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pgleesonpgleeson
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Regenerated with latest nml libs
1 parent bcbd470 commit 9fb7ea9

11 files changed

Lines changed: 84 additions & 89 deletions

‎NeuroML2/ConnectionsTest.net.nml‎

Lines changed: 12 additions & 12 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 v1.0.10
5+
libNeuroML v0.5.5
6+
pyNeuroML v1.1.1
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</notes>
88
<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"/>
99
<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"/>
@@ -17,38 +17,38 @@
1717
<property tag="radius" value="5"/>
1818
<property tag="color" value="0 0.6 0"/>
1919
<instance id="0">
20-
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20+
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</instance>
2222
<instance id="1">
23-
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23+
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2424
</instance>
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<instance id="2">
26-
<location x="-8.63946327112879" y="-58.505078738749702" z="48.108413536120366"/>
26+
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2727
</instance>
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<instance id="3">
29-
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29+
<location x="-52.406762043828394" y="6.010609135001554" z="-58.236579579123649"/>
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</instance>
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<instance id="4">
32-
<location x="9.410821864814789" y="-67.150951044248657" z="-5.539973054629277"/>
32+
<location x="-84.522276311302463" y="-27.093766860654476" z="-28.20137345446372"/>
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</instance>
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</population>
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<population id="pop_post" component="IF_cond_alpha_pop_post" size="5" type="populationList">
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<property tag="radius" value="5"/>
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<property tag="color" value="0 0.2 0.6"/>
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<instance id="0">
39-
<location x="-28.678926434693718" y="184.837404126174533" z="67.766118837628937"/>
39+
<location x="-10.963933858486152" y="160.214056107236161" z="-17.681929175932854"/>
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</instance>
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<instance id="1">
42-
<location x="10.594326616152161" y="283.075595791765863" z="-53.361320773272112"/>
42+
<location x="-65.391507421071694" y="215.929509183693398" z="53.214475027961086"/>
4343
</instance>
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<instance id="2">
45-
<location x="-40.595026343040686" y="184.199929560101282" z="85.56822054509729"/>
45+
<location x="-25.558099064460361" y="219.63712563909769" z="-87.608059485643892"/>
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</instance>
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<instance id="3">
48-
<location x="73.442669087700679" y="157.981140882509521" z="21.626005179957875"/>
48+
<location x="57.458557554047054" y="140.98406076648115" z="-24.288796136764446"/>
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</instance>
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<instance id="4">
51-
<location x="-68.040102348167693" y="233.599105418118029" z="-57.106869113278471"/>
51+
<location x="78.618467098550227" y="180.149183458113185" z="-55.213241499240318"/>
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</instance>
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</population>
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<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: 2 additions & 2 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 v1.0.10
5+
libNeuroML v0.5.5
6+
pyNeuroML v1.1.1
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</notes>
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<pulseGenerator id="DCSource_DCSource_0" delay="50.0ms" duration="350.0ms" amplitude="0.9nA"/>
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<compoundInput id="ACSource_ACSource_1">

‎NeuroML2/LEMS_Sim_Inputs.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
<!--
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This LEMS file has been generated from:
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PyNN v0.10.1
6-
libNeuroML v0.5.3
7-
pyNeuroML v1.0.10
6+
libNeuroML v0.5.5
7+
pyNeuroML v1.1.1
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-->
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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
<!--
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This LEMS file has been generated from:
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PyNN v0.10.1
6-
libNeuroML v0.5.3
7-
pyNeuroML v1.0.10
6+
libNeuroML v0.5.5
7+
pyNeuroML v1.1.1
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-->
99

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

‎NeuroML2/Positions.net.nml.h5‎

8 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
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</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"/>
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<network id="PyNN_NeuroML2_Export">
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<population id="pop_IF_curr_alpha" component="IF_curr_alpha_pop_IF_curr_alpha" size="3" type="populationList">
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<instance id="0">
21-
<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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<instance id="1">
24-
<location x="1." y="0." z="0."/>
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<location x="1.0" y="0.0" z="0.0"/>
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</instance>
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<instance id="2">
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<location x="2." y="0." z="0."/>
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<location x="2.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_IF_curr_exp" component="IF_curr_exp_pop_IF_curr_exp" size="1" type="populationList">
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<instance id="0">
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<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_IF_cond_alpha" component="IF_cond_alpha_pop_IF_cond_alpha" size="1" type="populationList">
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<instance id="0">
37-
<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_IF_cond_exp" component="IF_cond_exp_pop_IF_cond_exp" size="3" type="populationList">
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<instance id="0">
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<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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<instance id="1">
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<location x="1." y="0." z="0."/>
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<location x="1.0" y="0.0" z="0.0"/>
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</instance>
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<instance id="2">
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<location x="2." y="0." z="0."/>
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<location x="2.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_EIF_cond_exp_isfa_ista" component="EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista" size="1" type="populationList">
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<instance id="0">
53-
<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_HH_cond_exp" component="HH_cond_exp_pop_HH_cond_exp" size="1" type="populationList">
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<instance id="0">
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<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_post1" component="IF_cond_exp_pop_post1" size="1" type="populationList">
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<instance id="0">
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<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<population id="pop_post2" component="IF_cond_alpha_pop_post2" size="1" type="populationList">
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<instance id="0">
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<location x="0." y="0." z="0."/>
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</population>
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<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/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
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jLEMS v0.10.7
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org.neuroml.export v1.9.1
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org.neuroml.model v1.9.1
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jLEMS v0.10.8
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'''
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# Main PyNN script for: net1
@@ -51,7 +51,7 @@
5151
'b':-0.002,
5252
'c':-50.0,
5353
'd':0.1,
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'C':1.0E-4,
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'C':0.1,
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}
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# ---------------------------------------------

