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pgleesonpgleeson
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Merge pull request #8 from OpenSourceBrain/development
More tidying up & testing
2 parents fed0c8b + 32a79f1 commit 0e2d538

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8 files changed

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‎.gitignore‎

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@@ -48,3 +48,5 @@ report.*.txt
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/NeuroML2/nmllite/LEMS_SimNoisyExample.xml
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/NeuroML2/nmllite/NoisyExample.net.nml
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/NeuroML2/nmllite/NoisyExample__lems.xml
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/NeuroML2/arm64
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/NeuroML2/nmllite/arm64

‎.travis.yml‎

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‎NeuroML2/LEMS_NoisyCurrentInput.xml‎

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<inputList id="stimInput" component="pulseGen0" population="Pop0">
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<input id="0" target="../Pop0/0/IF_curr_exp" destination="synapses"/>
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</inputList>
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<inputList id="noisy1" component="noisyCurrentSource1" population="Pop0">
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<input id="0" target="../Pop0/1/IF_curr_exp" destination="synapses"/>
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</inputList>

‎NeuroML2/TestNoisySources.ipynb‎

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‎NeuroML2/nmllite/NoisyExample.json‎

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{
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"NoisyExample": {
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"version": "NeuroMLlite v0.2.1",
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"version": "NeuroMLlite v0.5.6",
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"notes": "Example with NoisyCurrentSource",
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"parameters": {
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"input_amp": 0.9
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},
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"notes": "Example with NoisyCurrentSource",
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"cells": [
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{
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"testcell": {
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"pynn_cell": "IF_cond_alpha",
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"parameters": {
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"tau_refrac": 5,
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"i_offset": 0
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}
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}
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},
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"cells": {
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"testcell": {
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"parameters": {
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"tau_refrac": 5,
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"i_offset": 0
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},
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"pynn_cell": "IF_cond_alpha"
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}
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],
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"input_sources": [
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{
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"i_clamp": {
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"pynn_input": "DCSource",
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"parameters": {
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"start": 200.0,
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"stop": 800.0,
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"amplitude": "input_amp"
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}
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}
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},
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{
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"noisyCurrentSource0": {
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"lems_source_file": "TestNCS.xml",
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"parameters": {
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"mean": "0.5nA"
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}
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}
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},
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"input_sources": {
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"i_clamp": {
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"parameters": {
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"amplitude": "input_amp",
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"start": 200.0,
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"stop": 800.0
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},
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"pynn_input": "DCSource"
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},
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"noisyCurrentSource0": {
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"parameters": {
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"mean": "0.5nA"
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},
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"lems_source_file": "TestNCS.xml"
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}
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],
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"regions": [
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{
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"region1": {
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"x": 0.0,
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"y": 0.0,
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"z": 0.0,
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"width": 1000.0,
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"height": 100.0,
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"depth": 1000.0
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}
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},
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"regions": {
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"region1": {
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"x": 0.0,
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"y": 0.0,
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"z": 0.0,
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"width": 1000.0,
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"height": 100.0,
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"depth": 1000.0
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}
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],
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"populations": [
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{
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"pop0": {
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"size": 1,
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"component": "testcell",
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"properties": {
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"color": "1 0 0"
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},
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"random_layout": {
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"region": "region1"
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}
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},
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"populations": {
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"pop0": {
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"size": 1,
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"component": "testcell",
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"properties": {
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"color": "1 0 0"
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},
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"random_layout": {
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"region": "region1"
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}
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},
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{
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"pop1": {
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"size": 3,
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"component": "testcell",
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"properties": {
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"color": "0 1 0"
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},
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"random_layout": {
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"region": "region1"
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}
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},
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"pop1": {
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"size": 3,
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"component": "testcell",
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"properties": {
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"color": "0 1 0"
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},
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"random_layout": {
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"region": "region1"
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}
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}
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],
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"inputs": [
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{
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"stim0": {
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"input_source": "i_clamp",
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"population": "pop0",
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"percentage": 100.0
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}
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},
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{
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"stim1": {
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"input_source": "noisyCurrentSource0",
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"population": "pop1",
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"percentage": 100.0
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}
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},
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"inputs": {
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"stim0": {
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"input_source": "i_clamp",
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"population": "pop0",
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"percentage": 100
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},
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"stim1": {
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"input_source": "noisyCurrentSource0",
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"population": "pop1",
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"percentage": 100
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}
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]
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}
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}
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}

‎NeuroML2/nmllite/NoisyExample.py‎

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duration='1000',
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dt='0.01',
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seed=1234,
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recordTraces={'all':'*'},
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recordSpikes={'all':'*'})
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record_traces={'all':'*'},
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record_spikes={'all':'*'})
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sim.to_json_file()
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‎NeuroML2/nmllite/SimNoisyExample.json‎

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{
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"SimNoisyExample": {
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"version": "NeuroMLlite v0.2.1",
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"network": "NoisyExample.json",
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"duration": 1000.0,
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"dt": 0.01,
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"seed": 1234,
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"recordTraces": {
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"version": "NeuroMLlite v0.5.6",
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"network": "NoisyExample.json",
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"duration": 1000.0,
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"dt": 0.01,
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"seed": 1234,
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"record_traces": {
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"all": "*"
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},
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"recordSpikes": {
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},
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"record_spikes": {
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"all": "*"
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}
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}

‎NeuroML2/scratch.ipynb‎

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