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Regeenrated example files #72

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Aug 19, 2024
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Regeenrated example files #72

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pgleeson Aug 19, 2024
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Merge branch 'development' into experimental
pgleeson Aug 19, 2024
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2 changes: 1 addition & 1 deletion docs/NeuroMLlite_specification.json
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{
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"specification": {
"Network": {
"definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",
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2 changes: 1 addition & 1 deletion docs/NeuroMLlite_specification.yaml
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version: NeuroMLlite v0.5.9
version: NeuroMLlite v0.6.0
specification:
Network:
definition: A Network containing multiple Population's, connected by Projection's
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2 changes: 1 addition & 1 deletion docs/README.md
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# Specification of NeuroMLlite v0.5.9
# Specification of NeuroMLlite v0.6.0
**Note: the NeuroMLlite specification is still in development! Subject to change...**

## Network
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2 changes: 1 addition & 1 deletion examples/Example10_Lorenz.json
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{
"Example10_Lorenz": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 10: Lorenz",
"parameters": {
"N": 1,
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2 changes: 1 addition & 1 deletion examples/Example11_Synapses.json
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{
"Example11_Synapses": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 11: synaptic properties",
"parameters": {
"input_amp": 0.23,
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2 changes: 1 addition & 1 deletion examples/Example11_Synapses.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example11_Synapses">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example11_Synapses
Generation seed: 1234
NeuroMLlite parameters:
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2 changes: 1 addition & 1 deletion examples/Example12_MultiComp.json
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{
"Example12_MultiComp": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 12: Multicompartmental cells...",
"parameters": {
"N": 20,
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2 changes: 1 addition & 1 deletion examples/Example1_TestNetwork.json
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{
"TestNetwork": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.",
"populations": {
"pop0": {
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2 changes: 1 addition & 1 deletion examples/Example2_TestNetwork.json
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{
"Example2_TestNetwork": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.",
"cells": {
"hhcell": {
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2 changes: 1 addition & 1 deletion examples/Example2_TestNetwork.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example2_TestNetwork">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example2_TestNetwork
Generation seed: 1234</notes>
<include href="test_files/inputs.nml"/>
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2 changes: 1 addition & 1 deletion examples/Example3_Network.json
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{
"Example3_Network": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.",
"cells": {
"hhcell": {
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2 changes: 1 addition & 1 deletion examples/Example3_Network.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example3_Network">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example3_Network
Generation seed: 1234</notes>
<include href="test_files/inputs.nml"/>
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2 changes: 1 addition & 1 deletion examples/Example4_PyNN.json
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{
"Example4_PyNN": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 4: a network with PyNN cells & inputs",
"parameters": {
"input_amp": 0.99
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2 changes: 1 addition & 1 deletion examples/Example4_PyNN.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example4_PyNN">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example4_PyNN
Generation seed: 1234
NeuroMLlite parameters:
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2 changes: 1 addition & 1 deletion examples/Example4_PyNN.yaml
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Example4_PyNN:
version: NeuroMLlite v0.5.9
version: NeuroMLlite v0.6.0
notes: 'Example 4: a network with PyNN cells & inputs'
parameters:
input_amp: 0.99
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2 changes: 1 addition & 1 deletion examples/Example6_PyNN.json
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{
"Example6_PyNN": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Another network for PyNN - work in progress...",
"parameters": {
"N_scaling": 0.005,
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2 changes: 1 addition & 1 deletion examples/Example6_PyNN.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example6_PyNN">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example6_PyNN
Generation seed: 1234
NeuroMLlite parameters:
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2 changes: 1 addition & 1 deletion examples/Example6_PyNN_noinputs.json
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{
"Example6_PyNN_noinputs": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Another network for PyNN - work in progress...",
"parameters": {
"N_scaling": 0.005,
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2 changes: 1 addition & 1 deletion examples/Example6_PyNN_noinputs.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example6_PyNN_noinputs">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example6_PyNN_noinputs
Generation seed: 1234
NeuroMLlite parameters:
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2 changes: 1 addition & 1 deletion examples/Example7_Brunel2000.json
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{
"Example7_Brunel2000": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 7: based on network of Brunel 2000",
"parameters": {
"g": 4,
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2 changes: 1 addition & 1 deletion examples/Example7_Brunel2000.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example7_Brunel2000">
<notes>Generated by NeuroMLlite v0.5.9
<notes>Generated by NeuroMLlite v0.6.0
Generated network: Example7_Brunel2000
Generation seed: 1234
NeuroMLlite parameters:
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2 changes: 1 addition & 1 deletion examples/Example8_Extension.json
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{
"Example8_Extension": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 8: general testing...",
"parameters": {
"N": 10,
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2 changes: 1 addition & 1 deletion examples/Example9_HindmarshRose.json
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{
"Example9_HindmarshRose": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example 9: HindmarshRose",
"parameters": {
"N": 1,
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2 changes: 1 addition & 1 deletion examples/LEMS_SimExample3.xml
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<!--

