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Dev pg #33

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6f69c2e
Regenerated
pgleeson Mar 27, 2020
a69c7ec
Additional files required
pgleeson Mar 27, 2020
6fba6f3
Run tests in local dir
pgleeson Mar 27, 2020
aee88e9
Update RateBased to match WilsonCowan
pgleeson May 4, 2020
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7 changes: 7 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -46,3 +46,10 @@ Matlab/*.png
/NeuroML2/temp
/NeuroML2/SimMejiasFig2_0.json
/NeuroML2/MejiasFig2.json
/NeuroML2/LEMS_SimInterareal_30_0.xml
/NeuroML2/LEMS_SimInterareal_4_0.xml
/NeuroML2/TestNetwork.json
/NeuroML2/LEMS_SimTestNetwork.xml
/NeuroML2/TestNetwork__lems.xml
/NeuroML2/LEMS_SimMejiasFig2_0.xml
/NeuroML2/MejiasFig2__lems.xml
8 changes: 6 additions & 2 deletions NeuroML2/GenerateNetwork.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
'''
Some initial test... No longer useful...
'''

from neuromllite import *

import random
Expand Down Expand Up @@ -43,8 +47,8 @@ def generate(wee = 1.5, wei = -3.25, wie = 3.5, wii = -2.5, interlaminar1=0,
suffix = '' if noise else '_flat'
suffix2 = '' if dt == 0.2 else '_smalldt'
l23ecell = Cell(id='L23_E_comp'+suffix+suffix2, lems_source_file='Prototypes.xml')
l23icell = Cell(id='L23_I_comp'+suffix+suffix2, lems_source_file='RateBased.xml') # hack to include this file too.
l56ecell = Cell(id='L56_E_comp'+suffix+suffix2, lems_source_file='NoisyCurrentSource.xml') # hack to include this file too.
l23icell = Cell(id='L23_I_comp'+suffix+suffix2, lems_source_file='Prototypes.xml') # hack to include this file too.
l56ecell = Cell(id='L56_E_comp'+suffix+suffix2, lems_source_file='Prototypes.xml') # hack to include this file too.
l56icell = Cell(id='L56_I_comp'+suffix+suffix2, lems_source_file='Prototypes.xml')

net.cells.append(l23ecell)
Expand Down
20 changes: 10 additions & 10 deletions NeuroML2/GenerateNeuroMLlite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,10 +158,10 @@ def generate(wee = 1.5, wei = -3.25, wie = 3.5, wii = -2.5,
print('Using a value for dt which is not supported!!')
quit()

l23ecell = Cell(id='L23_E_comp'+suffix+suffix2, lems_source_file='Prototypes.xml')
l23icell = Cell(id='L23_I_comp'+suffix+suffix2, lems_source_file='RateBased.xml') # hack to include this file too.
l56ecell = Cell(id='L56_E_comp'+suffix+suffix2, lems_source_file='NoisyCurrentSource.xml') # hack to include this file too.
l56icell = Cell(id='L56_I_comp'+suffix+suffix2, lems_source_file='Prototypes.xml')
l23ecell = Cell(id='L23_E_comp'+suffix+suffix2, lems_source_file='Prototypes.xml', parameters={'sig': 'sigma23'})
l23icell = Cell(id='L23_I_comp'+suffix+suffix2, lems_source_file='Prototypes.xml', parameters={'sig': 'sigma23'})
l56ecell = Cell(id='L56_E_comp'+suffix+suffix2, lems_source_file='Prototypes.xml', parameters={'sig': 'sigma56'})
l56icell = Cell(id='L56_I_comp'+suffix+suffix2, lems_source_file='Prototypes.xml', parameters={'sig': 'sigma56'})


net.cells.append(l23ecell)
Expand Down Expand Up @@ -515,7 +515,7 @@ def internal_connections(pops, W, pre_pop, post_pop):
incl_23 = True
incl_56 = False
incl_56 = True
traces, events = nmllr.run_once('/tmp')
traces, events = nmllr.run_once('.')
xs = []
ys = []
labels = []
Expand Down Expand Up @@ -688,7 +688,7 @@ def internal_connections(pops, W, pre_pop, post_pop):
nmllr = NeuroMLliteRunner('%s.json'%sim.id,
simulator=simulator)

traces, events = nmllr.run_once('/tmp')
traces, events = nmllr.run_once('.')

simulation[Iext][run] = {}
# For the purpose of this analysis we will save only the traces related to the excitatory L23 population
Expand Down Expand Up @@ -738,7 +738,7 @@ def internal_connections(pops, W, pre_pop, post_pop):

nmllr = NeuroMLliteRunner('%s.json' % sim.id,
simulator=simulator)
traces, events = nmllr.run_once('/tmp')
traces, events = nmllr.run_once('.')

