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pgleesonpgleeson
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Ordered receptor list for greater reproducability
1 parent 38a5f47 commit f131888

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+3067
-3072
lines changed

‎CElegans/pythonScripts/c302/c302.py

Lines changed: 3 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -15,9 +15,6 @@
1515
from neuroml import ElectricalConnectionInstanceW
1616
from neuroml import ContinuousProjection
1717
from neuroml import ContinuousConnectionInstanceW
18-
from neuroml import ExpTwoSynapse
19-
from neuroml import GapJunction
20-
from neuroml import GradedSynapse
2118
from neuroml import Property
2219
from neuroml import PulseGenerator
2320
from neuroml import SineGenerator
@@ -39,9 +36,6 @@
3936
from lxml import etree
4037
import re
4138

42-
from parameters_C0 import GradedSynapse2
43-
from parameters_C2 import DelayedGapJunction
44-
from parameters_C2 import DelayedGradedSynapse
4539
import collections
4640

4741
try:
@@ -732,8 +726,9 @@ def generate(net_id,
732726
all_neuron_info, all_muscle_info = _get_cell_info([cell])
733727
#neuron, neuron.type(), neuron.receptor(), neuron.neurotransmitter(), short, color
734728
pop0.properties.append(Property("color", all_neuron_info[cell][5]))
735-
pop0.properties.append(Property("type", str('; '.join(all_neuron_info[cell][1]))))
736-
pop0.properties.append(Property("receptor", str('; '.join(all_neuron_info[cell][2]))))
729+
pop0.properties.append(Property("type", str('; '.join(all_neuron_info[cell][1]))))
730+
recps = sorted(all_neuron_info[cell][2])
731+
pop0.properties.append(Property("receptor", str('; '.join(recps))))
737732
pop0.properties.append(Property("neurotransmitter", str('; '.join(all_neuron_info[cell][3]))))
738733
except:
739734
# It's only metadata...

‎CElegans/pythonScripts/c302/c302_utils.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -381,8 +381,8 @@ def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to=
381381
ax.set_yticks(np.arange(data.shape[0]) + 0.5,minor=True)
382382

383383

384-
ax.set_yticklabels([all_info_pre[k][4] for k in all_info_pre.keys()])
385-
ax.set_xticklabels([all_info_post[k][4] for k in all_info_post.keys()])
384+
ax.set_yticklabels([all_info_pre[k][4] for k in all_info_pre])
385+
ax.set_xticklabels([all_info_post[k][4] for k in all_info_post])
386386
ax.set_ylabel('presynaptic')
387387
tick_size = 10 if data.shape[0]<20 else (8 if data.shape[0]<40 else 6)
388388
ax.tick_params(axis='y', labelsize=tick_size)

‎CElegans/pythonScripts/c302/examples/c302_A_Full.net.nml

Lines changed: 236 additions & 236 deletions
Large diffs are not rendered by default.

‎CElegans/pythonScripts/c302/examples/c302_A_IClamp.net.nml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -79,7 +79,7 @@ Parameters and setting used to generate this network:
7979
<population id="PVCL" component="generic_neuron_iaf_cell" size="1" type="populationList">
8080
<property tag="color" value="1 0 .4"/>
8181
<property tag="type" value="interneuron"/>
82-
<property tag="receptor" value="SER-2; PDFR-1"/>
82+
<property tag="receptor" value="PDFR-1; SER-2"/>
8383
<property tag="neurotransmitter" value="Acetylcholine"/>
8484
<property tag="OpenWormBackerAssignedName" value="Ramana Kumar"/>
8585
<instance id="0">

‎CElegans/pythonScripts/c302/examples/c302_A_Muscles.net.nml

Lines changed: 107 additions & 107 deletions
Large diffs are not rendered by default.

