| 1 | <Lems xmlns="http://www.neuroml.org/lems/0.5" |
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| 2 | xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
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| 3 | xsi:schemaLocation="http://www.neuroml.org/lems/0.5 ../Schemas/LEMS/LEMS_v0.5.xsd" |
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| 4 | description="Defines voltage (and concentration) gated ion channel models. Ion channels will generally extend _baseIonChannel_. The most commonly used voltage dependent gate will extend _baseGate_."> |
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| 5 | |
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| 6 | <!-- A number of channel types for use in NeuroML 2 documents --> |
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| 7 | |
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| 8 | |
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| 9 | <!-- Including standard unit comp types & units for NeuroML v2.0 --> |
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| 10 | <Include file="NeuroMLCoreCompTypes.xml"/> |
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| 11 | |
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| 12 | |
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| 13 | <ComponentType name="baseVoltageDepRate" |
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| 14 | description="Base ComponentType for voltage dependent rate. Produces a time varying rate _r which depends on _v."> |
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| 15 | <Exposure name="r" dimension="per_time"/> |
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| 16 | <Requirement name="v" dimension="voltage"/> |
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| 17 | </ComponentType> |
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| 18 | |
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| 19 | <ComponentType name="baseVoltageConcDepRate" |
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| 20 | description="Base ComponentType for voltage and concentration dependent rate. Produces a time varying rate _r which depends on _v and _caConc." |
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| 21 | extends="baseVoltageDepRate"> |
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| 22 | <Requirement name="caConc" dimension="concentration"/> |
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| 23 | </ComponentType> |
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| 24 | |
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| 25 | |
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| 26 | <ComponentType name="baseHHRate" |
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| 27 | description="Base ComponentType for rate which follow one of the typical forms for rate equations in the standard HH formalism, using the parameters _rate, _midpoint and _scale" |
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| 28 | extends="baseVoltageDepRate"> |
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| 29 | <Parameter name="rate" dimension="per_time"/> |
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| 30 | <Parameter name="midpoint" dimension="voltage"/> |
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| 31 | <Parameter name="scale" dimension="voltage"/> |
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| 32 | </ComponentType> |
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| 33 | |
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| 34 | |
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| 35 | <ComponentType name="HHExpRate" |
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| 36 | extends="baseHHRate" |
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| 37 | description="Exponential form for rate equation (Q: Should these be renamed hhExpRate, etc?)"> |
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| 38 | <Behavior> |
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| 39 | <DerivedVariable name="r" exposure="r" value="rate * exp((v - midpoint)/scale)" dimension="per_time"/> |
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| 40 | </Behavior> |
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| 41 | </ComponentType> |
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| 42 | |
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| 43 | |
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| 44 | <ComponentType name="HHSigmoidRate" |
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| 45 | extends="baseHHRate" |
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| 46 | description="Sigmoidal form for rate equation"> |
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| 47 | <Behavior> |
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| 48 | <DerivedVariable name="r" exposure="r" value="rate / (1 + exp(0 - (v - midpoint)/scale))" dimension="per_time"/> |
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| 49 | </Behavior> |
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| 50 | </ComponentType> |
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| 51 | |
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| 52 | |
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| 53 | <ComponentType name="HHExpLinearRate" |
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| 54 | extends="baseHHRate" |
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| 55 | description="Exponential linear form for rate equation. Linear for large positive _v, exponentially decays for large negative _v."> |
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| 56 | <Behavior> |
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| 57 | <DerivedVariable name="x" value="(v - midpoint) / scale" dimension="none"/> |
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| 58 | <DerivedVariable name="r" exposure="r" value="rate * x / (1 - exp(0 - x))" dimension="per_time"/> |
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| 59 | </Behavior> |
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| 60 | </ComponentType> |
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| 61 | |
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| 62 | |
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| 63 | <ComponentType name="baseVoltageDepVariable" |
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| 64 | description="Base ComponentType for voltage dependent variable _x, which depends on _v. Can be used for inf/steady state of rate variable."> |
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| 65 | <Exposure name="x" dimension="none"/> |
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| 66 | <Requirement name="v" dimension="voltage"/> |
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| 67 | </ComponentType> |