rate_conn = np.stack((np.array(traces['V1_L23_E/0/L23_E_comp/r']),
np.array(traces['V1_L23_I/0/L23_I_comp/r']),
Expand Down Expand Up @@ -846,7 +846,7 @@ def internal_connections(pops, W, pre_pop, post_pop):

nmllr = NeuroMLliteRunner('%s.json' % sim.id,
simulator=simulator)
traces, events = nmllr.run_once('/tmp')
traces, events = nmllr.run_once('.')
rate_noconn = np.stack((np.array(traces['V1_L23_E/0/L23_E_comp/r']),
np.array(traces['V1_L23_I/0/L23_I_comp/r']),
np.array(traces['V1_L56_E/0/L56_E_comp/r']),
Expand Down Expand Up @@ -1013,7 +1013,7 @@ def internal_connections(pops, W, pre_pop, post_pop):

nmllr_rest = NeuroMLliteRunner('%s.json' %sim_rest.id,
simulator=simulator)
traces_rest, events_rest = nmllr_rest.run_once('/tmp')
traces_rest, events_rest = nmllr_rest.run_once('.')
# if -analysis is not passed generate a single network using the rest as default

# Run simulation with microsimulation
Expand All @@ -1028,7 +1028,7 @@ def internal_connections(pops, W, pre_pop, post_pop):

nmllr_stim = NeuroMLliteRunner('%s.json' %sim_stim.id,
simulator=simulator)
traces_stim, events_stim = nmllr_stim.run_once('/tmp')
traces_stim, events_stim = nmllr_stim.run_once('.')



Expand Down
72 changes: 42 additions & 30 deletions NeuroML2/Interareal.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"Interareal": {
"version": "NeuroMLlite v0.1.8",
"version": "NeuroMLlite v0.2.0",
"parameters": {
"wie": -3.25,
"iclamp_V1_L23_amp": "17nA",
Expand All @@ -24,22 +24,34 @@
"cells": [
{
"L23_E_comp": {
"lems_source_file": "Prototypes.xml"
"lems_source_file": "Prototypes.xml",
"parameters": {
"sig": "sigma23"
}
}
},
{
"L23_I_comp": {
"lems_source_file": "RateBased.xml"
"lems_source_file": "Prototypes.xml",
"parameters": {
"sig": "sigma23"
}
}
},
{
"L56_E_comp": {
"lems_source_file": "NoisyCurrentSource.xml"
"lems_source_file": "Prototypes.xml",
"parameters": {
"sig": "sigma56"
}
}
},
{
"L56_I_comp": {
"lems_source_file": "Prototypes.xml"
"lems_source_file": "Prototypes.xml",
"parameters": {
"sig": "sigma56"
}
}
}
],
Expand Down Expand Up @@ -254,7 +266,7 @@
"delay": 0,
"weight": "wee",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -267,7 +279,7 @@
"delay": 0,
"weight": "wei",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -280,7 +292,7 @@
"delay": 0,
"weight": "l2e_l5e",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -293,7 +305,7 @@
"delay": 0,
"weight": "FF_l2e_l2e",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -306,7 +318,7 @@
"delay": 0,
"weight": "wie",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -319,7 +331,7 @@
"delay": 0,
"weight": "wii",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -332,7 +344,7 @@
"delay": 0,
"weight": "l5e_l2i",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -345,7 +357,7 @@
"delay": 0,
"weight": "wee",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -358,7 +370,7 @@
"delay": 0,
"weight": "wei",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -371,7 +383,7 @@
"delay": 0,
"weight": "wie",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -384,7 +396,7 @@
"delay": 0,
"weight": "wii",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -397,7 +409,7 @@
"delay": 0,
"weight": "wee",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -410,7 +422,7 @@
"delay": 0,
"weight": "wei",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -423,7 +435,7 @@
"delay": 0,
"weight": "l2e_l5e",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -436,7 +448,7 @@
"delay": 0,
"weight": "wie",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -449,7 +461,7 @@
"delay": 0,
"weight": "wii",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -462,7 +474,7 @@
"delay": 0,
"weight": "FB_l5e_l2e",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -475,7 +487,7 @@
"delay": 0,
"weight": "FB_l5e_l2i",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -488,7 +500,7 @@
"delay": 0,
"weight": "FB_l5e_l5e",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -501,7 +513,7 @@
"delay": 0,
"weight": "FB_l5e_l2i",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -514,7 +526,7 @@
"delay": 0,
"weight": "l5e_l2i",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -527,7 +539,7 @@
"delay": 0,
"weight": "wee",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -540,7 +552,7 @@
"delay": 0,
"weight": "wei",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -553,7 +565,7 @@
"delay": 0,
"weight": "wie",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
},
Expand All @@ -566,7 +578,7 @@
"delay": 0,
"weight": "wii",
"random_connectivity": {
"probability": 1.0
"probability": 1
}
}
}
Expand Down
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