‎CElegans/pythonScripts/c302/examples/c302_A_Oscillator.net.nml

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ Parameters and setting used to generate this network:
5454
<population id="AVAL" component="generic_neuron_iaf_cell" size="1" type="populationList">
5555
<property tag="color" value="1 0 .4"/>
5656
<property tag="type" value="interneuron"/>
57-
<property tag="receptor" value="GLR-5; GLR-4; GLR-2; GLR-1; UNC-8; GGR-3; NPR-4; NMR-1; NMR-2"/>
57+
<property tag="receptor" value="GGR-3; GLR-1; GLR-2; GLR-4; GLR-5; NMR-1; NMR-2; NPR-4; UNC-8"/>
5858
<property tag="neurotransmitter" value=""/>
5959
<property tag="OpenWormBackerAssignedName" value="JUD"/>
6060
<instance id="0">
@@ -64,7 +64,7 @@ Parameters and setting used to generate this network:
6464
<population id="AVAR" component="generic_neuron_iaf_cell" size="1" type="populationList">
6565
<property tag="color" value="1 0 .4"/>
6666
<property tag="type" value="interneuron"/>
67-
<property tag="receptor" value="GLR-5; GLR-4; GLR-2; GLR-1; UNC-8; GGR-3; NPR-4; NMR-1; NMR-2"/>
67+
<property tag="receptor" value="GGR-3; GLR-1; GLR-2; GLR-4; GLR-5; NMR-1; NMR-2; NPR-4; UNC-8"/>
6868
<property tag="neurotransmitter" value=""/>
6969
<instance id="0">
7070
<location x="-3.5" y="-271.5" z="37.982999999999997"/>
@@ -73,7 +73,7 @@ Parameters and setting used to generate this network:
7373
<population id="DA2" component="generic_neuron_iaf_cell" size="1" type="populationList">
7474
<property tag="color" value=".5 .4 1"/>
7575
<property tag="type" value="motor"/>
76-
<property tag="receptor" value="CKR-2; DOP-1; UNC-8; NPR-3; DOP-3; SER-2"/>
76+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3; SER-2; UNC-8"/>
7777
<property tag="neurotransmitter" value="Acetylcholine"/>
7878
<property tag="OpenWormBackerAssignedName" value="Ruzila"/>
7979
<instance id="0">
@@ -83,7 +83,7 @@ Parameters and setting used to generate this network:
8383
<population id="DA3" component="generic_neuron_iaf_cell" size="1" type="populationList">
8484
<property tag="color" value=".5 .4 1"/>
8585
<property tag="type" value="motor"/>
86-
<property tag="receptor" value="DOP-3; DOP-1; UNC-8; NPR-3; CKR-2; SER-2"/>
86+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3; SER-2; UNC-8"/>
8787
<property tag="neurotransmitter" value="Acetylcholine"/>
8888
<property tag="OpenWormBackerAssignedName" value="Magoo"/>
8989
<instance id="0">
@@ -93,7 +93,7 @@ Parameters and setting used to generate this network:
9393
<population id="DB2" component="generic_neuron_iaf_cell" size="1" type="populationList">
9494
<property tag="color" value=".5 .4 1"/>
9595
<property tag="type" value="motor"/>
96-
<property tag="receptor" value="CKR-2; PDFR-1; DOP-3; NPR-3; DOP-1"/>
96+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3; PDFR-1"/>
9797
<property tag="neurotransmitter" value="Acetylcholine"/>
9898
<instance id="0">
9999
<location x="-0.2" y="-244.5" z="15.787000000000001"/>
@@ -102,7 +102,7 @@ Parameters and setting used to generate this network:
102102
<population id="DB3" component="generic_neuron_iaf_cell" size="1" type="populationList">
103103
<property tag="color" value=".5 .4 1"/>
104104
<property tag="type" value="motor"/>
105-
<property tag="receptor" value="DOP-3; CKR-2; NPR-3; DOP-1"/>
105+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3"/>
106106
<property tag="neurotransmitter" value="Acetylcholine"/>
107107
<instance id="0">
108108
<location x="-1.85" y="-195.275000000000006" z="-18.524999999999999"/>
@@ -111,7 +111,7 @@ Parameters and setting used to generate this network:
111111
<population id="DD2" component="generic_neuron_iaf_cell" size="1" type="populationList">
112112
<property tag="color" value=".5 .4 1"/>
113113
<property tag="type" value="motor"/>
114-
<property tag="receptor" value="NPR-1; DOP-3; MOD-1"/>
114+
<property tag="receptor" value="DOP-3; MOD-1; NPR-1"/>
115115
<property tag="neurotransmitter" value="GABA"/>
116116
<property tag="OpenWormBackerAssignedName" value="Evolver"/>
117117
<instance id="0">
@@ -121,7 +121,7 @@ Parameters and setting used to generate this network:
121121
<population id="DD3" component="generic_neuron_iaf_cell" size="1" type="populationList">
122122
<property tag="color" value=".5 .4 1"/>
123123
<property tag="type" value="motor"/>
124-
<property tag="receptor" value="NPR-1; DOP-3; MOD-1"/>
124+
<property tag="receptor" value="DOP-3; MOD-1; NPR-1"/>
125125
<property tag="neurotransmitter" value="GABA"/>
126126
<instance id="0">
127127
<location x="-1.9" y="-28.600002" z="-60.524999999999999"/>
