Skip to content

Commit b4bb14c

Browse files
pgleesonpgleeson
authored
Merge pull request #4 from OpenSourceBrain/development
Development
2 parents 74f206b + 9fb7ea9 commit b4bb14c

14 files changed

Lines changed: 103 additions & 108 deletions

‎NeuroML2/.test.exIzh.jnml.omt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,4 +13,4 @@ experiments:
1313
scaling: [1000, 1000]
1414
spike detection:
1515
method: threshold
16-
tolerance: 5.087e-05
16+
tolerance: 5.0862371508887715e-05

‎NeuroML2/.test.exPynn.jnml.omt‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ experiments:
1414
spike detection:
1515
method: threshold
1616
threshold: -55
17-
tolerance: 0.000125
17+
tolerance: 0.00012497396375755524
1818
EIF_cond_exp_isfa_ista:
1919
observables:
2020
spike times:
@@ -25,7 +25,7 @@ experiments:
2525
spike detection:
2626
method: threshold
2727
threshold: -45
28-
tolerance: 0.000429
28+
tolerance: 0.0004288690111505525
2929
pop_post2:
3030
observables:
3131
spike times:
@@ -36,4 +36,4 @@ experiments:
3636
spike detection:
3737
method: threshold
3838
threshold: -63.5
39-
tolerance: 0.000375
39+
tolerance: 0.0003740764986440312

