param)' >&2
+    exit 1
+fi
+
+# determine the path of the simulaton program
+SIM=`dirname $0`/../core/sim-$1
+if [ ! -x $SIM ]; then
+    echo "executable ($SIM) does not exist" >&2
+    exit 1
+fi
+
+# check if one of the input files is executable
+if [ -x $2 -o -x $3 -o -x $4 -o -x $5 -o -x $5 -o -x $6 -o -x $6 -o -x $7 -o -x $8 -o -x $9  ]; then
+    # yes -> interactive simulation
+    # create the FIFOs to communicate
+    echo Interactive spike program is not NOT IMPLEMENTED
+    exit 1
+else
+    # no -> static simulation
+    $SIM $2 $3 $4 $5 $6 $7 $8 $9 $10
+fi
diff --git a/code/matlab/Makefile b/code/matlab/Makefile
new file mode 100644
index 0000000..3546e44
--- /dev/null
+++ b/code/matlab/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all symlinks clean
+
+all: symlinks
+
+symlinks:
+	ls | grep '.m$$' | sed 's/\.m$$//' | xargs -n1 ln -f -s ../glue/exec-matlab
+
+clean:
+	ls | grep '.m$$' | sed 's/\.m$$//' | xargs rm || true 
+	rm *~ || true
\ No newline at end of file
diff --git a/code/matlab/analye-perfomance.m b/code/matlab/analye-perfomance.m
new file mode 100644
index 0000000..75b399b
--- /dev/null
+++ b/code/matlab/analye-perfomance.m
@@ -0,0 +1,14 @@
+%% load data
+perf = load('performance.out');
+perf = perf > 1.0;
+s = length(perf);
+
+%% compute sliding avergae
+ws = 250; % window size
+perf_avg = zeros(s-ws,1);
+for i = 1:(s-ws)
+   perf_avg(i,1) = mean(perf(i:(i+ws),1));
+end
+
+%% plot
+plot(perf_avg);
\ No newline at end of file
diff --git a/code/matlab/analye-stdp-freq-dep.m b/code/matlab/analye-stdp-freq-dep.m
new file mode 100644
index 0000000..85c4030
--- /dev/null
+++ b/code/matlab/analye-stdp-freq-dep.m
@@ -0,0 +1,12 @@
+
+raw = load('synapse.destilled');
+
+res = [];
+for i=1:(floor(length(raw) / 200)),
+  row = raw(((i*200)-199):((i*200)-99),2)';
+  res(i,:) = [mean(row), var(row)];
+end
+
+for i=1:length(res),
+    fprintf(2,'%d, %f, %f\n', int32(i), res(i,1), res(i,2))
+end
\ No newline at end of file
diff --git a/code/matlab/analyze_weight_development.m b/code/matlab/analyze_weight_development.m
new file mode 100644
index 0000000..da34cd4
--- /dev/null
+++ b/code/matlab/analyze_weight_development.m
@@ -0,0 +1,30 @@
+%% -- load the synapse file
+
+syn_raw = load('synapse.out');
+
+%% -- generate mean weights (and some config stuff)
+
+num_syn = 96227;
+num_steps = length(syn_raw) / num_syn;
+types = [ 1*ones(100,1); 2*ones(600,1); 3*ones(100,1); 4*ones(200,1) ];
+
+syn_mean = zeros(num_steps, 16);
+syn_count = zeros(num_steps, 16);
+for i = 1:num_steps
+    ba = (i-1)*num_syn+1;
+    for j = ba:(ba+num_syn-1)
+        l = syn_raw(j,:);
+        src = l(1,2) + 1;
+        dst = l(1,3) + 1;
+        w = l(1,5);
+        
+        syn_mean(i, 4*types(src)+types(dst)-4) = syn_mean(i, 4*types(src)+types(dst)-4) + w;
+        syn_count(i, 4*types(src)+types(dst)-4) = syn_count(i, 4*types(src)+types(dst)-4) + 1;
+    end
+end
+syn_mean = syn_mean ./ syn_count;
+
+%% plot it
+
+plot(syn_mean);
+legend('II', 'IB', 'IO', 'IX', 'BI', 'BB', 'BO', 'BX', 'OI', 'OB', 'OO', 'OX', 'XI', 'XB', 'XO', 'XX');
\ No newline at end of file
diff --git a/code/matlab/plot_stdp_param_scout.m b/code/matlab/plot_stdp_param_scout.m
new file mode 100644
index 0000000..2342fd7
--- /dev/null
+++ b/code/matlab/plot_stdp_param_scout.m
@@ -0,0 +1,51 @@
+%% load the raw data from synapses output file
+raw = load('synapse.out');
+
+
+%% get mean and variance from the 1000 neurons
+ns = 999;
+l = floor(length(raw)/ns);
+raw2 = zeros(l,1);
+raw2_var = zeros(l,1);
+for i=1:l,
+    % hint: adapted to read only the first 100 out of 1000 neurons
+    raw2(i,1) =    mean(raw((i*ns-ns+1):(i*ns-900), 4), 1);
+    raw2_var(i,1) = var(raw((i*ns-ns+1):(i*ns-900), 4), 1);
+end
+
+%% erase duplicate lines (the silence period of simulation)
+l2 = floor(l/2) - 1;
+raw3 = zeros(l2,1);
+raw3_var = zeros(l2,1);
+for i=0:l2,
+    raw3(i+1,1) = raw2((2*i+1),1);
+    raw3_var(i+1,1) = raw2_var((2*i+1),1);
+end
+
+%% display graphs
+nx = 4;
+nt = 100;
+res = zeros(nx,nx);
+k =1;
+for i=0:(nx-1),
+    for j=0:(nx-1),
+        cur = raw3( ((i*nx + j)*nt + 1):((i*nx + j)*nt + nt - 1), 1);
+        cur_var = raw3_var( ((i*nx + j)*nt + 1):((i*nx + j)*nt + nt - 1), 1);
+        tr = (cur(nt - 1) > 0) + 2 * (sum(cur < 0) > 0);
+        res(i+1,j+1) = tr;
+        
+         %if ((mod(i,5) == 0) && (mod(j,5) == 0)),
+         %if (tr == 2),
+         %if (i<=10 && j>10),
+            subplot(nx, nx, k); 
+            k = k + 1;
+            %if (tr == 3),
+                plot(  [ 1:0.5:(nt/2) ]', [ cur, zeros(nt-1, 1), cur-cur_var, cur+cur_var ]);
+                title( sprintf('i=%d, j=%d', i, j));
+            %end;
+            %axis([-1 (nt+1) -1 1])
+            set(gca,'xtick',0:10:(nt/2))
+            %set(gca,'ytick',[])
+         %end;
+    end;
+end;
\ No newline at end of file
diff --git a/code/matlab/random_spikes.m b/code/matlab/random_spikes.m
new file mode 100644
index 0000000..89baf02
--- /dev/null
+++ b/code/matlab/random_spikes.m
@@ -0,0 +1,15 @@
+% fill the extenrally
+%num_neurons = 2; % wich should receive a spike
+%spike_freq = 1; % local per neuron per second
+%duration = 2; % [s]
+
+current = 100; % this should drive my neurons crazy
+
+format long
+
+num = num_neurons * spike_freq * duration;
+res = [ sort(rand(num, 1) .* duration), floor(rand(num, 1) .* num_neurons), ones(num, 1) * current ];
+
+for i=1:length(res),
+    fprintf(2,'%f,%d,%f\n', res(i,1), int32(floor(res(i,2))), res(i,3))
+end
diff --git a/code/matlab/random_topo.m b/code/matlab/random_topo.m
new file mode 100644
index 0000000..73d94ac
--- /dev/null
+++ b/code/matlab/random_topo.m
@@ -0,0 +1,60 @@
+%% config
+% the values below should be set externally
+% num_neurons = 10;
+% connection_density = 0.5;
+% inhibitory_fraction = 0.2;
+
+min_weight = 0;
+max_weight = 0.004;
+fie = - 1;
+fei = 15 / 20;
+fii = 0;
+
+min_delay = 0.001; % >= 0.1 ms
