RxD bath application, updated replace_axon

examples/notebooks/neuromodulation/data/DA-bath-experiment.json

@@ -0,0 +1,38 @@
+{
+    "network_file": "networks/neuromodulation_bath/network-synapses.hdf5",
+    "input_file": "networks/neuromodulation_bath/input-spikes.hdf5",
+    "output_file": "networks/neuromodulation_bath/simulation/output.hdf5",
+    "log_file": "networks/neuromodulation_bath/log/network-simulation-bath.txt",
+    "time": 4.0,
+    "record_all_soma": true,
+    "record_rxd_species_all": [0, 1],
+    "record_density_mechanism": {	
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"naf_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_g": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_shift": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	}	
+    },
+    "rxd_enable_extracellular": false,
+    "bath_application": {
+	"DA": {
+	    "time": [0, 1.99, 2, 4],
+	    "concentration": [0, 0, 60e-6, 60e-6]
+	}
+    }
+}

examples/notebooks/neuromodulation/data/da_experiment_off.json

@@ -0,0 +1,15 @@
+{
+    "network_file": "networks/neuromodulation_ON_OFF/network-synapses.hdf5",
+    "input_file": "networks/neuromodulation_ON_OFF/input-spikes.hdf5",
+    "output_file": "networks/neuromodulation_ON_OFF/simulation/output_neuromodulation_OFF.hdf5",
+    "log_file": "networks/neuromodulation_ON_OFF/log/network-simulation-OFF.txt",
+    "time": 25.0,
+    "record_all_soma": true,
+    "record_density_mechanism": {
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [0, 0],
+	    "section_x": [0.5, 0.5]
+	}
+    }
+}

examples/notebooks/neuromodulation/data/da_experiment_off_bath.json

@@ -0,0 +1,15 @@
+{
+    "network_file": "networks/neuromodulation_ON_OFF_bath/network-synapses.hdf5",
+    "input_file": "networks/neuromodulation_ON_OFF_bath/input-spikes.hdf5",
+    "output_file": "networks/neuromodulation_ON_OFF_bath/simulation/output_neuromodulation_OFF.hdf5",
+    "log_file": "networks/neuromodulation_ON_OFF_bath/log/network-simulation-OFF.txt",
+    "time": 25.0,
+    "record_all_soma": true,
+    "record_density_mechanism": {
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [0, 0],
+	    "section_x": [0.5, 0.5]
+	}
+    }
+}

examples/notebooks/neuromodulation/data/da_experiment_on.json

@@ -0,0 +1,32 @@
+{
+    "network_file": "networks/neuromodulation_ON_OFF/network-synapses.hdf5",
+    "input_file": "networks/neuromodulation_ON_OFF/input-spikes.hdf5",
+    "output_file": "networks/neuromodulation_ON_OFF/simulation/output_neuromodulation_ON.hdf5",
+    "log_file": "networks/neuromodulation_ON_OFF/log/network-simulation-ON.txt",
+    "time": 25.0,
+    "record_all_soma": true,
+    "record_rxd_species_all": [0, 1],
+    "record_density_mechanism": {	
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"naf_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_g": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_shift": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	}	
+    },
+    "rxd_enable_extracellular": false
+}

examples/notebooks/neuromodulation/data/da_experiment_on_bath.json

@@ -0,0 +1,32 @@
+{
+    "network_file": "networks/neuromodulation_ON_OFF_bath/network-synapses.hdf5",
+    "input_file": "networks/neuromodulation_ON_OFF_bath/input-spikes.hdf5",
+    "output_file": "networks/neuromodulation_ON_OFF_bath/simulation/output_neuromodulation_ON.hdf5",
+    "log_file": "networks/neuromodulation_ON_OFF_bath/log/network-simulation-ON.txt",
+    "time": 25.0,
+    "record_all_soma": true,
+    "record_rxd_species_all": [0, 1],
+    "record_density_mechanism": {	
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"naf_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_g": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"kaf_ms.modulation_factor_shift": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	}	
+    },
+    "rxd_enable_extracellular": false
+}

examples/notebooks/neuromodulation/data/input_v6_bath_on_off.json

@@ -0,0 +1,23 @@
+{
+    "dspn": {
+	"cortical_background": {
+	    "generator": "poisson",
+	    "frequency": 1.2
+	},
+	"thalamic_background": {
+	    "generator": "poisson",
+	    "frequency": 1.2
+	},
+        "cortical" : {
+            "generator" : "poisson",
+            "start" : [0],
+            "end" : [10],
+            "frequency" : [10],
+            "conductance" : 0.5e-9,
+	    "input_correlation": 0.75,
+            "num_inputs" : 20,
+	    "parameter_file": "data/tmglut_DA_parameters.json",
+            "mod_file": "tmGlut"
+        }
+    }
+}