@@ -130,7 +130,7 @@ Parameters and setting used to generate this network:
130130
<population id="PLML" component="generic_neuron_iaf_cell" size="1" type="populationList">
131131
<property tag="color" value="1 .2 1"/>
132132
<property tag="type" value="sensory"/>
133-
<property tag="receptor" value="DOP-1; DES-2; GLR-8; MEC-2; MEC-6; MEC-4; MEC-9; PDFR-1; DEG-3"/>
133+
<property tag="receptor" value="DEG-3; DES-2; DOP-1; GLR-8; MEC-2; MEC-4; MEC-6; MEC-9; PDFR-1"/>
134134
<property tag="neurotransmitter" value="Glutamate"/>
135135
<property tag="OpenWormBackerAssignedName" value="Isaac Spear"/>
136136
<instance id="0">
@@ -140,7 +140,7 @@ Parameters and setting used to generate this network:
140140
<population id="PLMR" component="generic_neuron_iaf_cell" size="1" type="populationList">
141141
<property tag="color" value="1 .2 1"/>
142142
<property tag="type" value="sensory"/>
143-
<property tag="receptor" value="DOP-1; DES-2; GLR-8; MEC-2; MEC-6; MEC-4; MEC-9; PDFR-1; DEG-3"/>
143+
<property tag="receptor" value="DEG-3; DES-2; DOP-1; GLR-8; MEC-2; MEC-4; MEC-6; MEC-9; PDFR-1"/>
144144
<property tag="neurotransmitter" value="Glutamate"/>
145145
<property tag="OpenWormBackerAssignedName" value="Altman"/>
146146
<instance id="0">
@@ -150,7 +150,7 @@ Parameters and setting used to generate this network:
150150
<population id="VA2" component="generic_neuron_iaf_cell" size="1" type="populationList">
151151
<property tag="color" value=".5 .4 1"/>
152152
<property tag="type" value="motor"/>
153-
<property tag="receptor" value="CKR-2; LGC-53; DOP-3; NPR-3; DOP-1"/>
153+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; LGC-53; NPR-3"/>
154154
<property tag="neurotransmitter" value="Acetylcholine"/>
155155
<property tag="OpenWormBackerAssignedName" value="Marquam Hill"/>
156156
<instance id="0">
@@ -160,7 +160,7 @@ Parameters and setting used to generate this network:
160160
<population id="VA3" component="generic_neuron_iaf_cell" size="1" type="populationList">
161161
<property tag="color" value=".5 .4 1"/>
162162
<property tag="type" value="motor"/>
163-
<property tag="receptor" value="DOP-3; CKR-2; NPR-3; DOP-1; LGC-53"/>
163+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; LGC-53; NPR-3"/>
164164
<property tag="neurotransmitter" value="Acetylcholine"/>
165165
<instance id="0">
166166
<location x="-1.475" y="-184.099989999999991" z="-26.374998000000001"/>
@@ -169,7 +169,7 @@ Parameters and setting used to generate this network:
169169
<population id="VB2" component="generic_neuron_iaf_cell" size="1" type="populationList">
170170
<property tag="color" value=".5 .4 1"/>
171171
<property tag="type" value="sensory; motor"/>
172-
<property tag="receptor" value="DOP-3; CKR-2; NPR-3; DOP-1"/>
172+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3"/>
173173
<property tag="neurotransmitter" value="Acetylcholine"/>
174174
<property tag="OpenWormBackerAssignedName" value="Bloodgood"/>
175175
<instance id="0">
@@ -179,7 +179,7 @@ Parameters and setting used to generate this network:
179179
<population id="VB3" component="generic_neuron_iaf_cell" size="1" type="populationList">
180180
<property tag="color" value=".5 .4 1"/>
181181
<property tag="type" value="sensory; motor"/>
182-
<property tag="receptor" value="CKR-2; DOP-3; NPR-3; DOP-1"/>
182+
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3"/>
183183
<property tag="neurotransmitter" value="Acetylcholine"/>
184184
<property tag="OpenWormBackerAssignedName" value="Ramez Naam"/>
185185
<instance id="0">
@@ -189,7 +189,7 @@ Parameters and setting used to generate this network:
189189
<population id="VD2" component="generic_neuron_iaf_cell" size="1" type="populationList">
190190
<property tag="color" value=".5 .4 1"/>
191191
<property tag="type" value="motor"/>
192-
<property tag="receptor" value="SER-2; NPR-1; DOP-3; MOD-1"/>
192+
<property tag="receptor" value="DOP-3; MOD-1; NPR-1; SER-2"/>
193193
<property tag="neurotransmitter" value="GABA"/>
194194
<instance id="0">
195195
<location x="-0.65000004" y="-226.049990000000008" z="2.35"/>
@@ -198,7 +198,7 @@ Parameters and setting used to generate this network:
198198
<population id="VD3" component="generic_neuron_iaf_cell" size="1" type="populationList">
199199
<property tag="color" value=".5 .4 1"/>
200200
<property tag="type" value="motor"/>
201-
<property tag="receptor" value="SER-2; NPR-1; DOP-3; MOD-1"/>
201+
<property tag="receptor" value="DOP-3; MOD-1; NPR-1; SER-2"/>
202202
<property tag="neurotransmitter" value="GABA"/>
203203
<instance id="0">
204204
<location x="-0.8" y="-188.099999999999994" z="-23.449999999999999"/>

