diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index ed36379..3936aa4 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -17,10 +17,10 @@ jobs: python-version: [ 3.7, 3.9 ] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 63d13ea..5f69bff 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -18,10 +18,10 @@ jobs: engine: [ jNeuroML, jNeuroML_NEURON, Brian2 ] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} diff --git a/NeuroML2/GenerateNetwork.py b/NeuroML2/GenerateNetwork.py index 38fafa4..c906d44 100644 --- a/NeuroML2/GenerateNetwork.py +++ b/NeuroML2/GenerateNetwork.py @@ -85,7 +85,7 @@ def generate(wee = 1.5, wei = -3.25, wie = 3.5, wii = -2.5, interlaminar1=0, if not tgt in all_tgts: #and 'V' in tgt and 'V' in src: all_tgts.append(tgt) - print all_tgts + print(all_tgts) print(len(all_tgts)) f = open('Neuron_2015_Table.csv') diff --git a/NeuroML2/Interareal.json b/NeuroML2/Interareal.json index f615b15..e256f2d 100644 --- a/NeuroML2/Interareal.json +++ b/NeuroML2/Interareal.json @@ -1,6 +1,6 @@ { "Interareal": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "notes": "Testing...", "parameters": { "wee": 1.5, @@ -490,12 +490,12 @@ "modulation_V1_L23_E": { "input_source": "iclamp_V1_L23", "population": "V1_L23_E", - "percentage": 100.0 + "percentage": 100 }, "modulation_V1_L56_E": { "input_source": "iclamp_V1_L56", "population": "V1_L56_E", - "percentage": 100.0 + "percentage": 100 } } } diff --git a/NeuroML2/Interareal.net.nml b/NeuroML2/Interareal.net.nml index 915d1e2..51c31c9 100644 --- a/NeuroML2/Interareal.net.nml +++ b/NeuroML2/Interareal.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.3 + Generated by NeuroMLlite v0.5.8 Generated network: Interareal Generation seed: 1234 NeuroMLlite parameters: @@ -60,7 +60,7 @@ - + @@ -68,7 +68,7 @@ - + @@ -76,7 +76,7 @@ - + @@ -84,7 +84,7 @@ - + @@ -92,7 +92,7 @@ - + @@ -100,7 +100,7 @@ - + @@ -108,7 +108,7 @@ - + @@ -116,7 +116,7 @@ - + diff --git a/NeuroML2/Interareal_3.json b/NeuroML2/Interareal_3.json index 7d2aa41..270d965 100644 --- a/NeuroML2/Interareal_3.json +++ b/NeuroML2/Interareal_3.json @@ -1,935 +1,651 @@ { "Interareal_3": { - "version": "NeuroMLlite v0.1.8", + "version": "NeuroMLlite v0.5.8", + "notes": "Testing...", "parameters": { - "wie": -3.25, - "iclamp_V1_L23_amp": "2nA", - "l5e_l2i": 0.75, - "FF_l2e_l2e": 1.0, - "l2e_l5e": 1, - "wii": -2.5, - "FB_l5e_l2e": 0.1, - "wee": 1.5, - "FB_l5e_l5e": 0.9, - "duration_stim": "1e9ms", - "FB_l5e_l5i": 0.5, - "sigma56": 0.45, - "delay_stim": "0ms", - "FB_l5e_l2i": 0.5, - "iclamp_V1_L56_amp": "4nA", - "wei": 3.5, - "sigma23": 0.3 - }, - "notes": "Testing...", - "cells": [ - { - "L23_E_comp": { - "lems_source_file": "Prototypes.xml" - } - }, - { - "L23_I_comp": { - "lems_source_file": "RateBased.xml" - } - }, - { - "L56_E_comp": { - "lems_source_file": "NoisyCurrentSource.xml" - } - }, - { - "L56_I_comp": { - "lems_source_file": "Prototypes.xml" - } + "wee": 1.5, + "wei": 3.5, + "wie": -3.25, + "wii": -2.5, + "l5e_l2i": 0.75, + "l2e_l5e": 1, + "FF_l2e_l2e": 1.0, + "FB_l5e_l2i": 0.5, + "FB_l5e_l5e": 0.9, + "FB_l5e_l5i": 0.5, + "FB_l5e_l2e": 0.1, + "sigma23": 0.3, + "sigma56": 0.45, + "delay_stim": "0ms", + "duration_stim": "1e9ms", + "iclamp_V1_L23_amp": "2nA", + "iclamp_V1_L56_amp": "4nA" + }, + "cells": { + "L23_E_comp": { + "lems_source_file": "Prototypes.xml" + }, + "L23_I_comp": { + "lems_source_file": "Prototypes.xml" + }, + "L56_E_comp": { + "lems_source_file": "Prototypes.xml" + }, + "L56_I_comp": { + "lems_source_file": "Prototypes.xml" } - ], - "synapses": [ - { - "rs": { - "lems_source_file": "Prototypes.xml" - } + }, + "synapses": { + "rs": { + "lems_source_file": "Prototypes.xml" + }, + "silent1": { + "lems_source_file": "RateBased.xml" } - ], - "input_sources": [ - { - "iclamp_V1_L23": { - "neuroml2_input": "PulseGenerator", - "parameters": { - "delay": "delay_stim", - "duration": "duration_stim", - "amplitude": "iclamp_V1_L23_amp" - } - } - }, - { - "iclamp_V1_L56": { - "neuroml2_input": "PulseGenerator", - "parameters": { - "delay": "delay_stim", - "duration": "duration_stim", - "amplitude": "iclamp_V1_L56_amp" - } - } + }, + "input_sources": { + "iclamp_V1_L23": { + "parameters": { + "amplitude": "iclamp_V1_L23_amp", + "delay": "delay_stim", + "duration": "duration_stim" + }, + "neuroml2_input": "PulseGenerator" + }, + "iclamp_V1_L56": { + "parameters": { + "amplitude": "iclamp_V1_L56_amp", + "delay": "delay_stim", + "duration": "duration_stim" + }, + "neuroml2_input": "PulseGenerator" } - ], - "regions": [ - { - "V1_L23": { - "x": 0.0, - "y": 5.0, - "z": 0.0, - "width": 5.0, - "height": 30.0, - "depth": 5.0 - } - }, - { - "V1_L56": { - "x": 0.0, - "y": 0.0, - "z": 0.0, - "width": 5.0, - "height": 5.0, - "depth": 5.0 - } - }, - { - "V4_L23": { - "x": 15.0, - "y": 5.0, - "z": 0.0, - "width": 5.0, - "height": 30.0, - "depth": 5.0 - } - }, - { - "V4_L56": { - "x": 15.0, - "y": 0.0, - "z": 0.0, - "width": 5.0, - "height": 5.0, - "depth": 5.0 - } - }, - { - "MT_L23": { - "x": 30.0, - "y": 5.0, - "z": 0.0, - "width": 5.0, - "height": 30.0, - "depth": 5.0 - } - }, - { - "MT_L56": { - "x": 30.0, - "y": 0.0, - "z": 0.0, - "width": 5.0, - "height": 5.0, - "depth": 5.0 - } + }, + "regions": { + "V1_L23": { + "x": 0.0, + "y": 5.0, + "z": 0.0, + "width": 5.0, + "height": 30.0, + "depth": 5.0 + }, + "V1_L56": { + "x": 0.0, + "y": 0.0, + "z": 0.0, + "width": 5.0, + "height": 5.0, + "depth": 5.0 + 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0, + "weight": "1.0", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_I_MT_L23_E": { + "presynaptic": "MT_L23_I", + "postsynaptic": "MT_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_I_MT_L23_I": { + "presynaptic": "MT_L23_I", + "postsynaptic": "MT_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L23_I": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "0.75", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L56_E": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L56_I": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_I_MT_L56_E": { + "presynaptic": "MT_L56_I", + "postsynaptic": "MT_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_I_MT_L56_I": { + "presynaptic": "MT_L56_I", + "postsynaptic": "MT_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 } } - ], - "inputs": [ - { - "modulation_V1_L23_E": { - "input_source": "iclamp_V1_L23", - "population": "V1_L23_E", - "percentage": 100.0 - } - }, - { - "modulation_V1_L56_E": { - "input_source": "iclamp_V1_L56", - "population": "V1_L56_E", - "percentage": 100.0 - } + }, + "inputs": { + "modulation_V1_L23_E": { + "input_source": "iclamp_V1_L23", + "population": "V1_L23_E", + "percentage": 100 + }, + "modulation_V1_L56_E": { + "input_source": "iclamp_V1_L56", + "population": "V1_L56_E", + "percentage": 100 } - ] + } } } \ No newline at end of file diff --git a/NeuroML2/Interareal_3.net.nml b/NeuroML2/Interareal_3.net.nml index 47ed925..70276b4 100644 --- a/NeuroML2/Interareal_3.net.nml +++ b/NeuroML2/Interareal_3.net.nml @@ -1,5 +1,5 @@ - - Generated by NeuroMLlite v0.1.8 + + Generated by NeuroMLlite v0.5.8 Generated network: Interareal_3 Generation seed: 1234 NeuroMLlite parameters: @@ -23,6 +23,7 @@ + @@ -38,13 +39,8 @@ - - - - - @@ -55,14 +51,6 @@ - - - - - - - - @@ -72,102 +60,102 @@ Testing... - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -215,27 +203,12 @@ - - - - - - - - - - - - - - - @@ -266,30 +239,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/NeuroML2/Interareal_30.json b/NeuroML2/Interareal_30.json index 20f2a5d..0a9fce8 100644 --- a/NeuroML2/Interareal_30.json +++ b/NeuroML2/Interareal_30.json @@ -1,23248 +1,5424 @@ { "Interareal_30": { - "version": "NeuroMLlite v0.1.8", + "version": "NeuroMLlite v0.5.8", + "notes": "Testing...", "parameters": { - "wie": -3.25, - "iclamp_V1_L23_amp": "2nA", - "l5e_l2i": 