‎NeuroML2/ConnectionsTest.net.nml‎

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -2,53 +2,53 @@
22
<notes>
33
This NeuroML 2 file has been generated from:
44
PyNN v0.10.1
5-
libNeuroML v0.5.3
6-
pyNeuroML v1.0.8
5+
libNeuroML v0.5.5
6+
pyNeuroML v1.1.1
77
</notes>
8-
<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1." i_offset="0.9" tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
9-
<IF_cond_alpha id="IF_cond_alpha_pop_post" cm="1." i_offset="0.9" tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
10-
<alphaCondSynapse id="syn__pop_pre__TO__pop_post" tau_syn="2." e_rev="0."/>
11-
<alphaCondSynapse id="syn__AllToAllConnectorProj" tau_syn="2." e_rev="0."/>
12-
<alphaCondSynapse id="syn__OneToOneConnector" tau_syn="2." e_rev="0."/>
13-
<alphaCondSynapse id="syn__FixedProbabilityConnector" tau_syn="2." e_rev="0."/>
14-
<alphaCondSynapse id="syn__AllToAllConnectorProjSelection" tau_syn="2." e_rev="0."/>
8+
<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
9+
<IF_cond_alpha id="IF_cond_alpha_pop_post" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
10+
<alphaCondSynapse id="syn__pop_pre__TO__pop_post" tau_syn="2.0" e_rev="0.0"/>
11+
<alphaCondSynapse id="syn__AllToAllConnectorProj" tau_syn="2.0" e_rev="0.0"/>
12+
<alphaCondSynapse id="syn__OneToOneConnector" tau_syn="2.0" e_rev="0.0"/>
13+
<alphaCondSynapse id="syn__FixedProbabilityConnector" tau_syn="2.0" e_rev="0.0"/>
14+
<alphaCondSynapse id="syn__AllToAllConnectorProjSelection" tau_syn="2.0" e_rev="0.0"/>
1515
<network id="ConnectionsTest">
1616
<population id="pop_pre" component="IF_cond_alpha_pop_pre" size="5" type="populationList">
1717
<property tag="radius" value="5"/>
1818
<property tag="color" value="0 0.6 0"/>
1919
<instance id="0">
20-
<location x="5.541832845040129" y="59.921418584252393" z="20.857984592385105"/>
20+
<location x="-32.186643403808567" y="-17.354649054736583" z="-65.493481332544846"/>
2121
</instance>
2222
<instance id="1">
23-
<location x="34.466522868595085" y="87.638652592529724" z="-33.145933330040037"/>
23+
<location x="-67.354645297143236" y="-4.19796344220984" z="-43.49873410003169"/>
2424
</instance>
2525
<instance id="2">
26-
<location x="-65.704278939682226" y="-34.764594972583772" z="-62.279243529588157"/>
26+
<location x="71.797570419985519" y="18.947079504991638" z="-12.907315815267673"/>
2727
</instance>
2828
<instance id="3">
29-
<location x="-25.211843195842178" y="3.640852771338143" z="32.441587323651142"/>
29+
<location x="-52.406762043828394" y="6.010609135001554" z="-58.236579579123649"/>
3030
</instance>
3131
<instance id="4">
32-
<location x="-2.226433693613816" y="-6.999164118723655" z="56.311934654534902"/>
32+
<location x="-84.522276311302463" y="-27.093766860654476" z="-28.20137345446372"/>
3333
</instance>
3434
</population>
3535
<population id="pop_post" component="IF_cond_alpha_pop_post" size="5" type="populationList">
3636
<property tag="radius" value="5"/>
3737
<property tag="color" value="0 0.2 0.6"/>
3838
<instance id="0">
39-
<location x="-53.052248905203328" y="259.088479625842638" z="-24.729342611499305"/>
39+
<location x="-10.963933858486152" y="160.214056107236161" z="-17.681929175932854"/>
4040
</instance>
4141
<instance id="1">
42-
<location x="-5.605492121538203" y="210.161061349492314" z="54.437434010504695"/>
42+
<location x="-65.391507421071694" y="215.929509183693398" z="53.214475027961086"/>
4343
</instance>
4444
<instance id="2">
45-
<location x="4.660513826530521" y="186.333860539104307" z="-81.175402165055971"/>
45+
<location x="-25.558099064460361" y="219.63712563909769" z="-87.608059485643892"/>
4646
</instance>
4747
<instance id="3">
48-
<location x="61.944758456588779" y="195.847455277570702" z="59.736272625549326"/>
48+
<location x="57.458557554047054" y="140.98406076648115" z="-24.288796136764446"/>
4949
</instance>
5050
<instance id="4">
51-
<location x="9.177333646907693" y="181.683156874365778" z="-62.523285074325408"/>
51+
<location x="78.618467098550227" y="180.149183458113185" z="-55.213241499240318"/>
5252
</instance>
5353
</population>
5454
<projection id="pop_pre__TO__pop_post" presynapticPopulation="pop_pre" postsynapticPopulation="pop_post" synapse="syn__pop_pre__TO__pop_post">

‎NeuroML2/Inputs.net.nml‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
<notes>
33
This NeuroML 2 file has been generated from:
44
PyNN v0.10.1
5-
libNeuroML v0.5.3
6-
pyNeuroML v1.0.8
5+
libNeuroML v0.5.5
6+
pyNeuroML v1.1.1
77
</notes>
88
<pulseGenerator id="DCSource_DCSource_0" delay="50.0ms" duration="350.0ms" amplitude="0.9nA"/>
99
<compoundInput id="ACSource_ACSource_1">
@@ -16,20 +16,20 @@
1616
<pulseGenerator id="step_2" delay="350.0ms" duration="60.0ms" amplitude="-0.2nA"/>
1717
<pulseGenerator id="step_3" delay="410.0ms" duration="999999590.0ms" amplitude="0.2nA"/>
1818
</compoundInput>
19-
<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1." i_offset="0.1" tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
19+
<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1.0" i_offset="0.1" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
2020
<network id="Inputs">
2121
<population id="pop_pre" component="IF_cond_alpha_pop_pre" size="4" type="populationList">
2222
<instance id="0">
23-
<location x="0." y="0." z="0."/>
23+
<location x="0.0" y="0.0" z="0.0"/>
2424
</instance>
2525
<instance id="1">
26-
<location x="1." y="0." z="0."/>
26+
<location x="1.0" y="0.0" z="0.0"/>
2727
</instance>
2828
<instance id="2">
29-
<location x="2." y="0." z="0."/>
29+
<location x="2.0" y="0.0" z="0.0"/>
3030
</instance>
3131
<instance id="3">
32-
<location x="3." y="0." z="0."/>
32+
<location x="3.0" y="0.0" z="0.0"/>
3333
</instance>
3434
</population>
3535
<inputList id="Input_DCSource_DCSource_0" population="pop_pre" component="DCSource_DCSource_0">