+max_delay = 0.005;  % < 2 ms
+
+
+%% init weights
+
+weights = min_weight + (max_weight - min_weight) * rand(num_neurons);
+weights = weights .* (rand(num_neurons) < connection_density);
+
+l = num_neurons - inhibitory_fraction * num_neurons + 1;
+h = num_neurons;
+
+% make incoming and outgoing weight of each inhibitory neuron proportional
+weights(1:(l-1), l:h) = weights(l:h, 1:(l-1))';
+
+% scaling weights for inhibitory connections
+weights(l:h, 1:(l-1)) = fie * weights(l:h, 1:(l-1));
+weights(l:h, l:h)     = fii * weights(l:h, l:h);
+weights(1:(l-1), l:h) = fei * weights(1:(l-1), l:h);
+
+
+%% init delays
+
+delay = min_delay + (max_delay - min_delay) * rand(num_neurons);
+
+% make inhibitory delays shorter
+delay(1:(l-1), l:h) = 0.1 * delay(1:(l-1), l:h);
+delay(l:h, 1:(l-1)) = 0.1 * delay(l:h, 1:(l-1));
+
+
+%% print resulting topology config
+
+[ a, b ] = find(weights ~= 0); 
+index = find(weights ~= 0);
+
+format long
+
+res = [ a, b, delay(index), weights(index) ];
+
+for i=1:length(res),
+  constness = (max(res(i,1:2)) / num_neurons >= 1 - inhibitory_fraction) % is src or dst and inhibitory neuron?
+  if (constness)
+    fprintf(2,'%d,%d,1,%f,%f\n', int32(res(i,1))-1, int32(res(i,2))-1, res(i,3), res(i,4));
+  else
+    fprintf(2,'%d,%d,0,%f,%f\n', int32(res(i,1))-1, int32(res(i,2))-1, res(i,3), res(i,4));
+  end
+end
+
diff --git a/code/trainer/Makefile b/code/trainer/Makefile
new file mode 100644
index 0000000..1fc48d1
--- /dev/null
+++ b/code/trainer/Makefile
@@ -0,0 +1,29 @@
+# HINT: the paradigm is not to create object files to allow all otpimizations
+#	take place even though the code is scattered across many files
+
+CC=g++
+CCFLAGS=-O3 -ggdb
+LDFLAGS=-lpthread -lm
+INCLUDE=-I/home/huwald/src/boost -I../core
+
+BASE_SRC_FILES=../core/model_switch.h ../core/fileutils.h ../core/fileutils.cpp
+
+.PHONY: all clean wordcount
+
+all: reinforce_synapse check_stdp_freq-dep
+
+clean:
+	rm -f *~ trainer massif.*.* reinforce_synapse-* check_stdp_freq-dep-*
+
+.PHONY: reinforce_synapse
+reinforce_synapse: reinforce_synapse-dalif
+reinforce_synapse-%: reinforce_synapse.cpp reinforce_synapse.h ../core/models/%.h $(BASE_SRC_FILES)
+	$(CC) -o $@ $(CCFLAGS) reinforce_synapse.cpp $(INCLUDE) $(LDFLAGS) -DMODEL_`echo $* | tr '[:lower:]' '[:upper:]'`
+
+.PHONY: check_stdp_freq-dep
+check_stdp_freq-dep: check_stdp_freq-dep-dalif
+check_stdp_freq-dep-%: check_stdp_freq-dep.cpp check_stdp_freq-dep.h ../core/models/%.h $(BASE_SRC_FILES)
+	$(CC) -o $@ $(CCFLAGS) check_stdp_freq-dep.cpp $(INCLUDE) $(LDFLAGS) -DMODEL_`echo $* | tr '[:lower:]' '[:upper:]'`
+
+wordcount:
+	wc *h *cpp Makefile
diff --git a/code/trainer/check_stdp_freq-dep.cpp b/code/trainer/check_stdp_freq-dep.cpp
new file mode 100644
index 0000000..f606d81
--- /dev/null
+++ b/code/trainer/check_stdp_freq-dep.cpp
@@ -0,0 +1,160 @@
+#include <stdlib.h>
+#include "fileutils.h"
+#include "math.h"
+#include "unistd.h"
+
+#include "check_stdp_freq-dep.h"
+#include "fileutils.cpp"
+#include "model_switch.h"
+
+using namespace std;
+
+int main(int argc, char **argv) {
+  // check cmd line sanity
+  if (argc != 5) {
+    fprintf(stderr, "Wrong argument count\n\n"
+	    "Call format:\n"
+	    "%s\n\t"
+	    "performance out\n\t"
+	    "trace cmd out\n\t"
+	    "global out\n\t"
+	    "spike out\n\t"
+	    "\n"
+	    "Special names allowed:\n\t- (standart input)\n\t0 (/dev/null)\n", argv[0]);
+    return -1;
+  }
+
+  Trainer *t = new Trainer(argc, argv);
+  t->run();
+
+  pthread_join(t->thread_write, NULL);
+}
+
+Trainer::Trainer(int argc, char** argv) {
+  // init vars
+  currentEpoch  = 0;
+  epochDuration  = 10.0; // [s]
+  neurons        = 1000; // number of neurons to send noise to
+  voltage        = 0.1;  // [V]
+  md             = 1.2; // 10.0;
+  mss            = 1.1; //1.2;
+  fs             = 100;   // number of frequencies to try
+  frd            = 1.0;  // relative difference between to frequencies (f_i+1 = frd * f_i)
+  fad            = 0.5;  // absolute difference between to frequencies (f_i+1 = fad + f_i)
+  
+  // open all file descriptors in an order complementary to the simulators one
+  // to avoid deadlocks
+  fd_spike_out       = fd_magic(argv[4], true);
+  fd_global_out      = fd_magic(argv[3], true);
+  fd_performance_out = fd_magic(argv[1], true);
+  fd_trace_out       = fd_magic(argv[2], true);
+
+  // create read and write threads
+  pthread_create(&thread_write, NULL, (void* (*)(void*)) &write_spikes, this);
+}
+
+void Trainer::run() {
+  char *str_trace = "%f; synapse\n";
+
+  // init global sim variables
+  MS_Global msg;
+  msg_init(msg);
+  msg.dopamin_level = 0.0;
+  
+  double ta = 0.009821, //0.0088541,
+         la = 0.140249; // 0.126445;
+
+  /*
+  // loop over both vars to examine
+  for (msg.stdp_tau_plus  = msg.stdp_tau_minus / md;
+       msg.stdp_tau_plus <= msg.stdp_tau_minus * md;
+       msg.stdp_tau_plus *= mss) {
+    for (msg.stdp_lambda_plus  = msg.stdp_lambda_minus / md;
+	 msg.stdp_lambda_plus <= msg.stdp_lambda_minus * md;
+	 msg.stdp_lambda_plus *= mss) {*/
+  // loop over both vars to examine
+  for (msg.stdp_tau_plus  = ta / md;
+       msg.stdp_tau_plus <= ta * md;
+       msg.stdp_tau_plus *= mss) {
+    for (msg.stdp_lambda_plus  = la / md;
+	 msg.stdp_lambda_plus <= la * md;
+	 msg.stdp_lambda_plus *= mss) {
+      
+      // print the parameters to the performance output
+      msg_print(msg, fd_performance_out);
+      fprintf(fd_performance_out, "\n");
+
+      // print the global params
+      fprintf(fd_global_out, "%f, ", currentEpoch * epochDuration);
+      msg_print(msg, fd_global_out);
+      fprintf(fd_global_out, "\n");
+
+      // let the simulation proceed
+      fprintf(fd_trace_out, str_trace, epochDuration);
+      currentEpoch++;
+ 
+      // repeat this 2*n-1 times (n=number of different frequency trials)
+      for (int i=0; i < 2*fs-1; i++) {
+	fprintf(fd_trace_out, "\n");
+	currentEpoch++;
+      }