0.75, - "FF_l2e_l2e": 1.0, - "l2e_l5e": 1, - "wii": -2.5, - "FB_l5e_l2e": 0.1, - "wee": 1.5, - "FB_l5e_l5e": 0.9, - "duration_stim": "1e9ms", - "FB_l5e_l5i": 0.5, - "sigma56": 0.45, - "delay_stim": "0ms", - "FB_l5e_l2i": 0.5, - "iclamp_V1_L56_amp": "4nA", - "wei": 3.5, - "sigma23": 0.3 - }, - "notes": "Testing...", - "cells": [ - { - "L23_E_comp": { - "lems_source_file": "Prototypes.xml" - } - }, - { - "L23_I_comp": { - "lems_source_file": "RateBased.xml" - } - }, - { - "L56_E_comp": { - "lems_source_file": "NoisyCurrentSource.xml" - } - }, - { - "L56_I_comp": { - "lems_source_file": "Prototypes.xml" - } + "wee": 1.5, + "wei": 3.5, + "wie": -3.25, + "wii": -2.5, + "l5e_l2i": 0.75, + 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- "delay": 0, - "weight": "FB_l5e_l2e * 0.5294351866321437", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_V4_L23_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "V4_L23_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l2i * 0.5294351866321437", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_V4_L56_E": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "V4_L56_E", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l5e * 0.5294351866321437", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_V4_L56_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "V4_L56_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l5i * 0.5294351866321437", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_MT_L23_E": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "MT_L23_E", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l2e * 0.1670831081915849", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_MT_L23_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "MT_L23_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l2i * 0.1670831081915849", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_MT_L56_E": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "MT_L56_E", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l5e * 0.1670831081915849", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_MT_L56_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "MT_L56_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "FB_l5e_l5i * 0.1670831081915849", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_TEO_L23_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "TEO_L23_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "0.75", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_TEO_L56_E": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "TEO_L56_E", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "1.5", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_E_TEO_L56_I": { - "presynaptic": "TEO_L56_E", - "postsynaptic": "TEO_L56_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "3.5", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_I_TEO_L56_E": { - "presynaptic": "TEO_L56_I", - "postsynaptic": "TEO_L56_E", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "-3.25", - "random_connectivity": { - "probability": 1.0 - } - } - }, - { - "proj_TEO_L56_I_TEO_L56_I": { - "presynaptic": "TEO_L56_I", - "postsynaptic": "TEO_L56_I", - "synapse": "rs", - "type": "continuousProjection", - "delay": 0, - "weight": "-2.5", - "random_connectivity": { - "probability": 1.0 - } + }, + "projections": { + "proj_V1_L23_E_V1_L23_E": { + "presynaptic": "V1_L23_E", + "postsynaptic": "V1_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_E_V1_L23_I": { + "presynaptic": "V1_L23_E", + "postsynaptic": "V1_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_E_V1_L56_E": { + "presynaptic": "V1_L23_E", + "postsynaptic": "V1_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.0", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_E_V4_L23_E": { + "presynaptic": "V1_L23_E", + "postsynaptic": "V4_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "FF_l2e_l2e * 