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| 68 | |
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| 69 | <ComponentType name="baseVoltageConcDepVariable" |
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| 70 | description="Base ComponentType for voltage and calcium concentration dependent variable _x, which depends on _v and _caConc." |
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| 71 | extends="baseVoltageDepVariable"> |
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| 72 | <Requirement name="caConc" dimension="concentration"/> |
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| 73 | </ComponentType> |
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| 74 | |
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| 75 | <ComponentType name="baseHHVariable" |
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| 76 | description="Base ComponentType for voltage dependent dimensionless variable which follow one of the typical forms for variable equations in the standard HH formalism, using the parameters _rate, _midpoint, _scale" |
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| 77 | extends="baseVoltageDepVariable"> |
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| 78 | <Parameter name="rate" dimension="none"/> |
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| 79 | <Parameter name="midpoint" dimension="voltage"/> |
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| 80 | <Parameter name="scale" dimension="voltage"/> |
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| 81 | </ComponentType> |
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| 82 | |
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| 83 | |
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| 84 | <ComponentType name="HHExpVariable" |
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| 85 | extends="baseHHVariable" |
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| 86 | description="Exponential form for variable equation"> |
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| 87 | <Behavior> |
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| 88 | <DerivedVariable name="x" dimension="none" exposure="x" value="rate * exp((v - midpoint)/scale)"/> |
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| 89 | </Behavior> |
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| 90 | </ComponentType> |
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| 91 | |
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| 92 | |
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| 93 | <ComponentType name="HHSigmoidVariable" |
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| 94 | extends="baseHHVariable" |
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| 95 | description="Sigmoidal form for variable equation"> |
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| 96 | <Behavior> |
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| 97 | <DerivedVariable name="x" dimension="none" exposure="x" value="rate / (1 + exp(0 - (v - midpoint)/scale))"/> |
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| 98 | </Behavior> |
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| 99 | </ComponentType> |
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| 100 | |
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| 101 | |
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| 102 | <ComponentType name="HHExpLinearVariable" |
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| 103 | extends="baseHHVariable" |
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| 104 | description="Exponential linear form for variable equation. Linear for large positive _v, exponentially decays for large negative _v."> |
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| 105 | <Behavior> |
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| 106 | <DerivedVariable name="a" dimension="none" value="(v - midpoint) / scale"/> |
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| 107 | <DerivedVariable name="x" dimension="none" exposure="x" value="rate * a / (1 - exp(0 - a))"/> |
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| 108 | </Behavior> |
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| 109 | </ComponentType> |
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| 110 | |
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| 111 | |
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| 112 | <ComponentType name="baseVoltageDepTime" |
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| 113 | description="Base type for voltage dependent ComponentType producing value _t with dimension time (e.g. for time course of rate variable). Note: time course would not normally be fit to exp/sigmoid etc."> |
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| 114 | <Exposure name="t" dimension="time"/> |
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| 115 | <Requirement name="v" dimension="voltage"/> |
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| 116 | </ComponentType> |
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| 117 | |
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| 118 | <ComponentType name="fixedTimeCourse" |
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| 119 | extends="baseVoltageDepTime" |
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| 120 | description="Time course of a fixed magnitude _tau which can be used for the time course in _gateHH_"> |
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| 121 | |
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| 122 | <Parameter name="tau" dimension="time"/> |
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| 123 | <Behavior> |
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| 124 | <DerivedVariable name="t" dimension="time" exposure="t" value="tau"/> |
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| 125 | </Behavior> |
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| 126 | </ComponentType> |
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| 127 | |
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| 128 | |
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| 129 | |
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| 130 | <ComponentType name="baseQ10Settings" |
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| 131 | description="Base ComponentType for a scaling to apply to gating variable time course, usually temperature dependent"> |
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| 132 | |
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| 133 | <Exposure name="q10" dimension="none"/> |
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| 134 | <Requirement name="temperature" dimension="temperature"/> |
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| 135 | |
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| 136 | </ComponentType> |