+    }
+  }
+
+  fclose(fd_trace_out);
+  fclose(fd_global_out);
+}
+
+// ---- send indepenent poisson noise w/ increasing fequency----
+void *write_spikes(Trainer *t) {
+  // calculate how often we have to try all frequencies (=outer loop)
+  // WARN: ignore minor numerical instabilities
+  int max = (int) floor(2.0 * log(t->md) / log(t->mss) ) + 1;
+  max *= max; // there are two nested loops of the same size
+
+  double time = 0.0; // global time (that one send to the simulator)
+
+  // for each paramter config (set in the main routine)
+  for (int i=0; i<max; i++) {
+
+    double freq = 1.0;
+
+    // examine a set of frequencies
+    for (int j=0; j < t->fs; j++) {
+      // send out the spikes
+      double localtime = 0.0;
+      double nextRefSpike = 0.0;
+      double refFreq = 10.0; // [Hz]
+      int dst = -1;
+      while (localtime < t->epochDuration) {
+	// starting with the second call ...
+	if (dst != -1) {
+	  // check if we have to send a spike to the ref neuron
+	  if (localtime > nextRefSpike) {
+	    fprintf(t->fd_spike_out, "%f, %d, %f\n", time + nextRefSpike, 0, t->voltage);
+	    nextRefSpike += 1.0 / refFreq;
+	  }
+
+	  // send spike to the simulator
+	  fprintf(t->fd_spike_out, "%f, %d, %f\n", time + localtime, dst, t->voltage);
+	}else{
+	}
+
+	localtime -= log(1.0 - drand48()) / (freq * t->neurons); // possion distributed spike timing
+	dst = 1 + rand() % (t->neurons - 1); // random neuron (except reference neuron 0)
+      }
+
+      // increase time (twice because of the silence period after each noise period)
+      time = (i * t->fs + j) * 2.0 * t->epochDuration;
+
+      // increase frequency
+      freq *= t->frd;
+      freq += t->fad;
+    } 
+  }
+
+  // close fd because fscanf sucks
+  fclose(t->fd_spike_out);
+
+  return NULL;
+}
diff --git a/code/trainer/check_stdp_freq-dep.h b/code/trainer/check_stdp_freq-dep.h
new file mode 100644
index 0000000..cf429b6
--- /dev/null
+++ b/code/trainer/check_stdp_freq-dep.h
@@ -0,0 +1,46 @@
+#ifndef TRAINER_H
+#define TRAINER_H
+
+#include <stdio.h>
+#include <pthread.h>
+#include <map>
+#include <queue>
+#include "boost/tuple/tuple.hpp"
+
+
+using namespace std;
+
+class Trainer {
+ public:
+  FILE *fd_spike_out,
+    *fd_global_out,
+    *fd_trace_out,
+    *fd_performance_out;
+
+  // init stuff
+  Trainer(int argc, char** argv);
+
+  // main routine
+  void run();
+
+  // state vars
+  long currentEpoch;
+
+  // thread related
+  pthread_t thread_write;
+
+  // configuration
+  double md; // multiplicative difference (>1)
+  double mss; // multiplicative step size (>1)
+  double fs, frd, fad; // number of frequency steps and relative step size
+  double epochDuration;
+  double voltage; // per outgoing (random) spike
+  long neurons;
+};
+
+// seperate thread to read all spikes neccessary because reading and
+// writing to these descriptors could block and thus cause a deadlock
+void *read_spikes(Trainer *t);
+void *write_spikes(Trainer *t);
+
+#endif // TRAINER_H
diff --git a/code/trainer/mem1.cpp b/code/trainer/mem1.cpp
new file mode 100644
index 0000000..3b522b4
--- /dev/null
+++ b/code/trainer/mem1.cpp
@@ -0,0 +1,412 @@
+#include <stdlib.h>
+#include "fileutils.h"
+#include "math.h"
+
+#include "reinforce_synapse.h"
+#include "fileutils.cpp"
+#include "model_switch.h"
+
+using namespace std;
+
+int main(int argc, char **argv) {
+  // check cmd line sanity
+  if (argc != 7) {
+    fprintf(stderr, "Wrong argument count\n\n"
+	    "Call format:\n"
+	    "%s\n\t"
+	    "performance out\n\t"
+	    "trace cmd out\n\t"
+	    "global out\n\t"
+	    "global in\n\t"
+	    "spike out\n\t"
+	    "spike in\n\t"
+	    "\n"
+	    "Special names allowed:\n\t- (standart input)\n\t0 (/dev/null)\n", argv[0]);
+    return -1;
+  }
+
+  Trainer *t = new Trainer(argc, argv);
+  t->run();
+}
+
+//===== Initialisation =====================================
+
+Trainer::Trainer(int argc, char** argv) {
+  initConfig();
+  initState();
+  initGroups(); // determine input and output neurons
+
+  initFiles();
+  initThreads();
+}
+
+void Trainer::initConfig() {
+  neurons           = 1000; 
+  neuronsPerSymbol  = 200;
+  noiseFreq         = 10.0; // [Hz]
+  noiseVoltage      = 0.03; // [V]
+  reward            = 0.1;
+
+  epochDuration     = 1.0; // [s]
+  numTrials         = 1000;
+  numSymbols        = 2;
+  //readoutDelay      = 1;
+  refractoryPeriods = 3;
+}
+
+void Trainer::initState() {
+ dopamin_level = 0.0;
+ currentTrial  = 0;
+ state = 0;
+
+ msg_init(msg);
+ msg.dopamin_level = dopamin_level;
+
+ groupFreq.resize(numSymbols);
+ for (int i=0; i<numSymbols; i++) {
+   groupFreq[i] = 0;
+ }
+}
+
+void Trainer::initGroups() {
+  ioNeurons[i] = new set<int>();
+  for (int j=0; j<neuronsPerSymbol;) {
+    int n = rand() % numNeurons;
+    if (!isNeurons[i]->count(n)) {
+      ioNeurons[i]->insert(n);
+      j++;
+    }
+  }
+}
+
+void Trainer::initFiles() {
+  // open all file descriptors in an order complementary to the simulators one
+  // to avoid deadlocks
+  fd_spike_in        = fd_magic(argv[6], false);
+  fd_global_in       = fd_magic(argv[4], false);
+  fd_spike_out       = fd_magic(argv[5], true);
+  fd_global_out      = fd_magic(argv[3], true);
+  fd_performance_out = fd_magic(argv[1], true);
+  fd_trace_out       = fd_magic(argv[2], true);
+}
+
+void Trainer::initThreads() {
+  // init locks
+  pthread_mutex_init(&incomingSpikeLock, NULL);
+  pthread_mutex_init(&writerLock, NULL);
+
+  // create read and write threads
+  pthread_create(&thread_read, NULL, (void* (*)(void*)) &read_spikes, this);
+  pthread_create(&thread_write, NULL, (void* (*)(void*)) &write_spikes, this);
+}
+
+//===== Core trainer ====================================
+
+void Trainer::pushGlobal(double time) {
+  fprintf(fd_global_out, "%f, ", time);
+  msg_print(msg, fd_global_out);
+  fprintf(fd_global_out, "\n");
+  fflush(fd_global_out);
+}
+
+// hint time is delta time!