0.19192441275410568", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_E_MT_L23_E": { + "presynaptic": "V1_L23_E", + "postsynaptic": "MT_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "FF_l2e_l2e * 0.0888694940343316", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_E_TEO_L23_E": { + "presynaptic": "V1_L23_E", + "postsynaptic": "TEO_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "FF_l2e_l2e * 0.039008034094570536", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_I_V1_L23_E": { + "presynaptic": "V1_L23_I", + "postsynaptic": "V1_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L23_I_V1_L23_I": { + "presynaptic": "V1_L23_I", + "postsynaptic": "V1_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L56_E_V1_L23_I": { + "presynaptic": "V1_L56_E", + "postsynaptic": "V1_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "0.75", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L56_E_V1_L56_E": { + "presynaptic": "V1_L56_E", + "postsynaptic": "V1_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L56_E_V1_L56_I": { + "presynaptic": "V1_L56_E", + "postsynaptic": "V1_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L56_I_V1_L56_E": { + "presynaptic": "V1_L56_I", + "postsynaptic": "V1_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V1_L56_I_V1_L56_I": { + "presynaptic": "V1_L56_I", + "postsynaptic": "V1_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L23_E_V4_L23_E": { + "presynaptic": "V4_L23_E", + "postsynaptic": "V4_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L23_E_V4_L23_I": { + "presynaptic": "V4_L23_E", + "postsynaptic": "V4_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L23_E_V4_L56_E": { + "presynaptic": "V4_L23_E", + "postsynaptic": "V4_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.0", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L23_I_V4_L23_E": { + "presynaptic": "V4_L23_I", + "postsynaptic": "V4_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L23_I_V4_L23_I": { + "presynaptic": "V4_L23_I", + "postsynaptic": "V4_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L56_E_V4_L23_I": { + "presynaptic": "V4_L56_E", + "postsynaptic": "V4_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "0.75", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L56_E_V4_L56_E": { + "presynaptic": "V4_L56_E", + "postsynaptic": "V4_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L56_E_V4_L56_I": { + "presynaptic": "V4_L56_E", + "postsynaptic": "V4_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L56_I_V4_L56_E": { + "presynaptic": "V4_L56_I", + "postsynaptic": "V4_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_V4_L56_I_V4_L56_I": { + "presynaptic": "V4_L56_I", + "postsynaptic": "V4_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_E_MT_L23_E": { + "presynaptic": "MT_L23_E", + "postsynaptic": "MT_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_E_MT_L23_I": { + "presynaptic": "MT_L23_E", + "postsynaptic": "MT_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_E_MT_L56_E": { + "presynaptic": "MT_L23_E", + "postsynaptic": "MT_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.0", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_I_MT_L23_E": { + "presynaptic": "MT_L23_I", + "postsynaptic": "MT_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L23_I_MT_L23_I": { + "presynaptic": "MT_L23_I", + "postsynaptic": "MT_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L23_I": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "0.75", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L56_E": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_E_MT_L56_I": { + "presynaptic": "MT_L56_E", + "postsynaptic": "MT_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_I_MT_L56_E": { + "presynaptic": "MT_L56_I", + "postsynaptic": "MT_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_MT_L56_I_MT_L56_I": { + "presynaptic": "MT_L56_I", + "postsynaptic": "MT_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