‎NeuroML2/LEMS_Sim_Inputs.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
<!--
44
This LEMS file has been generated from:
55
PyNN v0.10.1
6-
libNeuroML v0.5.3
7-
pyNeuroML v1.0.8
6+
libNeuroML v0.5.5
7+
pyNeuroML v1.1.1
88
-->
99

1010
<!-- Specify which component to run -->

‎NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
<!--
44
This LEMS file has been generated from:
55
PyNN v0.10.1
6-
libNeuroML v0.5.3
7-
pyNeuroML v1.0.8
6+
libNeuroML v0.5.5
7+
pyNeuroML v1.1.1
88
-->
99

1010
<!-- Specify which component to run -->

‎NeuroML2/Positions.net.nml.h5‎

14 Bytes
Binary file not shown.

‎NeuroML2/PyNN_NeuroML2_Export.net.nml‎

Lines changed: 24 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -2,70 +2,70 @@
22
<notes>
33
This NeuroML 2 file has been generated from:
44
PyNN v0.10.1
5-
libNeuroML v0.5.3
6-
pyNeuroML v1.0.8
5+
libNeuroML v0.5.5
6+
pyNeuroML v1.1.1
77
</notes>
8-
<IF_curr_alpha id="IF_curr_alpha_pop_IF_curr_alpha" cm="1." i_offset="0.9" tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="10." v_reset="-62." v_rest="-65." v_thresh="-52."/>
9-
<IF_curr_exp id="IF_curr_exp_pop_IF_curr_exp" cm="1." i_offset="1." tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="8." v_reset="-70." v_rest="-65." v_thresh="-50."/>
10-
<IF_cond_alpha id="IF_cond_alpha_pop_IF_cond_alpha" cm="1." i_offset="0.9" tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
11-
<IF_cond_alpha id="IF_cond_alpha_pop_post2" cm="1." i_offset="0." tau_syn_E="5." tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="10." v_reset="-62." v_rest="-65." v_thresh="-52." e_rev_E="0." e_rev_I="-70."/>
12-
<IF_cond_exp id="IF_cond_exp_pop_IF_cond_exp" cm="1." i_offset="1." tau_syn_E="2." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-68." v_rest="-65." v_thresh="-52." e_rev_E="0." e_rev_I="-70."/>
13-
<IF_cond_exp id="IF_cond_exp_pop_post1" cm="1." i_offset="0." tau_syn_E="5." tau_syn_I="5." v_init="-65." tau_m="20." tau_refrac="10." v_reset="-62." v_rest="-65." v_thresh="-52." e_rev_E="0." e_rev_I="-70."/>
14-
<EIF_cond_exp_isfa_ista id="EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista" cm="0.281" i_offset="0.6" tau_syn_E="5." tau_syn_I="5." v_init="-70.599999999999994" tau_m="9.3667" tau_refrac="0." v_reset="-68." v_rest="-70.599999999999994" v_thresh="-52." e_rev_E="0." e_rev_I="-80." a="0." b="0.0805" delta_T="2." tau_w="144." v_spike="-40."/>
15-
<HH_cond_exp id="HH_cond_exp_pop_HH_cond_exp" cm="0.2" i_offset="0.2" tau_syn_E="0.2" tau_syn_I="2." v_init="-65." v_offset="-63." e_rev_E="0." e_rev_I="-80." e_rev_K="-90." e_rev_Na="50." e_rev_leak="-65." g_leak="0.01" gbar_K="6." gbar_Na="20."/>
16-
<expCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post1" tau_syn="5." e_rev="0."/>
17-
<alphaCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post2" tau_syn="5." e_rev="0."/>
8+
<IF_curr_alpha id="IF_curr_alpha_pop_IF_curr_alpha" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="10.0" v_reset="-62.0" v_rest="-65.0" v_thresh="-52.0"/>
9+
<IF_curr_exp id="IF_curr_exp_pop_IF_curr_exp" cm="1.0" i_offset="1.0" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="8.0" v_reset="-70.0" v_rest="-65.0" v_thresh="-50.0"/>
10+
<IF_cond_alpha id="IF_cond_alpha_pop_IF_cond_alpha" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
11+
<IF_cond_alpha id="IF_cond_alpha_pop_post2" cm="1.0" i_offset="0.0" tau_syn_E="5.0" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="10.0" v_reset="-62.0" v_rest="-65.0" v_thresh="-52.0" e_rev_E="0.0" e_rev_I="-70.0"/>
12+
<IF_cond_exp id="IF_cond_exp_pop_IF_cond_exp" cm="1.0" i_offset="1.0" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-68.0" v_rest="-65.0" v_thresh="-52.0" e_rev_E="0.0" e_rev_I="-70.0"/>
13+