+void Trainer::pushTrace(double time) {
+  const char *str_trace = "%f; spikes (0; 1); global; neuron (0; 1); synapse (0; 1)\n";
+  fprintf(fd_trace_out, str_trace, time);
+  fflush(fd_trace_out);
+}
+
+bool Trainer::readGlobal() {
+  double _foo_dbl;  
+  char str_raw[128],
+       str_msg[128];
+  str_raw[0] = 0;
+  
+  // read a single line
+  if (fgets((char*) str_raw, 128, fd_global_in) == NULL) {
+    fprintf(stderr, "ERROR: global status file descriptor from simulator closed unexpectedly\n");
+    return false;
+  }
+
+  // parse it
+  if ((sscanf((char*) str_raw, "%lf, %[^\n]\n", &_foo_dbl, (char*) str_msg) != 2)
+      || (!msg_parse(msg, (char*) str_msg))) {
+    fprintf(stderr, "ERROR: reading global status from simulator failed\n\t\"%s\"\n", (char*) str_raw);
+    return false;
+  }
+
+  return true;
+}
+
+void binIncomingSpikes() {
+  // reset bins
+  for (int i=0; i<groupFreq.size(); i++)
+    groupFreq[i] = 0;
+  
+  // lock spike queue
+  pthread_yield(); // give the spike reading thread chance to finish ... this is not more than ugly semifix wrong par!
+  pthread_mutex_lock(&incomingSpikeLock);
+  
+  // read all spikes in the correct time window
+  while ((!incomingSpikes.empty()) && (incomingSpikes.front().get<0>() <= currentEpoch * epochDuration)) {
+    // drop event out of queue
+    SpikeEvent se = incomingSpikes.front();
+    double time = se.get<0>();
+    int neuron = se.get<1>();
+    incomingSpikes.pop();
+    
+    // check if it belongs to the previous bin (and ignore it if this is the case)
+    if (time < (currentEpoch - 1) * epochDuration) {
+      fprintf(stderr, "WARN: spike reading thread to slow; unprocessed spike of the past discovered\n%f\t%f\t%d\t%f\n",
+	      time, (double) (currentEpoch - 1) * epochDuration, currentEpoch, epochDuration);
+      continue;
+    }
+    
+    // check membership in each group and increase group frequency
+    for (int i=0; i < ioNeurons.size(); i++)
+      if (ioNeuros[i]->count(neuron))
+	groupFreq[i]++;
+  }
+
+  pthread_mutex_unlock(&incomingSpikeLock);
+}
+
+void Trainer::addBaselineSpikes() {
+}
+
+void Trainer::addSymbolSpikes() {
+  
+}
+ 
+
+double Trainer::calcSignalStrength() {
+  if (symbolHist.empty()) {
+    fprintf(stderr, "Writer thread is too slow; missed the current symbol\n");
+    exit(-1);
+  }
+
+  int fs, fn = 0; // freq signal, freq noise
+  for (int i=0; i<numSymbols; i++) {
+    if (i == symbolHist.front()) {
+      fs = groupFreq[i];
+    }else{
+      fm = fmax(fm, groupFreq[i]);
+    }
+  }
+
+  if (fn == 0) {
+    return fs * INFINITY;
+  }else{
+    return ((double) fs) / fn;
+  }
+}
+
+void Trainer::run() {
+  // rough description of this function
+  //   . start an epoch
+  //   . wait for it's end
+  //   . process incomig spikes (binning)
+  //   . select if a reward takes place
+  //   . print reward value
+  //   . send out the reward signal
+
+  // send out the full trace command once (later it will be repeated by sending newline)
+  pushTrace(epochDuration);
+
+  // send the first two global states (at t=0 and t=1.5 [bintime] to allow the simulation to
+  // be initialized (before the causality of the loop below is met)
+  pushGlobal(0.0);
+  msg_process(msg, 1.5 * epochDuration);
+  dopamin_level = msg.dopamin_level;
+  pushGlobal(1.5 * epochDuration);
+  
+  // loop until the experiment is done
+  for (; currentEpoch * epochDuration < entireDuration; currentEpoch++) {
+
+    // send a new trace command (do it as early as possible although it is
+    // only executed after the new global is send out at the bottom of this loop)
+    if ((currentEpoch + 2) * epochDuration < entireDuration) {
+      // repeat the previous trace command
+      fprintf(fd_trace_out, "\n");
+      fflush(fd_trace_out);
+    }else{
+      pushTrace(entireDuration - (currentEpoch + 1) * epochDuration);
+    }
+
+    // send new spikes
+    pthread_mutex_lock(&outgoingSpikeLock);
+    addBaselineSpikes();
+    if (state == 0) addSymbolSpikes();
+    pthread_cond_signal(&outgoingSpikeCond);
+    pthread_mutex_unlock(&outgoingSpikeLock);
+
+    // wait for the end of the epoch (by reading the global state resulting from it)
+    if (!readGlobal())
+      break;
+
+    // process incomig spikes (binning) of the previous epoch
+    if (currentEpoch > 0) 
+      binIncomingSpikes();
+
+    // proceed the global state to keep it in sync with the simulator's global state
+    // the local dopamin level is kept seperately and aged only one epochDuration to
+    // avoid oscillation effects in dopamin level
+    msg_process(msg, 1.5 * epochDuration);
+    dopamin_level *= exp( - epochDuration / msg.dopamin_tau );
+
+    // do various actions depeding on state (thus lock mutex of the writer thread)
+
+    
+    switch (state) {
+    case 0: // a signal is sent
+      state++;
+
+    case 1: // we are waiting for the signal to be reproduce
+      // get fraction of the current symbol's freq compared to the strongest wrong symbol
+      double ss = calcSignalStrength();
+
+      // check if the reward condition is met
+      if (ss > 1) {
+	dopmain_level += reward;
+      }else{
+	state++; // lost signal -> next state (and finally a new trial)
+	currentSymbol = rand() % numSymbols; // determine new symbol to display
+      }
+
+      break;
+
+    default: // the signal has been lost (in the last round); refractory time
+      ++state %= refractoryPeriods;
+    }
+
+    /*if ((currentEpoch > 1) && ((*neuronFreq[0])[0] > 0) && ((*neuronFreq[1])[1] > 0)) {
+      dopamin_level += da_single_reward;
+      fprintf(fd_performance_out, "+");
+    }else{
+      fprintf(fd_performance_out, "-");
+    }*/
+
+    // performance and "debug" output
+    if (currentEpoch > 1) {