This LEMS file has been automatically generated using PyNeuroML v1.3.0 (libNeuroML v0.6.0)
This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)

-->

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2 changes: 1 addition & 1 deletion examples/LEMS_SimExample4.xml
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<!--

This LEMS file has been automatically generated using PyNeuroML v1.3.0 (libNeuroML v0.6.0)
This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)

-->

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2 changes: 1 addition & 1 deletion examples/SimExample10.json
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{
"SimExample10": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example10_Lorenz.json",
"duration": 10000.0,
"dt": 1.0,
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2 changes: 1 addition & 1 deletion examples/SimExample11.json
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{
"SimExample11": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example11_Synapses.json",
"duration": 1000.0,
"dt": 0.01,
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2 changes: 1 addition & 1 deletion examples/SimExample12_MultiComp.json
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{
"SimExample12_MultiComp": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example12_MultiComp.json",
"duration": 1000.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/SimExample3.json
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{
"SimExample3": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example3_Network.json",
"duration": 1000.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/SimExample4.json
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{
"SimExample4": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example4_PyNN.json",
"duration": 1000.0,
"dt": 0.01,
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2 changes: 1 addition & 1 deletion examples/SimExample4.yaml
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SimExample4:
version: NeuroMLlite v0.5.9
version: NeuroMLlite v0.6.0
network: Example4_PyNN.yaml
duration: 1000.0
dt: 0.01
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2 changes: 1 addition & 1 deletion examples/SimExample6_PyNN.json
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{
"SimExample6_PyNN": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example6_PyNN.json",
"duration": 100.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/SimExample7.json
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{
"SimExample7": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example7_Brunel2000.json",
"duration": 1000.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/SimExample8.json
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{
"SimExample8": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example8_Extension.json",
"duration": 1000.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/SimExample9.json
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{
"SimExample9": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Example9_HindmarshRose.json",
"duration": 1000000.0,
"dt": 25.0,
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2 changes: 1 addition & 1 deletion examples/arbor/ArborExample.json
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{
"ArborExample": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example for testing Arbor",
"parameters": {
"v_init": -50,
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2 changes: 1 addition & 1 deletion examples/arbor/ArborExample.yaml
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ArborExample:
version: NeuroMLlite v0.5.9
version: NeuroMLlite v0.6.0
notes: Example for testing Arbor
parameters:
v_init: -50
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2 changes: 1 addition & 1 deletion examples/arbor/SimArborExample.json
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{
"SimArborExample": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "ArborExample.json",
"duration": 100.0,
"dt": 0.01,
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2 changes: 1 addition & 1 deletion examples/arbor/SimArborExample.yaml
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SimArborExample:
version: NeuroMLlite v0.5.9
version: NeuroMLlite v0.6.0
network: ArborExample.yaml
duration: 100.0
dt: 0.01
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2 changes: 1 addition & 1 deletion examples/sonatatest/SimSonataExample.json
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{
"SimSonataExample": {
"version": "NeuroMLlite v0.5.8",
"version": "NeuroMLlite v0.6.0",
"network": "SonataExample.json",
"duration": 1000.0,
"dt": 0.01,
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2 changes: 1 addition & 1 deletion examples/sonatatest/SonataExample.json
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{
"SonataExample": {
"version": "NeuroMLlite v0.5.8",
"version": "NeuroMLlite v0.6.0",
"notes": "Example for testing Sonata",
"parameters": {
"input_amp": 0.19,
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2 changes: 1 addition & 1 deletion examples/spikeratetest/SimSpikers.json
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{
"SimSpikers": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"network": "Spikers.json",
"duration": 10000.0,
"dt": 0.025,
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2 changes: 1 addition & 1 deletion examples/spikeratetest/Spikers.json
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{
"Spikers": {
"version": "NeuroMLlite v0.5.9",
"version": "NeuroMLlite v0.6.0",
"notes": "Example with spiking entities..",
"parameters": {
"N": 10,
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