<IF_cond_exp id="IF_cond_exp_pop_post1" cm="1.0" i_offset="0.0" tau_syn_E="5.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="10.0" v_reset="-62.0" v_rest="-65.0" v_thresh="-52.0" e_rev_E="0.0" e_rev_I="-70.0"/>
14+
<EIF_cond_exp_isfa_ista id="EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista" cm="0.281" i_offset="0.6" tau_syn_E="5.0" tau_syn_I="5.0" v_init="-70.599999999999994" tau_m="9.3667" tau_refrac="0.0" v_reset="-68.0" v_rest="-70.599999999999994" v_thresh="-52.0" e_rev_E="0.0" e_rev_I="-80.0" a="0.0" b="0.0805" delta_T="2.0" tau_w="144.0" v_spike="-40.0"/>
15+
<HH_cond_exp id="HH_cond_exp_pop_HH_cond_exp" cm="0.2" i_offset="0.2" tau_syn_E="0.2" tau_syn_I="2.0" v_init="-65.0" v_offset="-63.0" e_rev_E="0.0" e_rev_I="-80.0" e_rev_K="-90.0" e_rev_Na="50.0" e_rev_leak="-65.0" g_leak="0.01" gbar_K="6.0" gbar_Na="20.0"/>
16+
<expCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post1" tau_syn="5.0" e_rev="0.0"/>
17+
<alphaCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post2" tau_syn="5.0" e_rev="0.0"/>
1818
<network id="PyNN_NeuroML2_Export">
1919
<population id="pop_IF_curr_alpha" component="IF_curr_alpha_pop_IF_curr_alpha" size="3" type="populationList">
2020
<instance id="0">
21-
<location x="0." y="0." z="0."/>
21+
<location x="0.0" y="0.0" z="0.0"/>
2222
</instance>
2323
<instance id="1">
24-
<location x="1." y="0." z="0."/>
24+
<location x="1.0" y="0.0" z="0.0"/>
2525
</instance>
2626
<instance id="2">
27-
<location x="2." y="0." z="0."/>
27+
<location x="2.0" y="0.0" z="0.0"/>
2828
</instance>
2929
</population>
3030
<population id="pop_IF_curr_exp" component="IF_curr_exp_pop_IF_curr_exp" size="1" type="populationList">
3131
<instance id="0">
32-
<location x="0." y="0." z="0."/>
32+
<location x="0.0" y="0.0" z="0.0"/>
3333
</instance>
3434
</population>
3535
<population id="pop_IF_cond_alpha" component="IF_cond_alpha_pop_IF_cond_alpha" size="1" type="populationList">
3636
<instance id="0">
37-
<location x="0." y="0." z="0."/>
37+
<location x="0.0" y="0.0" z="0.0"/>
3838
</instance>
3939
</population>
4040
<population id="pop_IF_cond_exp" component="IF_cond_exp_pop_IF_cond_exp" size="3" type="populationList">
4141
<instance id="0">
42-
<location x="0." y="0." z="0."/>
42+
<location x="0.0" y="0.0" z="0.0"/>
4343
</instance>
4444
<instance id="1">
45-
<location x="1." y="0." z="0."/>
45+
<location x="1.0" y="0.0" z="0.0"/>
4646
</instance>
4747
<instance id="2">
48-
<location x="2." y="0." z="0."/>
48+
<location x="2.0" y="0.0" z="0.0"/>
4949
</instance>
5050
</population>
5151
<population id="pop_EIF_cond_exp_isfa_ista" component="EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista" size="1" type="populationList">
5252
<instance id="0">
53-
<location x="0." y="0." z="0."/>
53+
<location x="0.0" y="0.0" z="0.0"/>
5454
</instance>
5555
</population>
5656
<population id="pop_HH_cond_exp" component="HH_cond_exp_pop_HH_cond_exp" size="1" type="populationList">
5757
<instance id="0">
58-
<location x="0." y="0." z="0."/>
58+
<location x="0.0" y="0.0" z="0.0"/>
5959
</instance>
6060
</population>
6161
<population id="pop_post1" component="IF_cond_exp_pop_post1" size="1" type="populationList">
6262
<instance id="0">
63-
<location x="0." y="0." z="0."/>
63+
<location x="0.0" y="0.0" z="0.0"/>
6464
</instance>
6565
</population>
6666
<population id="pop_post2" component="IF_cond_alpha_pop_post2" size="1" type="populationList">
6767
<instance id="0">
68-
<location x="0." y="0." z="0."/>
68+
<location x="0.0" y="0.0" z="0.0"/>
6969
</instance>
7070
</population>
7171
<projection id="pop_EIF_cond_exp_isfa_ista__TO__pop_post1" presynapticPopulation="pop_EIF_cond_exp_isfa_ista" postsynapticPopulation="pop_post1" synapse="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post1">