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| 137 | |
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| 138 | |
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| 139 | <ComponentType name="q10Fixed" |
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| 140 | extends="baseQ10Settings" |
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| 141 | description="A fixed value, _fixedQ10, for the scaling of the time course of the gating variable"> |
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| 142 | <Parameter name="fixedQ10" dimension="none"/> |
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| 143 | <Behavior> |
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| 144 | <DerivedVariable name="q10" exposure="q10" dimension="none" value="fixedQ10"/> |
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| 145 | </Behavior> |
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| 146 | </ComponentType> |
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| 147 | |
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| 148 | |
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| 149 | <ComponentType name="q10ExpTemp" |
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| 150 | extends="baseQ10Settings" |
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| 151 | description="A value for the Q10 scaling which varies as a standard function of the difference between the current temperature, _temperature, and the temperature at which the gating variable equations were determined, _experimentalTemp"> |
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| 152 | |
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| 153 | <Parameter name="q10Factor" dimension="none"/> |
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| 154 | <Parameter name="experimentalTemp" dimension="temperature"/> |
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| 155 | |
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| 156 | <Behavior> |
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| 157 | <DerivedVariable name="q10" exposure="q10" dimension="none" value="q10Factor^((temperature - experimentalTemp)/10)"/> |
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| 158 | </Behavior> |
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| 159 | </ComponentType> |
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| 160 | |
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| 161 | <ComponentType name="baseConductanceScaling" |
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| 162 | description="Base ComponentType for a scaling to apply to a gate's conductance, e.g. temperature dependent scaling"> |
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| 163 | |
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| 164 | <Exposure name="factor" dimension="none"/> |
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| 165 | <Requirement name="temperature" dimension="temperature"/> |
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| 166 | |
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| 167 | </ComponentType> |
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| 168 | |
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| 169 | |
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| 170 | <ComponentType name="q10ConductanceScaling" |
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| 171 | extends="baseConductanceScaling" |
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| 172 | description="A value for the conductance scaling which varies as a standard function of the difference between the current temperature, _temperature, and the temperature at which the conductance was originally determined, _experimentalTemp"> |
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| 173 | |
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| 174 | <Parameter name="q10Factor" dimension="none"/> |
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| 175 | <Parameter name="experimentalTemp" dimension="temperature"/> |
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| 176 | |
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| 177 | <Behavior> |
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| 178 | <DerivedVariable name="factor" exposure="factor" dimension="none" value="q10Factor^((temperature - experimentalTemp)/10)"/> |
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| 179 | </Behavior> |
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| 180 | </ComponentType> |
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| 181 | |
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| 182 | <ComponentType name="baseGate" |
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| 183 | description="Base ComponentType for a voltage and/or concentration dependent gate"> |
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| 184 | <Parameter name="instances" dimension="none"/> |
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| 185 | <Exposure name="fcond" dimension="none"/> |
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| 186 | <Exposure name="q" dimension="none"/> |
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| 187 | |
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| 188 | </ComponentType> |
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| 189 | |
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| 190 | <ComponentType name="gateHH" |
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| 191 | extends="baseGate" |
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| 192 | description="Gate which follows the general Hodgkin Huxley formalism"> |
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| 193 | |
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| 194 | <Child name="notes" type="notes"/> |
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| 195 | <Child name="q10Settings" type="baseQ10Settings"/> |
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| 196 | |
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| 197 | <Child name="forwardRate" type="baseVoltageDepRate"/> |
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| 198 | <Child name="reverseRate" type="baseVoltageDepRate"/> |
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| 199 | |
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| 200 | <Child name="timeCourse" type="baseVoltageDepTime" /> |
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| 201 | |
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| 202 | <Child name="steadyState" type="baseVoltageDepVariable" /> |
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| 203 | |
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| 204 | <Exposure name="alpha" dimension="per_time"/> |
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| 205 | <Exposure name="beta" dimension="per_time"/> |
