Updated neurmodulation notebooks

Hjorthmedh · Oct 17, 2024 · b313653 · b313653
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Showing 7 changed files with 187,834 additions and 53,054 deletions.
diff --git a/examples/notebooks/neuromodulation/bath_current_injection.json b/examples/notebooks/neuromodulation/bath_current_injection.json
@@ -1,10 +1,10 @@
 {
     "0": {
-	"time": [0, 0.5, 1, 10],
-	"current": [0, 600e-12, 0, 0]
+	"time": [0, 10],
+	"current": [700e-12, 700e-12]
     },
     "1": {
-	"time": [0, 0.5, 1, 10],
-	"current": [0, 500e-12, 0, 0]
+	"time": [0, 10],
+	"current": [600e-12, 600e-12]
     }
 }
diff --git a/examples/notebooks/neuromodulation/data/da_experiment_cur_inj_off_bath.json b/examples/notebooks/neuromodulation/data/da_experiment_cur_inj_off_bath.json
@@ -3,7 +3,7 @@
     "output_file": "networks/neuromodulation_bath_current/simulation/output_neuromodulation_OFF.hdf5",
     "log_file": "networks/neuromodulation_bath_current/log/network-simulation-OFF.txt",
     "time": 1.5,
-    "sim_dt": 0.001,
+    "!sim_dt": 0.005,
     "record_all_soma": true,
     "record_rxd_species_all": [0, 1],
     "record_density_mechanism": {	

diff --git a/examples/notebooks/neuromodulation/data/da_experiment_cur_inj_on_bath.json b/examples/notebooks/neuromodulation/data/da_experiment_cur_inj_on_bath.json
@@ -2,8 +2,8 @@
     "network_file": "networks/neuromodulation_bath_current/network-synapses.hdf5",
     "output_file": "networks/neuromodulation_bath_current/simulation/output_neuromodulation_ON.hdf5",
     "log_file": "networks/neuromodulation_bath_current/log/network-simulation-ON.txt",
-    "time": 70,
-    "sim_dt": 0.005,
+    "time": 2,
+    "!sim_dt": 0.005,
     "record_all_soma": true,
     "record_rxd_species_soma": [0, 1],
     "record_density_mechanism": {	
@@ -26,17 +26,36 @@
 	    "neuron_id": [0, 1],
 	    "section_id": [-1, -1],
 	    "section_x": [0.5, 0.5]
-	}	
+	},
+	"kas_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+
+	"cal12_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	},
+	"cal13_ms.modulation_factor": {
+	    "neuron_id": [0, 1],
+	    "section_id": [-1, -1],
+	    "section_x": [0.5, 0.5]
+	}
+
     },
     "rxd_enable_extracellular": false,
     "bath_application": {
 	"DA": {
 	    "!!time": [0, 0.9999, 1, 10.99, 11.0, 20.999, 21, 30.999, 31, 50],
 	    "!!concentration": [2e-9, 2e-9, 60e-6, 60e-6, 100e-6, 100e-6, 2e-9, 2e-9, 0, 0],
-	    "time": [0, 9.99, 10.0, 19.99, 20, 29.99, 30, 39.99, 40, 49.99, 50, 59.99, 60, 70],
-	    "concentration": [1e-9, 1e-9, 20e-9, 20e-9, 50e-9, 50e-9, 100e-9, 100e-9, 200e-9, 200e-9, 500e-9, 500e-9, 1e-6, 1e-6],
+	    "!time": [0, 9.99, 10.0, 19.99, 20, 29.99, 30, 39.99, 40, 49.99, 50, 59.99, 60, 70],
+	    "!concentration": [1e-9, 1e-9, 20e-9, 20e-9, 50e-9, 50e-9, 100e-9, 100e-9, 200e-9, 200e-9, 500e-9, 500e-9, 1e-6, 1e-6],
 	    "!time": [0, 100],
 	    "!concentration": [20e-9, 20e-9],
+	    "time": [0, 1, 1, 2, 2, 10],
+	    "concentration": [20e-9, 20e-9, 250e-9, 250e-9, 20e-9, 20e-9],
 	    "interpolate": true
 	}
     },