+      //fprintf(fd_performance_out, "\n");
+      fprintf(fd_performance_out, "\t%f\t%d\t%d\n", dopamin_level, (*neuronFreq[0])[0], (*neuronFreq[1])[1]);
+    }else{
+      // fake output as acutal data is not available, yet
+      fprintf(fd_performance_out, "\t%f\t%d\t%d\n", dopamin_level, (int) 0, (int) 0);
+    }
+
+    // set the new DA level
+    msg.dopamin_level = dopamin_level;
+
+    // print new global state
+    // (do this even if there has been no evaluation of the performance yet, 
+    //  because it is neccessary for the simulator to proceed)
+    pushGlobal(((double) currentEpoch + 2.5) * epochDuration);
+  }
+
+  fclose(fd_trace_out);
+
+  // terminate child threads
+  pthread_cancel(thread_read);
+  pthread_cancel(thread_write);
+}
+
+void *read_spikes(Trainer *t) {
+  double lastSpike = -INFINITY; // used to check if the spikes are coming in order
+
+  // read spikes until eternity
+  while (!feof(t->fd_spike_in)) {
+    // read one line from stdin (blocking)
+    char buf[128];
+    if (fgets((char*) buf, 128, t->fd_spike_in) == NULL) continue; // this should stop the loop because of EOF
+
+    // parse the input
+    double time, current;
+    int neuron;
+    switch (sscanf((char*) buf, "%lf, %d, %lf\n", &time, &neuron, &current)) {
+    case 3:
+      // format is ok, continue
+      break;
+    default:
+      // format is wrong, stop
+      fprintf(stderr, "ERROR: malformatted incoming spike:\n\t%s\n", &buf);
+      return NULL;
+    }
+
+    if (lastSpike > time) {
+      fprintf(stderr, "WARN: out of order spike detected (coming from simulator)\n\t%f\t%d\n", time, neuron);
+      continue;
+    }
+
+    lastSpike = time;
+
+    // add the spike to the queue of spikes
+    pthread_mutex_lock(&(t->incomingSpikeLock));
+    t->incomingSpikes.push(boost::make_tuple(time, neuron, current));
+    pthread_mutex_unlock(&(t->incomingSpikeLock));    
+  }
+
+  // we shouldn't reach this point in a non-error case
+  fprintf(stderr, "ERROR: EOF in incoming spike stream\n");
+  // TODO: kill entire programm
+  return NULL;
+}
+
+void *write_spikes(Trainer *t) {
+  // at the moment: generate noise until the file descriptor blocks
+  double time = 0.0;
+
+  // PAR HINT:
+  // loop until exactly one spike after the entire duration is send out
+  // this will block on full buffer on the file descriptor and thus keep
+  // the thread busy early enough
+
+
+  /* // ---- send 100% dependent spike train ---
+  time = 0.005;
+  while (time <= t->entireDuration) {
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, 0, 1.0);
+        time += 0.012;
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, 1, 1.0);
+    time += 1.0;
+  }*/
+
+  
+  /* // ---- send indepenent poisson noise ----
+  while (time <= t->entireDuration) {
+    // calc timing, intensity and destination of the spike
+    // HINT:
+    //   * log(...) is negative
+    //   * drand48() returns something in [0,1), to avoid log(0) we transform it to (0,1]
+    time -= log(1.0 - drand48()) / (t->freq * t->neurons);
+    int dst = rand() % t->neurons;
+    double current = t->voltage;
+    
+    // send it to the simulator
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, dst, current);
+    }*/
+
+  // ---- send indepenent poisson noise w7 increasing fequency----
+  double blafoo = 0;
+  t->freq = 1.0;
+  while (time <= t->entireDuration) {
+    if (time - blafoo > 100.0) {
+      blafoo += 200.0;
+      t->freq += 1.0;
+      time += 100.0; // time jump to let ET recover to zero
+    }
+    // calc timing, intensity and destination of the spike
+    // HINT:
+    //   * log(...) is negative
+    //   * drand48() returns something in [0,1), to avoid log(0) we transform it to (0,1]
+    time -= log(1.0 - drand48()) / (t->freq * t->neurons);
+    int dst = rand() % t->neurons;
+    double current = t->voltage;
+    
+    // send it to the simulator
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, dst, current);
+  }
+
+  // close fd because fscanf sucks
+  fclose(t->fd_spike_out);
+}
diff --git a/code/trainer/mem1.h b/code/trainer/mem1.h
new file mode 100644
index 0000000..31fc2b0
--- /dev/null
+++ b/code/trainer/mem1.h
@@ -0,0 +1,72 @@
+#ifndef TRAINER_H
+#define TRAINER_H
+
+#include <stdio.h>
+#include <pthread.h>
+#include <map>
+#include <queue>
+#include "boost/tuple/tuple.hpp"
+
+
+using namespace std;
+
+class Trainer {
+ public:
+  FILE *fd_spike_in,
+    *fd_spike_out,
+    *fd_global_out,
+    *fd_global_in,
+    *fd_trace_out,
+    *fd_performance_out;
+
+  // init stuff
+  Trainer(int argc, char** argv);
+  void initConfig();
+  void initState();
+  void initGroups();
+  void initFiles();
+  void initThreads();
+
+  // main routine
+  void run();
+
+  // state vars
+  long currentTrial;
+  vector<int> groupFreq; // spikes fired during epoch for each symbol (=group of neurons)
+  vector< set<int>* > ioNeurons; // a set of neurons for each symbol to which the symbol is written and from wich it is read later
+  //queue< int > symbolHist; // stores the symbols displayed; written by thread_write, read by main thread
+  int currentSymbol;
+  double dopamin_level;
+  int state;
+  MS_Global msg;
+
+  // synchronisation vars
+  typedef boost::tuple<double, int, double> SpikeEvent; // <what time, wich neuron, current>
+  queue<SpikeEvent> incomingSpikes;
+  // TODO: outgoingSpikes;
+  pthread_mutex_t incomingSpikeLock, writerLock;
+  // TODO: , outgoingSpikeLock; (including a condition for the writer to wakeup upon if a previously empyt queue has been filled)
+  pthread_t thread_read, thread_write;
+
+  // configuration
+  // network
+  long neurons; // total number of neurons
+  long neuronsPerSymbol;
+  double noiseFreq; // of poisson noise (per neuron)
+  double noiseVoltage; // per noise spike
