-
Notifications
You must be signed in to change notification settings - Fork 1
/
Figure5_NMDA.xml
157 lines (134 loc) · 7.32 KB
/
Figure5_NMDA.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
<Lems>
<Target component="sim1"/>
<!-- Include standard NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>
<!-- custom ComponentTypes -->
<ComponentType name="rampCell">
<Parameter name="v0" dimension="voltage"/>
<Parameter name="v1" dimension="voltage"/>
<Parameter name="tau" dimension="time"/>
<Attachments name="synapses" type="basePointCurrent"/>
<Exposure name="v" dimension="voltage" description="Membrane potential"/>
<Children name="blockingPlasticSynapse" type="blockingPlasticSynapse"/>
<Dynamics>
<DerivedVariable name="v" dimension="voltage" exposure="v" value="v0 + (t*(v1-v0)/tau)"/>
</Dynamics>
</ComponentType>
<!-- component definitions -->
<spikeGenerator id="spikeGen" period="15ms" />
<rampCell id="vClampCell" v0="100 mV" v1="100 mV" tau="1 ms"/>
<blockingPlasticSynapse id="nmdaSyn" gbase="2nS" erev="0mV"
tauRise="2ms" tauDecay="20ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="1 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
<plasticityMechanism type="tsodyksMarkramDepFacMechanism"
initReleaseProb="0.25" tauFac="50 ms" tauRec="150 ms"/>
</blockingPlasticSynapse>
<rampCell id="cell0" v0="-100 mV" v1="100 mV" tau="200 ms">
<blockingPlasticSynapse id="nmdaSyn0" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="0.001 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
</blockingPlasticSynapse>
<blockingPlasticSynapse id="nmdaSyn1" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="0.01 mM"
scalingConc= "2 mM"
scalingVolt="15 mV"/>
</blockingPlasticSynapse>
<blockingPlasticSynapse id="nmdaSyn2" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="0.1 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
</blockingPlasticSynapse>
<blockingPlasticSynapse id="nmdaSyn3" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="1 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
</blockingPlasticSynapse>
<blockingPlasticSynapse id="nmdaSyn4" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="10 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
</blockingPlasticSynapse>
<blockingPlasticSynapse id="nmdaSyn5" gbase="0.5nS" erev="0mV"
tauRise="2ms" tauDecay="8ms">
<blockMechanism type="voltageConcDepBlockMechanism"
species="mg" blockConcentration="100 mM"
scalingConc= "2 mM" scalingVolt="15 mV"/>
</blockingPlasticSynapse>
</rampCell>
<network id="net">
<population id="srcPop" component="spikeGen" size="1"/>
<population id="clampPop" component="vClampCell" size="1"/>
<!--<population id="rampPop" component="cell0" size="1"/>-->
<synapticConnection from="srcPop[0]" to="clampPop[0]"
synapse="nmdaSyn" destination="synapses"/>
</network>
<!-- Simulation configuration -->
<Simulation id="sim1" length="200ms" step="0.01ms" target="net">
<Display id="d1" title="Synaptic conductance for vClampCell" timeScale="1ms" xmin="-20" xmax="220" ymin="-0.05" ymax="1.05">
<Line id="g (nS)" quantity="clampPop[0]/nmdaSyn/g" scale="1nS"
color="#086A87" timeScale="1ms"/>
<Line id="U" quantity="clampPop[0]/nmdaSyn/plasticityMechanism/U" scale="1"
color="#DBA901" timeScale="1ms"/>
<Line id="R" quantity="clampPop[0]/nmdaSyn/plasticityMechanism/R" scale="1"
color="#8A0886" timeScale="1ms"/>
</Display>
<OutputFile id="conductances" fileName="nmda.dat">
<OutputColumn id="g" quantity="clampPop[0]/nmdaSyn/g"/>
<OutputColumn id="U" quantity="clampPop[0]/nmdaSyn/plasticityMechanism/U"/>
<OutputColumn id="R" quantity="clampPop[0]/nmdaSyn/plasticityMechanism/R"/>
</OutputFile>
<!--
<Display id="d2" title="block factor for rampCell" timeScale="1ms" xmin="-20" xmax="220" ymin="-0.2" ymax="1.2">
<Line id="0.001 mM"
quantity="rampPop[0]/nmdaSyn0/blockMechanism/blockFactor"
scale="1" color="#DBA901" timeScale="1ms"/>
<Line id="0.01 mM"
quantity="rampPop[0]/nmdaSyn1/blockMechanism/blockFactor"
scale="1" color="#AEB404" timeScale="1ms"/>
<Line id="0.1 mM"
quantity="rampPop[0]/nmdaSyn2/blockMechanism/blockFactor"
scale="1" color="#298A08" timeScale="1ms"/>
<Line id="1 mM"
quantity="rampPop[0]/nmdaSyn3/blockMechanism/blockFactor"
scale="1" color="#086A87" timeScale="1ms"/>
<Line id="10 mM"
quantity="rampPop[0]/nmdaSyn4/blockMechanism/blockFactor"
scale="1" color="#29088A" timeScale="1ms"/>
<Line id="100 mM"
quantity="rampPop[0]/nmdaSyn5/blockMechanism/blockFactor"
scale="1" color="#8A0886" timeScale="1ms"/>
</Display>
<OutputFile id="of1" fileName="nmda.dat">
<OutputColumn id="0" quantity="clampPop[0]/nmdaSyn/g"/>
<OutputColumn id="1"
quantity="clampPop[0]/nmdaSyn/plasticityMechanism/U"/>
<OutputColumn id="2"
quantity="clampPop[0]/nmdaSyn/plasticityMechanism/R"/>
<OutputColumn id="3"
quantity="rampPop[0]/v"/>
<OutputColumn id="4"
quantity="rampPop[0]/nmdaSyn0/blockMechanism/blockFactor"/>
<OutputColumn id="5"
quantity="rampPop[0]/nmdaSyn1/blockMechanism/blockFactor"/>
<OutputColumn id="6"
quantity="rampPop[0]/nmdaSyn2/blockMechanism/blockFactor"/>
<OutputColumn id="7"
quantity="rampPop[0]/nmdaSyn3/blockMechanism/blockFactor"/>
<OutputColumn id="8"
quantity="rampPop[0]/nmdaSyn4/blockMechanism/blockFactor"/>
<OutputColumn id="9"
quantity="rampPop[0]/nmdaSyn5/blockMechanism/blockFactor"/>
</OutputFile> -->
</Simulation>
</Lems>