L23_E_TEO_L23_E": { + "presynaptic": "TEO_L23_E", + "postsynaptic": "TEO_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L23_E_TEO_L23_I": { + "presynaptic": "TEO_L23_E", + "postsynaptic": "TEO_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L23_E_TEO_L56_E": { + "presynaptic": "TEO_L23_E", + "postsynaptic": "TEO_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.0", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L23_I_TEO_L23_E": { + "presynaptic": "TEO_L23_I", + "postsynaptic": "TEO_L23_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L23_I_TEO_L23_I": { + "presynaptic": "TEO_L23_I", + "postsynaptic": "TEO_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L56_E_TEO_L23_I": { + "presynaptic": "TEO_L56_E", + "postsynaptic": "TEO_L23_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "0.75", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L56_E_TEO_L56_E": { + "presynaptic": "TEO_L56_E", + "postsynaptic": "TEO_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "1.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L56_E_TEO_L56_I": { + "presynaptic": "TEO_L56_E", + "postsynaptic": "TEO_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "3.5", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L56_I_TEO_L56_E": { + "presynaptic": "TEO_L56_I", + "postsynaptic": "TEO_L56_E", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-3.25", + "random_connectivity": { + "probability": 1 + } + }, + "proj_TEO_L56_I_TEO_L56_I": { + "presynaptic": "TEO_L56_I", + "postsynaptic": "TEO_L56_I", + "synapse": "rs", + "type": "continuousProjection", + "delay": 0, + "weight": "-2.5", + "random_connectivity": { + "probability": 1 } } - ], - "inputs": [ - { - "modulation_V1_L23_E": { - "input_source": "iclamp_V1_L23", - "population": "V1_L23_E", - "percentage": 100.0 - } - }, - { - "modulation_V1_L56_E": { - "input_source": "iclamp_V1_L56", - "population": "V1_L56_E", - "percentage": 100.0 - } + }, + "inputs": { + "modulation_V1_L23_E": { + "input_source": "iclamp_V1_L23", + "population": "V1_L23_E", + "percentage": 100 + }, + "modulation_V1_L56_E": { + "input_source": "iclamp_V1_L56", + "population": "V1_L56_E", + "percentage": 100 } - ] + } } } \ No newline at end of file diff --git a/NeuroML2/Interareal_4.net.nml b/NeuroML2/Interareal_4.net.nml index f92563d..19c710f 100644 --- a/NeuroML2/Interareal_4.net.nml +++ b/NeuroML2/Interareal_4.net.nml @@ -1,5 +1,5 @@ - - Generated by NeuroMLlite v0.1.8 + + Generated by NeuroMLlite v0.5.8 Generated network: Interareal_4 Generation seed: 1234 NeuroMLlite parameters: @@ -23,6 +23,7 @@ + @@ -39,14 +40,8 @@ - - - - - - @@ -55,17 +50,8 @@ - - - - - - - - - @@ -76,14 +62,6 @@ - - - - - - - - @@ -93,134 +71,134 @@ Testing... - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -271,30 +249,12 @@ - - - - - - - - - - - - - - - - - - @@ -319,39 +279,12 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -382,30 +315,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/NeuroML2/Interlaminar.json b/NeuroML2/Interlaminar.json index ae89675..5a7d248 100644 --- a/NeuroML2/Interlaminar.json +++ b/NeuroML2/Interlaminar.json @@ -1,6 +1,6 @@ { "Interlaminar": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "notes": "Testing...", "parameters": { "wee": 1.5, @@ -248,12 +248,12 @@ "modulation_V1_L23_E": { "input_source": "iclamp_V1_L23", "population": "V1_L23_E", - "percentage": 100.0 + "percentage": 100 }, "modulation_V1_L56_E": { "input_source": "iclamp_V1_L56", "population": "V1_L56_E", - "percentage": 100.0 + "percentage": 100 } } } diff --git a/NeuroML2/Interlaminar.net.nml b/NeuroML2/Interlaminar.net.nml index cb7c4da..fe8bd84 100644 --- a/NeuroML2/Interlaminar.net.nml +++ b/NeuroML2/Interlaminar.