‎CElegans/pythonScripts/c302/examples/c302_A_Pharyngeal.net.nml

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@ Parameters and setting used to generate this network:
5353
<population id="I1L" component="generic_neuron_iaf_cell" size="1" type="populationList">
5454
<property tag="color" value="1 0 .4"/>
5555
<property tag="type" value="sensory; interneuron"/>
56-
<property tag="receptor" value="GLR-7; DOP-4; FRPR-4; PDFR-1; GLR-8"/>
56+
<property tag="receptor" value="DOP-4; FRPR-4; GLR-7; GLR-8; PDFR-1"/>
5757
<property tag="neurotransmitter" value="Acetylcholine"/>
5858
<property tag="OpenWormBackerAssignedName" value="sitructa"/>
5959
<instance id="0">
@@ -63,7 +63,7 @@ Parameters and setting used to generate this network:
6363
<population id="I1R" component="generic_neuron_iaf_cell" size="1" type="populationList">
6464
<property tag="color" value="1 0 .4"/>
6565
<property tag="type" value="sensory; interneuron"/>
66-
<property tag="receptor" value="GLR-7; DOP-4; FRPR-4; PDFR-1; GLR-8"/>
66+
<property tag="receptor" value="DOP-4; FRPR-4; GLR-7; GLR-8; PDFR-1"/>
6767
<property tag="neurotransmitter" value="Acetylcholine"/>
6868
<property tag="OpenWormBackerAssignedName" value="Jesus Martinez"/>
6969
<instance id="0">
@@ -73,7 +73,7 @@ Parameters and setting used to generate this network:
7373
<population id="I2L" component="generic_neuron_iaf_cell" size="1" type="populationList">
7474
<property tag="color" value="1 0 .4"/>
7575
<property tag="type" value="sensory; interneuron"/>
76-
<property tag="receptor" value="GLR-7; DOP-4; SER-7; NTR-1; GLR-8"/>
76+
<property tag="receptor" value="DOP-4; GLR-7; GLR-8; NTR-1; SER-7"/>
7777
<property tag="neurotransmitter" value="Glutamate"/>
7878
<property tag="OpenWormBackerAssignedName" value="MetaMal"/>
7979
<instance id="0">
@@ -83,7 +83,7 @@ Parameters and setting used to generate this network:
8383
<population id="I2R" component="generic_neuron_iaf_cell" size="1" type="populationList">
8484
<property tag="color" value="1 0 .4"/>
8585
<property tag="type" value="sensory; interneuron"/>
86-
<property tag="receptor" value="GLR-7; DOP-4; SER-7; NTR-1; GLR-8"/>
86+
<property tag="receptor" value="DOP-4; GLR-7; GLR-8; NTR-1; SER-7"/>
8787
<property tag="neurotransmitter" value=""/>
8888
<property tag="OpenWormBackerAssignedName" value="Flying Armbar"/>
8989
<instance id="0">
@@ -93,7 +93,7 @@ Parameters and setting used to generate this network:
9393
<population id="I3" component="generic_neuron_iaf_cell" size="1" type="populationList">
9494
<property tag="color" value="1 0 .4"/>
9595
<property tag="type" value="sensory; interneuron"/>
96-
<property tag="receptor" value="GLR-7; SER-7; GLR-8"/>
96+
<property tag="receptor" value="GLR-7; GLR-8; SER-7"/>
9797
<property tag="neurotransmitter" value=""/>
9898
<instance id="0">
9999
<location x="-2.05" y="-296.550020000000018" z="58.25"/>
@@ -130,7 +130,7 @@ Parameters and setting used to generate this network:
130130
<population id="M1" component="generic_neuron_iaf_cell" size="1" type="populationList">
131131
<property tag="color" value=".5 .4 1"/>
132132
<property tag="type" value="motor"/>
133-
<property tag="receptor" value="SER-4; GLR-2; AVR-14"/>
133+
<property tag="receptor" value="AVR-14; GLR-2; SER-4"/>
134134
<property tag="neurotransmitter" value="Acetylcholine"/>
135135
<property tag="OpenWormBackerAssignedName" value="albertwenger"/>
136136
<instance id="0">