+  double reward; // per succesful trial
+  
+  // learning task
+  double epochDuration; // a trial consists of several epochs
+  long numTrials;
+  int numSymbols; // number of different things to remember
+  //int readoutDelay; // number of epochs between symbol-write and symbol-read-epoch
+  int refractoryPeriods; // how many epochs to wait after a trial finished until we start with a new trial
+};
+
+// seperate thread to read all spikes neccessary because reading and
+// writing to these descriptors could block and thus cause a deadlock
+void *read_spikes(Trainer *t);
+void *write_spikes(Trainer *t);
+
+#endif // TRAINER_H
diff --git a/code/trainer/reinforce_synapse.cpp b/code/trainer/reinforce_synapse.cpp
new file mode 100644
index 0000000..bf6fc7f
--- /dev/null
+++ b/code/trainer/reinforce_synapse.cpp
@@ -0,0 +1,302 @@
+#include <stdlib.h>
+#include "fileutils.h"
+#include "math.h"
+
+#include "reinforce_synapse.h"
+#include "fileutils.cpp"
+#include "model_switch.h"
+
+using namespace std;
+
+int main(int argc, char **argv) {
+  // check cmd line sanity
+  if (argc != 7) {
+    fprintf(stderr, "Wrong argument count\n\n"
+	    "Call format:\n"
+	    "%s\n\t"
+	    "performance out\n\t"
+	    "trace cmd out\n\t"
+	    "global out\n\t"
+	    "global in\n\t"
+	    "spike out\n\t"
+	    "spike in\n\t"
+	    "\n"
+	    "Special names allowed:\n\t- (standart input)\n\t0 (/dev/null)\n", argv[0]);
+    return -1;
+  }
+
+  Trainer *t = new Trainer(argc, argv);
+  t->run();
+  // TODO: finalize
+}
+
+Trainer::Trainer(int argc, char** argv) {
+  // init vars
+  currentEpoch  = 0;
+  dopamin_level = 0.0;
+
+  epochDuration  = 0.01; // [s]
+  //epochDuration  = 1.0; // [s]
+  entireDuration = 20000.0; // [s]
+  neurons        = 2;    // number of neurons to send noise to
+  freq           = 1.0; // [Hz] per Neuron
+  voltage        = 0.1; // [V]
+  da_single_reward = 0.01;
+
+  neuronFreq[0] = (map<int, int>*) NULL;
+  neuronFreq[1] = (map<int, int>*) NULL;
+
+  // open all file descriptors in an order complementary to the simulators one
+  // to avoid deadlocks
+  fd_spike_in        = fd_magic(argv[6], false);
+  fd_global_in       = fd_magic(argv[4], false);
+  fd_spike_out       = fd_magic(argv[5], true);
+  fd_global_out      = fd_magic(argv[3], true);
+  fd_performance_out = fd_magic(argv[1], true);
+  fd_trace_out       = fd_magic(argv[2], true);
+
+  // init locks
+  pthread_mutex_init(&incomingSpikeLock, NULL);
+
+  // create read and write threads
+  pthread_create(&thread_read, NULL, (void* (*)(void*)) &read_spikes, this);
+  pthread_create(&thread_write, NULL, (void* (*)(void*)) &write_spikes, this);
+}
+
+void Trainer::run() {
+  // start an epoch
+  // wait for it's end
+  // process incomig spikes (binning)
+  // select if a reward takes place
+  // print reward value (TODO: into a seperate, externally given file descriptor)
+  // send out the reward signal
+
+  char *str_trace = "%f; spikes (0; 1); global; neuron (0; 1); synapse (0; 1)\n";
+
+  // send out the full trace commande once (later it will be repeated by sending newline)
+  fprintf(fd_trace_out, str_trace, epochDuration);
+  fflush(fd_trace_out);
+
+  // send the first two global states (at t=0 and t=1.5 [bintime] to allow the simulation to
+  // be initialized (before the causality of the loop below is met)
+  MS_Global msg;
+  msg_init(msg);
+  msg.dopamin_level = dopamin_level;
+
+  // set the tau-levels like in Izhi's network
+  msg.stdp_tau_minus = 1.5 * msg.stdp_tau_plus;
+  msg.stdp_lambda_plus = msg.stdp_lambda_minus;
+
+  fprintf(fd_global_out, "0.0, ");
+  msg_print(msg, fd_global_out);
+  fprintf(fd_global_out, "\n");
+
+  msg_process(msg, 1.5 * epochDuration);
+  dopamin_level = msg.dopamin_level;
+
+
+  fprintf(fd_global_out, "%f, ", 1.5 * epochDuration);
+  msg_print(msg, fd_global_out);
+  fprintf(fd_global_out, "\n");
+
+  fflush(fd_global_out);
+  
+  // loop until the experiment is done
+  for (; currentEpoch * epochDuration < entireDuration; currentEpoch++) {
+    // send a new trace command (do it as early as possible although it is
+    // only executed after the new global is send out at the bottom of this loop)
+    if ((currentEpoch + 2) * epochDuration < entireDuration) {
+      // repeat the previous trace command
+      fprintf(fd_trace_out, "\n");
+    }else{
+      fprintf(fd_trace_out, str_trace, entireDuration - (currentEpoch + 1) * epochDuration);
+    }
+    fflush(fd_trace_out);
+
+    // wait for the end of the epoch (by reading the global state resulting from it)
+    char str_raw[128], str_msg[128]; str_raw[0] = 0;
+    double _foo_dbl;
+    if (fgets((char*) str_raw, 128, fd_global_in) == NULL) {
+      fprintf(stderr, "ERROR: global status file descriptor from simulator closed unexpectedly\n");
+      break;
+    }
+    if ((sscanf((char*) str_raw, "%lf, %[^\n]\n", &_foo_dbl, (char*) str_msg) != 2)
+	|| (!msg_parse(msg, (char*) str_msg))) {
+      fprintf(stderr, "ERROR: reading global status from simulator failed\n\t\"%s\"\n", (char*) str_raw);
+      break;
+    }
+
+    // process incomig spikes (binning) of the previous epoch
+    if (currentEpoch > 0) {
+      // shift the bins
+      if (neuronFreq[0]) {
+	delete neuronFreq[0];
+	neuronFreq[0] = neuronFreq[1];
+      }else{
+	neuronFreq[0] = new map<int, int>();
+      }
+      neuronFreq[1] = new map<int, int>();
+
+      // read all spikes in the correct time window
+      pthread_mutex_lock(&incomingSpikeLock);
+      while ((!incomingSpikes.empty()) && (incomingSpikes.front().get<0>() <= currentEpoch * epochDuration)) {
+	// drop event out of queue
+	SpikeEvent se = incomingSpikes.front();
+	double time = se.get<0>();
+	int neuron = se.get<1>();
+	incomingSpikes.pop();
+
