-
Notifications
You must be signed in to change notification settings - Fork 53
/
custom_muscle_components.xml
330 lines (204 loc) · 12.5 KB
/
custom_muscle_components.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="cell_C">
<ionChannel id="slo-2" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="m" instances="1">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="10.237 mV"/>
</gateHHtauInf>
<!--<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="5.237 mV"/>
</gateHHtauInf>-->
</ionChannel>
<ionChannel id="shk-1" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="m" instances="1">
<timeCourse type="fixedTimeCourse" tau="10 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="13.237 mV"/>
</gateHHtauInf>
<!--<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="10.237 mV"/>
</gateHHtauInf>-->
</ionChannel>
<ionChannel id="egl-19" conductance="10pS" type="ionChannelHH" species="ca">
<notes></notes>
<gateHHtauInf id="m" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="-5.7 mV"/>
</gateHHtauInf>
<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="50 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="0.7 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="n" instances="4">
<timeCourse type="fixedTimeCourse" tau="190 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="1.237 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_fast_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes>K fast channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="p" instances="4">
<timeCourse type="fixedTimeCourse" tau="2.25518 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="7.42636 mV" midpoint="-8.05232 mV"/>
</gateHHtauInf>
<gateHHtauInf id="q" instances="1">
<timeCourse type="fixedTimeCourse" tau="149.963 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="-9.97468 mV" midpoint="-15.6456 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_slow_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes>K slow channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="n" instances="1">
<timeCourse type="fixedTimeCourse" tau="25.0007 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="15.8512 mV" midpoint="19.8741 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="ca_boyle_muscle" conductance="10pS" type="ionChannelHH" species="ca">
<notes>Ca channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="e" instances="2">
<timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
</gateHHtauInf>
<gateHHtauInf id="f" instances="1">
<timeCourse type="fixedTimeCourse" tau="150.88 ms"/>
<!-- Note!!!
f gate is "inactivation" a/c B&C 2008 p172
but the scale value from Table A1 (kf) is positive (5mV), i.e. steady
state is zero for v << midpoint and 1 for v >> midpoint
Couple this with a very slow time course & the ion channel never
conducts as e^2 x f is always ~0
Using -5.03176mV NOT 5mV for k/scale to make this INACTIVATION
This is suggested by the value used here:
https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/MatlabSupport/Main_Version/data/input.csv#L20
see also
https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/PythonSupport/Main_Version/compareToNeuroML2.py
-->
<steadyState type="HHSigmoidVariable" rate="1" scale="-5.03176 mV" midpoint="25.1815 mV"/>
</gateHHtauInf>
<customHGate id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/>
</ionChannel>
<ionChannel id="ca_muscle" conductance="10pS" type="ionChannelHH" species="ca">
<notes></notes>
<gateHHtauInf id="m" instances="2">
<timeCourse type="fixedTimeCourse" tau="1 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="6.7 mV"/>
</gateHHtauInf>
<gateHHtauInf id="h" instances="1">
<timeCourse type="fixedTimeCourse" tau="7 ms"/>
<steadyState type="MuscleSigmoidVariableCaInact" a="0.516" b="13.508 mV" c="19.48 mV"/>
</gateHHtauInf>
</ionChannel>
<ComponentType name="MuscleSigmoidVariable"
extends="baseVoltageDepVariable"
description="Sigmoidal form for variable equation">
<Parameter name="midpoint" dimension="voltage" />
<Parameter name="scale" dimension="voltage" />
<Dynamics>
<DerivedVariable name="x" dimension="none" exposure="x" value="1 / (1 + exp((-(v-midpoint)) / scale))"/>
</Dynamics>
</ComponentType>
<ComponentType name="MuscleSigmoidVariableCaInact"
extends="baseVoltageDepVariable"
description="Sigmoidal form for variable equation">
<Parameter name="a" dimension="none" />
<Parameter name="b" dimension="voltage" />
<Parameter name="c" dimension="voltage" />
<Dynamics>
<DerivedVariable name="x" dimension="none" exposure="x" value="1 - a * exp((-(v - b)*(v - b)) / (2 * c * c))"/>
</Dynamics>
</ComponentType>
<ComponentType name="muscleConcentrationModel"
extends="fixedFactorConcentrationModel"