@@ -167,7 +167,7 @@ Parameters and setting used to generate this network:
167167
<population id="M3R" component="generic_neuron_iaf_cell" size="1" type="populationList">
168168
<property tag="color" value=".5 .4 1"/>
169169
<property tag="type" value="sensory; motor"/>
170-
<property tag="receptor" value="NPR-1; GLR-8; SER-7"/>
170+
<property tag="receptor" value="GLR-8; NPR-1; SER-7"/>
171171
<property tag="neurotransmitter" value="Glutamate"/>
172172
<instance id="0">
173173
<location x="-8.050000000000001" y="-295.399999999999977" z="48.149999999999999"/>
@@ -176,7 +176,7 @@ Parameters and setting used to generate this network:
176176
<population id="M4" component="generic_neuron_iaf_cell" size="1" type="populationList">
177177
<property tag="color" value=".5 .4 1"/>
178178
<property tag="type" value="motor"/>
179-
<property tag="receptor" value="SER7b; GLR-8; SER-7"/>
179+
<property tag="receptor" value="GLR-8; SER-7; SER7b"/>
180180
<property tag="neurotransmitter" value="Acetylcholine"/>
181181
<instance id="0">
182182
<location x="-2.033" y="-288.932979999999986" z="57.582999999999998"/>
@@ -195,7 +195,7 @@ Parameters and setting used to generate this network:
195195
<population id="MCL" component="generic_neuron_iaf_cell" size="1" type="populationList">
196196
<property tag="color" value=".5 .4 1"/>
197197
<property tag="type" value="sensory; motor"/>
198-
<property tag="receptor" value="TYRA-2; SER-7; GLR-8"/>
198+
<property tag="receptor" value="GLR-8; SER-7; TYRA-2"/>
199199
<property tag="neurotransmitter" value="Acetylcholine"/>
200200
<instance id="0">
201201
<location x="3.2" y="-296.149999999999977" z="52.299999999999997"/>
@@ -204,7 +204,7 @@ Parameters and setting used to generate this network:
204204
<population id="MCR" component="generic_neuron_iaf_cell" size="1" type="populationList">
205205
<property tag="color" value=".5 .4 1"/>
206206
<property tag="type" value="sensory; motor"/>
207-
<property tag="receptor" value="TYRA-2; GLR-8; SER-7"/>
207+
<property tag="receptor" value="GLR-8; SER-7; TYRA-2"/>
208208
<property tag="neurotransmitter" value="Acetylcholine"/>
209209
<instance id="0">
210210
<location x="-7.25" y="-296.149999999999977" z="52.299999999999997"/>
@@ -223,7 +223,7 @@ Parameters and setting used to generate this network:
223223
<population id="NSML" component="generic_neuron_iaf_cell" size="1" type="populationList">
224224
<property tag="color" value=".5 .4 1"/>
225225
<property tag="type" value="sensory; motor"/>
226-
<property tag="receptor" value="GLR-7; DOP-3; SER-2; SER-4; AEX-2; GLR-8; TYRA-2"/>
226+
<property tag="receptor" value="AEX-2; DOP-3; GLR-7; GLR-8; SER-2; SER-4; TYRA-2"/>
227227
<property tag="neurotransmitter" value="Serotonin"/>
228228
<instance id="0">
229229
<location x="2.6000001" y="-292.25" z="51.799999999999997"/>
@@ -232,7 +232,7 @@ Parameters and setting used to generate this network:
232232
<population id="NSMR" component="generic_neuron_iaf_cell" size="1" type="populationList">
233233
<property tag="color" value=".5 .4 1"/>
234234
<property tag="type" value="sensory; motor"/>
235-
<property tag="receptor" value="GLR-7; DOP-3; SER-2; SER-4; AEX-2; GLR-8; TYRA-2"/>
235+
<property tag="receptor" value="AEX-2; DOP-3; GLR-7; GLR-8; SER-2; SER-4; TYRA-2"/>
236236
<property tag="neurotransmitter" value="Serotonin"/>
237237
<instance id="0">
238238
<location x="-6.3500004" y="-292.25" z="51.799999999999997"/>

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