‎PyNN/RS.mod‎

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Original file line numberDiff line numberDiff line change
@@ -3,17 +3,17 @@ TITLE Mod file for component: Component(id=RS type=izhikevich2007Cell)
33
COMMENT
44

55
This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
6-
org.neuroml.export v1.9.0
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org.neuroml.model v1.9.0
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jLEMS v0.10.7
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org.neuroml.export v1.9.1
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org.neuroml.model v1.9.1
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jLEMS v0.10.8
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ENDCOMMENT
1111

1212
NEURON {
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POINT_PROCESS RS
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16-
NONSPECIFIC_CURRENT i : To ensure v of section follows v_I
16+
NONSPECIFIC_CURRENT i : To ensure v of section follows v_I
1717
RANGE v0 : parameter
1818
RANGE k : parameter
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RANGE vr : parameter
@@ -24,13 +24,9 @@ NEURON {
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RANGE c : parameter
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RANGE d : parameter
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RANGE C : parameter
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RANGE iSyn : exposure
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RANGE iMemb : exposure
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RANGE copy_v : copy of v on section
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3430
}
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3632
UNITS {
@@ -42,47 +38,45 @@ UNITS {
4238
(mV) = (millivolt)
4339
(mS) = (millisiemens)
4440
(uS) = (microsiemens)
41+
(nF) = (nanofarad)
4542
(molar) = (1/liter)
4643
(kHz) = (kilohertz)
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(mM) = (millimolar)
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(um) = (micrometer)
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(umol) = (micromole)
47+
(pC) = (picocoulomb)
5048
(S) = (siemens)
5149

5250
}
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5452
PARAMETER {
5553

56-
v0 = -60 (mV)
57-
k = 7.0E-4 (uS / mV)
58-
vr = -60 (mV)
59-
vt = -40 (mV)
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vpeak = 35 (mV)
61-
a = 0.030000001 (kHz)
62-
b = -0.002 (uS)
63-
c = -50 (mV)
64-
d = 0.1 (nA)
65-
C = 1.0E-4 (microfarads)
54+
v0 = -60 (mV) : was: -0.06 (voltage)
55+
k = 7.0E-4 (uS / mV) : was: 7.0E-7 (conductance_per_voltage)
56+
vr = -60 (mV) : was: -0.06 (voltage)
57+
vt = -40 (mV) : was: -0.04 (voltage)
58+
vpeak = 35 (mV) : was: 0.035 (voltage)
59+
a = 0.030000001 (kHz) : was: 30.0 (per_time)
60+
b = -0.002 (uS) : was: -2.0E-9 (conductance)
61+
c = -50 (mV) : was: -0.05 (voltage)
62+
d = 0.1 (nA) : was: 1.0E-10 (current)
63+
C = 0.1 (nF) : was: 1.0E-10 (capacitance)
6664
}
6765

6866
ASSIGNED {
6967
v (mV)
70-
i (mA/cm2)
71-
72-
copy_v (mV)
73-
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v_I (nA)
75-
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iSyn (nA) : derived variable
68+
i (nA) : the point process current
7769

78-
iMemb (nA) : derived variable
70+
v_I (mV/ms) : for rate of change of voltage
71+
iSyn (nA) : derived variable
72+
iMemb (nA) : derived variable
7973
rate_v (mV/ms)
8074
rate_u (nA/ms)
8175

8276
}
8377

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STATE {
85-
u (nA)
79+
u (nA) : dimension: current
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}
8882

@@ -101,7 +95,6 @@ BREAKPOINT {
10195
SOLVE states METHOD cnexp
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copy_v = v
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i = v_I * C
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}
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‎PyNN/RS_Iext.mod‎

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=RS_Iext type=pulseGenerator)
33
COMMENT
44

55
This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
6-
org.neuroml.export v1.9.0
7-
org.neuroml.model v1.9.0
8-
jLEMS v0.10.7
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org.neuroml.export v1.9.1
7+
org.neuroml.model v1.9.1
8+
jLEMS v0.10.8
99

1010
ENDCOMMENT
1111

@@ -28,25 +28,27 @@ UNITS {
2828
(mV) = (millivolt)
2929
(mS) = (millisiemens)
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(uS) = (microsiemens)
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(nF) = (nanofarad)
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(molar) = (1/liter)
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(kHz) = (kilohertz)
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(mM) = (millimolar)
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(um) = (micrometer)
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(umol) = (micromole)
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(pC) = (picocoulomb)
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(S) = (siemens)
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}
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PARAMETER {
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weight = 1
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delay = 0 (ms)
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duration = 520 (ms)
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amplitude = 0.1 (nA)
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delay = 0 (ms) : was: 0.0 (time)
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duration = 520 (ms) : was: 0.52 (time)
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amplitude = 0.1 (nA) : was: 1.0E-10 (current)
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}
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STATE {
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i (nA)
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i (nA) : dimension: current
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}
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‎PyNN/RS_Iext_inputdefinition.py‎

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Original file line numberDiff line numberDiff line change
@@ -9,9 +9,9 @@
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---------------------------------------------
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This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
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org.neuroml.export v1.9.0
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org.neuroml.model v1.9.0
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jLEMS v0.10.7
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org.neuroml.export v1.9.1
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org.neuroml.model v1.9.1
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jLEMS v0.10.8
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'''
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# Input file for Component: RS_Iext

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