+	// check if it belongs to the previous bin (and ignore it if this is the case)
+	if (time < (currentEpoch - 1) * epochDuration) {
+	  fprintf(stderr, "WARN: spike reading thread to slow; unprocessed spike of the past discovered\n%f\t%f\t%d\t%f\n", time, (double) (currentEpoch - 1) * epochDuration, currentEpoch, epochDuration);
+	  continue;
+	}
+
+	// increment the frequency counter (relies on int being default constructable to value 0)
+	(*neuronFreq[1])[neuron]++;
+      }
+
+      pthread_mutex_unlock(&incomingSpikeLock);
+    }
+
+    // proceed the global state to keep it in sync with the simulator's global state
+    // the local dopamin level is kept seperately and aged only one epochDuration to
+    // avoid oscillation effects in dopamin level
+    msg_process(msg, 1.5 * epochDuration);
+    dopamin_level *= exp( - epochDuration / msg.dopamin_tau );
+
+    // select if the reward takes place
+    if ((currentEpoch > 1) && ((*neuronFreq[0])[0] > 0) && ((*neuronFreq[1])[1] > 0)) {
+      dopamin_level += da_single_reward;
+      fprintf(fd_performance_out, "+");
+    }else{
+      fprintf(fd_performance_out, "-");
+    }
+
+    if (currentEpoch > 1) {
+      //fprintf(fd_performance_out, "\n");
+      fprintf(fd_performance_out, "\t%f\t%d\t%d\n", dopamin_level, (*neuronFreq[0])[0], (*neuronFreq[1])[1]);
+    }else{
+      // fake output as acutal data i not available, yet
+      fprintf(fd_performance_out, "\t%f\t%d\t%d\n", dopamin_level, (int) 0, (int) 0);
+    }
+
+    // set the new DA level
+    msg.dopamin_level = dopamin_level;
+
+    // print new global state
+    // (do this even if there has been no evaluation of the performance yet, 
+    //  because it is neccessary for the simulator to proceed)
+
+    fprintf(fd_global_out, "%f, ", ((double) currentEpoch + 2.5) * epochDuration);
+    msg_print(msg, fd_global_out);
+    fprintf(fd_global_out, "\n");
+    fflush(fd_global_out);
+  }
+
+  fclose(fd_trace_out);
+
+  // terminate child threads
+  pthread_cancel(thread_read);
+  pthread_cancel(thread_write);
+}
+
+void *read_spikes(Trainer *t) {
+  double lastSpike = -INFINITY; // used to check if the spikes are coming in order
+
+  // read spikes until eternity
+  while (!feof(t->fd_spike_in)) {
+    // read one line from stdin (blocking)
+    char buf[128];
+    if (fgets((char*) buf, 128, t->fd_spike_in) == NULL) continue; // this should stop the loop because of EOF
+
+    // parse the input
+    double time, current;
+    int neuron;
+    switch (sscanf((char*) buf, "%lf, %d, %lf\n", &time, &neuron, &current)) {
+    case 3:
+      // format is ok, continue
+      break;
+    default:
+      // format is wrong, stop
+      fprintf(stderr, "ERROR: malformatted incoming spike:\n\t%s\n", &buf);
+      return NULL;
+    }
+
+    if (lastSpike > time) {
+      fprintf(stderr, "WARN: out of order spike detected (coming from simulator)\n\t%f\t%d\n", time, neuron);
+      continue;
+    }
+
+    lastSpike = time;
+
+    // add the spike to the queue of spikes
+    pthread_mutex_lock(&(t->incomingSpikeLock));
+    t->incomingSpikes.push(boost::make_tuple(time, neuron, current));
+    pthread_mutex_unlock(&(t->incomingSpikeLock));    
+  }
+
+  // we shouldn't reach this point in a non-error case
+  fprintf(stderr, "ERROR: EOF in incoming spike stream\n");
+  // TODO: kill entire programm
+  return NULL;
+}
+
+void *write_spikes(Trainer *t) {
+  // at the moment: generate noise until the file descriptor blocks
+  double time = 0.0;
+
+  // PAR HINT:
+  // loop until exactly one spike after the entire duration is send out
+  // this will block on full buffer on the file descriptor and thus keep
+  // the thread busy early enough
+
+
+  /* // ---- send 100% dependent spike train ---
+  time = 0.005;
+  while (time <= t->entireDuration) {
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, 0, 1.0);
+        time += 0.012;
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, 1, 1.0);
+    time += 1.0;
+  }*/
+
+  
+  // ---- send indepenent poisson noise ----
+  while (time <= t->entireDuration) {
+    // calc timing, intensity and destination of the spike
+    // HINT:
+    //   * log(...) is negative
+    //   * drand48() returns something in [0,1), to avoid log(0) we transform it to (0,1]
+    time -= log(1.0 - drand48()) / (t->freq * t->neurons);
+    int dst = rand() % t->neurons;
+    double current = t->voltage;
+    
+    // send it to the simulator
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, dst, current);
+  }
+
+  /*// ---- send indepenent poisson noise w7 increasing fequency----
+  double blafoo = 0;
+  t->freq = 1.0;
+  while (time <= t->entireDuration) {
+    if (time - blafoo > 100.0) {
+      blafoo += 200.0;
+      t->freq += 1.0;
+      time += 100.0; // time jump to let ET recover to zero
+    }
+    // calc timing, intensity and destination of the spike
+    // HINT:
+    //   * log(...) is negative
+    //   * drand48() returns something in [0,1), to avoid log(0) we transform it to (0,1]
+    time -= log(1.0 - drand48()) / (t->freq * t->neurons);
+    int dst = rand() % t->neurons;
+    double current = t->voltage;
+    
+    // send it to the simulator
+    fprintf(t->fd_spike_out, "%f, %d, %f\n", time, dst, current);
+  }*/
+
+  // close fd because fscanf sucks
+  fclose(t->fd_spike_out);
+}
diff --git a/code/trainer/reinforce_synapse.h b/code/trainer/reinforce_synapse.h
new file mode 100644
index 0000000..46b0083
--- /dev/null
+++ b/code/trainer/reinforce_synapse.h
@@ -0,0 +1,55 @@
+#ifndef TRAINER_H
+#define TRAINER_H
+
+#include <stdio.h>
+#include <pthread.h>
+#include <map>
+#include <queue>
+#include "boost/tuple/tuple.hpp"
+
+
+using namespace std;
+
+class Trainer {
+ public:
+  FILE *fd_spike_in,
+    *fd_spike_out,
