adjustments for Arbor v0.9.0; README update

.gitignore

@@ -0,0 +1,2 @@
+*.so
+*.dat

AdEx/arbor_adex.py

@@ -104,11 +104,11 @@ def cell_description(self, gid):
         adex.set("tau_w", neuron_config["tau_w"])
 
         decor.paint('(all)', arbor.density(adex))
-        decor.place('"center"', arbor.spike_detector(v_thresh), "spike_detector")
+        decor.place('"center"', arbor.threshold_detector(v_thresh), "spike_detector")
 
         decor.place('"center"', arbor.iclamp(stimulus_config["amplitude"]/1e-9), "iclamp")
 
-        return arbor.cable_cell(tree, labels, decor)
+        return arbor.cable_cell(tree, decor, labels)
 
     def event_generators(self, gid):
         """Return event generators on gid."""
@@ -140,7 +140,7 @@ def main(variant):
 
     context = arbor.context()
     domains = arbor.partition_load_balance(recipe, context)
-    sim = arbor.simulation(recipe, domains, context)
+    sim = arbor.simulation(recipe, context, domains)
 
     sim.record(arbor.spike_recording.all)
 

README.md

@@ -1,22 +1,22 @@
 # FIPPA: The Functional Interplay between Plasticity Processes on Arbor
 
-The goal of FIPPA is to extend the neural network simulator
+The goal of the FIPPA project was to extend the neural network simulator
 [Arbor](https://arbor-sim.github.io) by key plasticity processes that
-will allow to simulate and analyze the long-term adaptive dynamics of
-large-scale, morphologically-detailed neuronal networks.The models
-that will be ported and augmented are based on the neuro-theoretical
-framework by [tetzlab.com](https://tetzlab.com). These models already
-indicated that the interplay between the plasticity processes of
-synaptic plasticity, synaptic scaling, and structural plasticity
-yields the formation and organization of motor memories.The research
-question is how multi-compartment neuron models with detailed synaptic
-dynamics can be utilized to improve the performance of such
-networks. Our main hypothesis is that the adaptive dynamics on the
-network level enforces the specialization of branches by the formation
-of synaptic clusters leading to the formation of self-sustaining
-long-term memories and an overall increase in storage capacity.
+allow to simulate and analyze the long-term adaptive dynamics of
+large-scale, morphologically-detailed neuronal networks. The models
+were ported and augmented in correspondence to neuro-theoretical
+investigations by the [Tetzlaff research group](https://tetzlab.com) at
+University of Göttingen.
 
-# Outputs
+## Arbor implementations -- FIPPA output
 
-* [Event-driven plasticity](STDP)
+* [Spike-timing-dependent plasticity (STDP)](STDP)
 * [Spike-based homeostasis](spike_based_homeostasis)
+* [Adaptive exponential integrate-and-fire (AdEx) neuron](AdEx)
+* [Synaptic tagging and capture (STC) in recurrent networks of point neurons](https://github.com/tetzlab/arbor_network_consolidation)
+
+## Arbor implementations -- based on FIPPA
+
+* Calcium-based synaptic plasticity
+* Heterosynaptic calcium-based plasticity in dendrites
+* Synaptic tagging and capture (STC) in recurrent networks of morphological neurons

STDP/Makefile

@@ -1,6 +1,6 @@
 .DEFAULT_GOAL := comparison_brian2_arbor.png
 
-BUILD_CATALOGUE_SCRIPT := build-catalogue
+BUILD_CATALOGUE_SCRIPT := arbor-build-catalogue
 
 custom-catalogue.so: $(wildcard mechanisms/*.mod)
 	$(BUILD_CATALOGUE_SCRIPT) custom mechanisms

STDP/arbor_lif_stdp.py

@@ -23,7 +23,7 @@ def __init__(self, config):
         self.the_props = arbor.neuron_cable_properties()
         self.the_cat = arbor.load_catalogue("./custom-catalogue.so")
         self.the_cat.extend(arbor.default_catalogue(), "")
-        self.the_props.register(self.the_cat)
+        self.the_props.catalogue = self.the_cat
 
         self.config = config
 
@@ -73,8 +73,8 @@ def cell_description(self, gid):
         lif.set("g_reset", neuron_config["g_reset"])
         lif.set("g_leak", neuron_config["g_leak"])
         lif.set("tau_refrac", neuron_config["tau_refrac"])
-        decor.paint('(all)', lif)
-        decor.place('"center"', arbor.spike_detector(v_thresh), "spike_detector")
+        decor.paint('(all)', arbor.density(lif))
+        decor.place('"center"', arbor.threshold_detector(v_thresh), "spike_detector")
 
         # plastic excitatory synapse
         syn_config_stdp = self.config["synapses"]["cond_exp_stdp"]
@@ -86,16 +86,16 @@ def cell_description(self, gid):
         mech_expsyn_exc.set('Apre', syn_config_stdp["A_pre"])
         mech_expsyn_exc.set('Apost', syn_config_stdp["A_post"])
         mech_expsyn_exc.set('max_weight', 50)
-        decor.place('"center"', mech_expsyn_exc, "expsyn_stdp_exc")
+        decor.place('"center"', arbor.synapse(mech_expsyn_exc), "expsyn_stdp_exc")
 