description="Model of buffering of concentration of an ion (currently hard coded to be calcium, due to requirement for _iCa) which has a baseline level _restingConc and tends to this value with time course _decayConstant. A fixed factor _rho is used to scale the incoming current INDEPENDENTLY OF THE SIZE OF THE COMPARTMENT to produce a concentration change.">
<Parameter name="restingConc" dimension="concentration"/>
<Parameter name="decayConstant" dimension="time"/>
<Parameter name="rho" dimension="rho_factor"/>
<Requirement name="iCa" dimension="current"/>
<Requirement name="surfaceArea" dimension="area"/>
<Text name="ion"/> <!-- TODO: check why this isn't inherited from concentrationModel -->
<Dynamics>
<StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
<!--<StateVariable name="x" dimension="concentration"/>
<StateVariable name="iCaSigmoid" dimension="none"/>
<StateVariable name="iCaSigmoidMid" dimension="current"/>
<StateVariable name="iCaSigmoidSlope" dimension="current"/>
<StateVariable name="xSigmoid" dimension="none"/>
<StateVariable name="xSigmoidMid" dimension="concentration"/>
<StateVariable name="xSigmoidSlope" dimension="concentration"/>
<StateVariable name="xDecay" dimension="time"/>-->
<!--<DerivedVariable name="iCaSigmoid" dimension="none" value="1 / (1 + exp((iCaSigmoidMid - iCa) / iCaSigmoidSlope))"/>
<DerivedVariable name="xSigmoid" dimension="none" value="1 / (1 + exp((xSigmoidMid - x) / xSigmoidSlope))"/>
<TimeDerivative variable="x" value="iCaSigmoid * (iCa/surfaceArea) * rho/10 - (x / xDecay)"/>-->
<TimeDerivative variable="concentration" value="(iCa/surfaceArea) * rho - ((concentration - restingConc) / decayConstant)"/>
<OnStart>
<StateAssignment variable="concentration" value="initialConcentration"/>
<StateAssignment variable="extConcentration" value="initialExtConcentration"/>
<!--<StateAssignment variable="x" value="initialConcentration"/>
<StateAssignment variable="iCaSigmoidMid" value="0.1"/>
<StateAssignment variable="iCaSigmoidSlope" value="0.1"/>
<StateAssignment variable="xSigmoidMid" value="0.1"/>
<StateAssignment variable="xSigmoidSlope" value="0.1"/>
<StateAssignment variable="xDecay" value="0.1"/>-->
</OnStart>
<OnCondition test="concentration .lt. 0">
<StateAssignment variable="concentration" value="0"/>
</OnCondition>
<!--<OnCondition test="x .lt. 0">
<StateAssignment variable="x" value="0"/>
</OnCondition>-->
</Dynamics>
</ComponentType>
<!-- <ComponentType name="muscleConcentrationModel2"
extends="concentrationModel"
description="">
<Parameter name="restingConc" dimension="concentration"/>
<Parameter name="decayConstant" dimension="time"/>
<Parameter name="rho" dimension="rho_factor"/>
<Parameter name="xRho" dimension="rho_factor"/>
<Parameter name="iCaSigmoidMid" dimension="current"/>
<Parameter name="iCaSigmoidSlope" dimension="current"/>
<Parameter name="xSigmoidMid" dimension="concentration"/>
<Parameter name="xSigmoidSlope" dimension="concentration"/>
<Parameter name="xDecay" dimension="time"/>
<Parameter name="xrest" dimension="concentration"/>
<Requirement name="iCa" dimension="current"/>
<Requirement name="v" dimension="voltage"/>
<Requirement name="surfaceArea" dimension="area"/>
<Exposure name="xx" dimension="concentration" />
<Text name="ion"/>
<Dynamics>
<StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
<StateVariable name="xx" exposure="xx" dimension="concentration"/>
<StateVariable name="tmpConc" dimension="concentration"/>
<StateVariable name="tmpX" dimension="concentration"/>
<DerivedVariable name="tmp" dimension="concentration" value="concentration" />
<DerivedVariable name="z" dimension="none" value="0" />
<DerivedVariable name="iCaSigmoid" dimension="none" value="(1 / (1 + exp((iCaSigmoidMid - iCa) / iCaSigmoidSlope)))"/>
<DerivedVariable name="xSigmoid" dimension="none" value="(1 / (1 + exp((xSigmoidMid - tmpConc) / xSigmoidSlope)))"/>
<TimeDerivative variable="xx" value="((iCa)/surfaceArea) * xRho - ((xx-xrest) / xDecay)"/>
<TimeDerivative variable="concentration" value="((iCa)/surfaceArea) * xRho - ((concentration-xrest) / xDecay)"/>
<OnStart>
<StateAssignment variable="concentration" value="initialConcentration"/>
<StateAssignment variable="extConcentration" value="initialExtConcentration"/>
<StateAssignment variable="xx" value="initialConcentration"/>
</OnStart>
<OnCondition test="concentration .lt. 0">
<StateAssignment variable="concentration" value="0"/>
</OnCondition>
<OnCondition test="t .gt. 0">
<StateAssignment variable="tmpConc" value="concentration"/>
<StateAssignment variable="tmpX" value="xx"/>
</OnCondition>
<OnCondition test="xx .lt. 0">
<StateAssignment variable="xx" value="0"/>
</OnCondition>
</Dynamics>
</ComponentType>
-->
</neuroml>