+    *fd_global_out,
+    *fd_global_in,
+    *fd_trace_out,
+    *fd_performance_out;
+
+  // init stuff
+  Trainer(int argc, char** argv);
+
+  // main routine
+  void run();
+
+  // state vars
+  long currentEpoch;
+  map<int, int> *neuronFreq[2]; // stores if a surveilled neuron fired during the current or last epoch
+  double dopamin_level;
+
+  // synchronisation vars
+  typedef boost::tuple<double, int, double> SpikeEvent; // <what time, wich neuron, current>
+  queue<SpikeEvent> incomingSpikes;
+  // TODO: outgoingSpikes;
+  pthread_mutex_t incomingSpikeLock;
+  // TODO: , outgoingSpikeLock; (including a condition for the writer to wakeup upon if a previously empyt queue has been filled)
+  pthread_t thread_read, thread_write;
+
+  // configuration
+  double epochDuration;
+  double entireDuration;
+  double freq; // of outgoing noise per neuron
+  double voltage; // per outgoing (random) spike
+  long neurons;
+  double da_single_reward;
+};
+
+// seperate thread to read all spikes neccessary because reading and
+// writing to these descriptors could block and thus cause a deadlock
+void *read_spikes(Trainer *t);
+void *write_spikes(Trainer *t);
+
+#endif // TRAINER_H
diff --git a/code/trainer/test.cpp b/code/trainer/test.cpp
new file mode 100644
index 0000000..ceb2484
--- /dev/null
+++ b/code/trainer/test.cpp
@@ -0,0 +1,13 @@
+#include <stdio.h>
+#include <math.h>
+
+int main() {
+  fprintf("aaa\n");
+  while (true);/*
+  double d=0;
+  printf("aa %lf\n", d);
+  d = 0;
+  scanf("%lf\n", &d);
+  printf("%lf\n", d);*/
+  return 0;
+}
diff --git a/model_input/Makefile b/model_input/Makefile
new file mode 100644
index 0000000..11358d6
--- /dev/null
+++ b/model_input/Makefile
@@ -0,0 +1,5 @@
+.PHONY: all
+all:
+	cd topology && make
+	cd neurons && make
+	cd spikes && make
diff --git a/model_input/global/if/default b/model_input/global/if/default
new file mode 100644
index 0000000..e69de29
diff --git a/model_input/neurons/Makefile b/model_input/neurons/Makefile
new file mode 100644
index 0000000..8c205d2
--- /dev/null
+++ b/model_input/neurons/Makefile
@@ -0,0 +1,11 @@
+.PHONY: all
+all: if/1000_nocharge
+
+if/%_nocharge :
+	rm -f $@
+	I=0; while [ $* -gt $$I ]; do echo 0 >> $@; I=$$(( $$I + 1 )); done
+
+dalif/%_nocharge :
+	rm -f $@
+	I=0; while [ $* -gt $$I ]; do echo "-0.1" >> $@; I=$$(( $$I + 1 )); done
+
diff --git a/model_input/neurons/dalif/1000_randomcharge b/model_input/neurons/dalif/1000_randomcharge
new file mode 100644
index 0000000..5434321
--- /dev/null
+++ b/model_input/neurons/dalif/1000_randomcharge
@@ -0,0 +1,1000 @@
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diff --git a/model_input/neurons/if/1_smallcharge b/model_input/neurons/if/1_smallcharge
new file mode 100644
index 0000000..209e3ef
--- /dev/null
+++ b/model_input/neurons/if/1_smallcharge
@@ -0,0 +1 @@
+20
diff --git a/model_input/neurons/if/3_supercharge b/model_input/neurons/if/3_supercharge
new file mode 100644
index 0000000..f6f7853
--- /dev/null
+++ b/model_input/neurons/if/3_supercharge
@@ -0,0 +1,3 @@
+10000
+10000
+10000
diff --git a/model_input/spikes/Makefile b/model_input/spikes/Makefile
new file mode 100644
index 0000000..3a4f512
--- /dev/null
+++ b/model_input/spikes/Makefile
@@ -0,0 +1,7 @@
+.PHONY: all
+all: 1000N_10s_10Hz_random 1N_10s_10Hz_random
+
+%_random : ../../code/matlab/random_spikes.m
+	../../code/matlab/random_spikes `echo $* | sed 's/^/num_neurons=/' | sed 's/N\_/;duration=/' | sed 's/s\_/;spike_freq=/' | sed 's/Hz$$/;/'` >/dev/null 2> $@
+
+
diff --git a/model_input/topology/Makefile b/model_input/topology/Makefile
new file mode 100644
index 0000000..22424b0
--- /dev/null
+++ b/model_input/topology/Makefile
@@ -0,0 +1,12 @@
+.PHONY: all
+all: if/1000_random
+
+if/%_random : ../../code/matlab/random_topo.m
+	../../code/matlab/random_topo "num_neurons=$*; connection_density=0.1; inhibitory_fraction=0.2;" 1>/dev/null 2> $@
+
+if/1_to_%:
+	rm -f $@
+	for I in $$(seq 1 $$(echo "$@" | egrep -o '[0-9]+$$')); do echo "0, $$I, 0.01, 0.001" >> $@; done
+
+dalif/%: if/%
+	cat $< | sed 's/^.*$$/0.0/' | paste -d"," $< - > $@
diff --git a/model_input/topology/README b/model_input/topology/README
new file mode 100644
index 0000000..b3d3685
--- /dev/null
+++ b/model_input/topology/README
@@ -0,0 +1 @@
+the first number denotes the number of neurons used
diff --git a/model_input/topology/if/2circle b/model_input/topology/if/2circle
new file mode 100644
index 0000000..446d25c
--- /dev/null
+++ b/model_input/topology/if/2circle
@@ -0,0 +1,2 @@
+0, 1, 0.01, 0.001
+1, 0, 0.01, 0.001
diff --git a/model_input/topology/if/3circle2 b/model_input/topology/if/3circle2
new file mode 100644
index 0000000..35bbc5d
--- /dev/null
+++ b/model_input/topology/if/3circle2
@@ -0,0 +1,6 @@
+0, 1, 0.333, 0.9
+0, 2, 0.4, 0.9
+1, 2, 0.334, 0.9
+1, 0, 0.39, 0.9
+2, 0, 0.333, 0.9
+2, 1, 0.3, 0.9
diff --git a/model_input/trace/10s_10ms_all b/model_input/trace/10s_10ms_all
new file mode 100644
index 0000000..a3ee5a3
--- /dev/null
+++ b/model_input/trace/10s_10ms_all
@@ -0,0 +1,1000 @@
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+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
+0.01; neuron; synapse; global; spikes
diff --git a/model_input/trace/10s_10s_all b/model_input/trace/10s_10s_all
new file mode 100644
index 0000000..71eabd3
--- /dev/null
+++ b/model_input/trace/10s_10s_all
@@ -0,0 +1 @@
+10; neuron; synapse; global; spikes
diff --git a/model_input/trace/README b/model_input/trace/README
new file mode 100644
index 0000000..1f15812
--- /dev/null
+++ b/model_input/trace/README
@@ -0,0 +1,3 @@
+to have a repetitive trace command every x ms use
+
+code/glue/repeat-trace-cmd duration trace_interval "trace commands"
-- 
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