         # inhibitory synapse
         syn_config = self.config["synapses"]["cond_exp"]
         mech_expsyn_inh = arbor.mechanism('expsyn')
         mech_expsyn_inh.set('tau', syn_config["tau"])
         mech_expsyn_inh.set('e', syn_config["reversal_potential"])
-        decor.place('"center"', mech_expsyn_inh, "expsyn_inh")
+        decor.place('"center"', arbor.synapse(mech_expsyn_inh), "expsyn_inh")
 
-        return arbor.cable_cell(tree, labels, decor)
+        return arbor.cable_cell(tree, decor, labels)
 
     def event_generators(self, gid):
         """Return event generators on gid."""
@@ -141,7 +141,7 @@ def main(variant):
 
     context = arbor.context()
     domains = arbor.partition_load_balance(recipe, context)
-    sim = arbor.simulation(recipe, domains, context)
+    sim = arbor.simulation(recipe, context, domains)
 
     sim.record(arbor.spike_recording.all)
 

set_arbor_env

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Script that sets environment variables required to run custom Arbor installation
+
+# check if PATH exists and set environment variable accordingly
+if [[ ! -v PATH ]]; then
+	export PATH=$(readlink -f ~/arbor_v0.9.0/bin)
+else
+	export PATH=$(readlink -f ~/arbor_v0.9.0/bin):$PATH
+fi
+
+# check if LD_LIBRARY_PATH exists and set environment variable accordingly
+if [[ ! -v LD_LIBRARY_PATH ]]; then
+	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.0/lib)
+else
+	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.0/lib):$LD_LIBRARY_PATH
+fi
+
+# check if PYTHONPATH exists and set environment variable accordingly
+if [[ ! -v PYTHONPATH ]]; then
+	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.0/lib/python3.8/site-packages) # or: .../python3.6/..., etc.
+else
+	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.0/lib/python3.8/site-packages):$PYTHONPATH # or: .../python3.6/..., etc.
+fi
+
+# set CMAKE_PREFIX_PATH environment variable
+export CMAKE_PREFIX_PATH=$(readlink -f ~/arbor_v0.9.0)

spike_based_homeostasis/Makefile

@@ -1,6 +1,6 @@
 .DEFAULT_GOAL := homeostasis.svg
 
-BUILD_CATALOGUE_SCRIPT := build-catalogue
+BUILD_CATALOGUE_SCRIPT := arbor-build-catalogue
 CONFIG := config.json
 
 homeostasis-catalogue.so: $(wildcard mechanisms/*.mod)

spike_based_homeostasis/arbor_homeostasis.py

@@ -38,7 +38,7 @@ def __init__(self, config, catalogue):
         self.the_props = arbor.neuron_cable_properties()
         self.the_cat = catalogue
         self.the_cat.extend(arbor.default_catalogue(), "")
-        self.the_props.register(self.the_cat)
+        self.the_props.catalogue = self.the_cat
 
         self.config = config
 
@@ -88,8 +88,8 @@ def cell_description(self, gid):
         lif.set("g_reset", neuron_config["g_reset"])
         lif.set("g_leak", neuron_config["g_leak"])
         lif.set("tau_refrac", neuron_config["tau_refrac"])
-        decor.paint('(all)', lif)
-        decor.place('"center"', arbor.spike_detector(v_thresh), "spike_detector")
+        decor.paint('(all)', arbor.density(lif))
+        decor.place('"center"', arbor.threshold_detector(v_thresh), "spike_detector")
 
         # plastic synapse
         syn_config_homeostasis = self.config["stimulus"]["steady"]
@@ -98,16 +98,16 @@ def cell_description(self, gid):
         mech_expsyn_homeostasis.set('e', syn_config_homeostasis["reversal_potential"])
         mech_expsyn_homeostasis.set('dw_plus', syn_config_homeostasis["dw_plus"])
         mech_expsyn_homeostasis.set('dw_minus', syn_config_homeostasis["dw_minus"])
-        decor.place('"center"', mech_expsyn_homeostasis, "expsyn_homeostasis")
+        decor.place('"center"', arbor.synapse(mech_expsyn_homeostasis), "expsyn_homeostasis")
 
         # static synapse
         syn_config = self.config["stimulus"]["varying"]
         mech_expsyn_varying = arbor.mechanism('expsyn')
         mech_expsyn_varying.set('tau', syn_config["tau"])
         mech_expsyn_varying.set('e', syn_config["reversal_potential"])
-        decor.place('"center"', mech_expsyn_varying, "expsyn")
+        decor.place('"center"', arbor.synapse(mech_expsyn_varying), "expsyn")
 
-        return arbor.cable_cell(tree, labels, decor)
+        return arbor.cable_cell(tree, decor, labels)
 
     def event_generators(self, gid):
         """Return event generators on gid."""
@@ -158,7 +158,7 @@ def main(config, catalogue):
 
     context = arbor.context()
     domains = arbor.partition_load_balance(recipe, context)
-    sim = arbor.simulation(recipe, domains, context)
+    sim = arbor.simulation(recipe, context, domains)
 
     sim.record(arbor.spike_recording.all)