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Merge pull request #427 from Hjorthmedh/neuromod_redux2
RxD bath application, updated replace_axon
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38 changes: 38 additions & 0 deletions
38
examples/notebooks/neuromodulation/data/DA-bath-experiment.json
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| { | ||
| "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] | ||
| } | ||
| } | ||
| } |
15 changes: 15 additions & 0 deletions
15
examples/notebooks/neuromodulation/data/da_experiment_off.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| { | ||
| "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] | ||
| } | ||
| } | ||
| } |
15 changes: 15 additions & 0 deletions
15
examples/notebooks/neuromodulation/data/da_experiment_off_bath.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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] | ||
| } | ||
| } | ||
| } |
32 changes: 32 additions & 0 deletions
32
examples/notebooks/neuromodulation/data/da_experiment_on.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } |
32 changes: 32 additions & 0 deletions
32
examples/notebooks/neuromodulation/data/da_experiment_on_bath.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } |
23 changes: 23 additions & 0 deletions
23
examples/notebooks/neuromodulation/data/input_v6_bath_on_off.json
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| Original file line number | Diff line number | Diff line change |
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| { | ||
| "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" | ||
| } | ||
| } | ||
| } |
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