‎PyNN/.test.pynn9nest.omt‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ experiments:
1414
spike detection:
1515
method: threshold
1616
threshold: -55
17-
tolerance: 0.0003082
17+
tolerance: 0.00030816640986148277
1818
EIF_cond_exp_isfa_ista:
1919
observables:
2020
spike times:
@@ -25,7 +25,7 @@ experiments:
2525
spike detection:
2626
method: threshold
2727
threshold: -45
28-
tolerance: 0.0001675
28+
tolerance: 0.00016744809109184723
2929
pop_post2:
3030
observables:
3131
spike times:
@@ -36,7 +36,7 @@ experiments:
3636
spike detection:
3737
method: threshold
3838
threshold: -63.5
39-
tolerance: 0.0001403
39+
tolerance: 0.00014027868699162797
4040

4141
spike_rate_IF_curr_alpha_0:
4242
observables:

‎PyNN/LEMS_2007One_pynn.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,9 @@
99
1010
1111
This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
12-
org.neuroml.export v1.9.0
13-
org.neuroml.model v1.9.0
14-
jLEMS v0.10.7
12+
org.neuroml.export v1.9.1
13+
org.neuroml.model v1.9.1
14+
jLEMS v0.10.8
1515
1616
'''
1717
# Main PyNN script for: net1
@@ -51,7 +51,7 @@
5151
'b':-0.002,
5252
'c':-50.0,
5353
'd':0.1,
54-
'C':1.0E-4,
54+
'C':0.1,
5555
}
5656

5757
# ---------------------------------------------

0 commit comments

Comments
 (0)