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.3 + Generated by NeuroMLlite v0.5.8 Generated network: Interlaminar Generation seed: 1234 NeuroMLlite parameters: @@ -40,7 +40,7 @@ - + @@ -48,7 +48,7 @@ - + @@ -56,7 +56,7 @@ - + @@ -64,7 +64,7 @@ - + diff --git a/NeuroML2/Interlaminar__lems.xml b/NeuroML2/Interlaminar__lems.xml index 28e9d72..febe710 100644 --- a/NeuroML2/Interlaminar__lems.xml +++ b/NeuroML2/Interlaminar__lems.xml @@ -14,7 +14,6 @@ - @@ -68,30 +67,12 @@ - - - - - - - - - - - - - - - - - - @@ -135,11 +116,12 @@ + - + @@ -149,7 +131,7 @@ - + diff --git a/NeuroML2/Intralaminar.json b/NeuroML2/Intralaminar.json index 159267f..c428342 100644 --- a/NeuroML2/Intralaminar.json +++ b/NeuroML2/Intralaminar.json @@ -1,6 +1,6 @@ { "Intralaminar": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "notes": "Testing...", "parameters": { "wee": 1.5, @@ -248,12 +248,12 @@ "modulation_V1_L23_E": { "input_source": "iclamp_V1_L23", "population": "V1_L23_E", - "percentage": 100.0 + "percentage": 100 }, "modulation_V1_L56_E": { "input_source": "iclamp_V1_L56", "population": "V1_L56_E", - "percentage": 100.0 + "percentage": 100 } } } diff --git a/NeuroML2/Intralaminar.net.nml b/NeuroML2/Intralaminar.net.nml index a89224e..7bbf8f1 100644 --- a/NeuroML2/Intralaminar.net.nml +++ b/NeuroML2/Intralaminar.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.3 + Generated by NeuroMLlite v0.5.8 Generated network: Intralaminar Generation seed: 1234 NeuroMLlite parameters: @@ -38,7 +38,7 @@ - + @@ -46,7 +46,7 @@ - + @@ -54,7 +54,7 @@ - + @@ -62,7 +62,7 @@ - + diff --git a/NeuroML2/Intralaminar__lems.xml b/NeuroML2/Intralaminar__lems.xml index 28e9d72..febe710 100644 --- a/NeuroML2/Intralaminar__lems.xml +++ b/NeuroML2/Intralaminar__lems.xml @@ -14,7 +14,6 @@ - @@ -68,30 +67,12 @@ - - - - - - - - - - - - - - - - - - @@ -135,11 +116,12 @@ + - + @@ -149,7 +131,7 @@ - + diff --git a/NeuroML2/RateBased.xml b/NeuroML2/RateBased.xml index 84e17d5..6b54f26 100644 --- a/NeuroML2/RateBased.xml +++ b/NeuroML2/RateBased.xml @@ -41,7 +41,7 @@ - + @@ -128,6 +128,7 @@ + - @@ -261,11 +261,13 @@ + + - + @@ -284,7 +286,7 @@ - + diff --git a/NeuroML2/SimInterareal_0.json b/NeuroML2/SimInterareal_0.json index e4357d8..c7fbbd9 100644 --- a/NeuroML2/SimInterareal_0.json +++ b/NeuroML2/SimInterareal_0.json @@ -1,6 +1,6 @@ { "SimInterareal_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Interareal.json", "duration": 40000.0, "dt": 0.2, diff --git a/NeuroML2/SimInterareal_30_0.json b/NeuroML2/SimInterareal_30_0.json index 5ef1cb1..46bb62e 100644 --- a/NeuroML2/SimInterareal_30_0.json +++ b/NeuroML2/SimInterareal_30_0.json @@ -1,6 +1,6 @@ { "SimInterareal_30_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Interareal_30.json", "duration": 40000.0, "dt": 0.2, diff --git a/NeuroML2/SimInterareal_3_0.json b/NeuroML2/SimInterareal_3_0.json index acafd72..24b4c54 100644 --- a/NeuroML2/SimInterareal_3_0.json +++ b/NeuroML2/SimInterareal_3_0.json @@ -1,6 +1,6 @@ { "SimInterareal_3_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Interareal_3.json", "duration": 40000.0, "dt": 0.2, diff --git a/NeuroML2/SimInterareal_4_0.json b/NeuroML2/SimInterareal_4_0.json index 07bca6d..223c690 100644 --- a/NeuroML2/SimInterareal_4_0.json +++ b/NeuroML2/SimInterareal_4_0.json @@ -1,6 +1,6 @@ { "SimInterareal_4_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Interareal_4.json", "duration": 40000.0, "dt": 0.2, diff --git a/NeuroML2/SimInterlaminar_0.json b/NeuroML2/SimInterlaminar_0.json index b127682..1f6e8eb 100644 --- a/NeuroML2/SimInterlaminar_0.json +++ b/NeuroML2/SimInterlaminar_0.json @@ -1,6 +1,6 @@ { "SimInterlaminar_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Interlaminar.json", "duration": 1000.0, "dt": 0.2, diff --git a/NeuroML2/SimIntralaminar_0.json b/NeuroML2/SimIntralaminar_0.json index 735cb41..7d3c495 100644 --- a/NeuroML2/SimIntralaminar_0.json +++ b/NeuroML2/SimIntralaminar_0.json @@ -1,6 +1,6 @@ { "SimIntralaminar_0": { - "version": "NeuroMLlite v0.5.3", + "version": "NeuroMLlite v0.5.8", "network": "Intralaminar.json", "duration": 25000.0, "dt": 0.2,