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| 206 | |
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| 207 | <Exposure name="tau" dimension="time"/> |
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| 208 | <Exposure name="inf" dimension="none"/> |
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| 209 | |
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| 210 | <Exposure name="rateScale" dimension="none"/> |
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| 211 | |
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| 212 | <Behavior> |
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| 213 | <StateVariable name="q" exposure="q" dimension="none"/> |
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| 214 | |
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| 215 | <DerivedVariable name="rateScale" exposure="rateScale" dimension="none" select="q10Settings/q10" onAbsent="1"/> |
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| 216 | |
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| 217 | <DerivedVariable name="alpha" dimension="per_time" exposure="alpha" select="forwardRate/r" onAbsent="-1"/> |
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| 218 | <DerivedVariable name="beta" dimension="per_time" exposure="beta" select="reverseRate/r" onAbsent="-1"/> |
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| 219 | |
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| 220 | <DerivedVariable name="fcond" exposure="fcond" dimension="none" value="q^instances"/> |
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| 221 | |
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| 222 | <!-- Perhaps not the neatest solution... --> |
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| 223 | <DerivedVariable name="tauExplicit" dimension="time" select="timeCourse/t" onAbsent="-1"/> |
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| 224 | <DerivedVariable name="infExplicit" dimension="none" select="steadyState/x" onAbsent="-1"/> |
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| 225 | |
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| 226 | <DerivedVariable name="inf" dimension="none" exposure="inf" value="infExplicit" valueCondition="infExplicit .geq. 0" valueIfFalse="alpha/(alpha+beta)"/> |
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| 227 | |
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| 228 | <DerivedVariable name="tau" dimension="time" exposure="tau" value="tauExplicit / rateScale" valueCondition="tauExplicit .geq. 0" valueIfFalse="1/((alpha+beta) * rateScale)"/> |
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| 229 | |
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| 230 | <TimeDerivative variable="q" value="(inf - q) / tau"/> |
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| 231 | |
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| 232 | <OnStart> |
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| 233 | <StateAssignment variable="q" value="inf"/> |
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| 234 | </OnStart> |
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| 235 | |
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| 236 | </Behavior> |
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| 237 | </ComponentType> |
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| 238 | |
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| 239 | |
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| 240 | |
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| 241 | <!-- |
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| 242 | <ComponentType name="gateHHTauInf" extends="gate"> |
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| 243 | |
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| 244 | |
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| 245 | <Child name="notes" type="notes"/> |
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| 246 | <Child name="q10Settings" type="q10Settings"/> |
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| 247 | |
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| 248 | <Child name="alpha" type="HHRate"/> may be absent.. |
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| 249 | <Child name="beta" type="HHRate"/> may be absent... |
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| 250 | |
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| 251 | |
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| 252 | <Child type="timeCourse" name="timeCourse"/> |
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| 253 | |
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| 254 | <Exposure name="tau" dimension="time"/> |
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| 255 | <Exposure name="inf" dimension="none"/> |
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| 256 | |
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| 257 | |
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| 258 | <Behavior> |
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| 259 | <StateVariable name="q" exposure="q" dimension="none"/> |
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| 260 | |
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| 261 | <DerivedVariable name="rateScale" dimension="none" select="q10Settings/q10" onAbsent="1"/> |
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| 262 | |
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| 263 | <DerivedVariable name="inf" dimension="none" exposure="inf" value="1"/> |
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| 264 | <DerivedVariable name="tau" dimension="time" exposure="tau" value="1"/> |
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| 265 | |
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| 266 | <DerivedVariable name="fcond" exposure="fcond" dimension="none" value="q^instances"/> |
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| 267 | <OnStart> |
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| 268 | <StateAssignment variable="q" value="inf"/> |
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| 269 | </OnStart> |
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| 270 | |
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| 271 | |
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| 272 | </Behavior> |
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| 273 | </ComponentType> |
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| 274 | |
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| 275 | |
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| 276 | |
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| 277 | <ComponentType name="gateTauInfComplex" extends="gate"> |
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| 278 | <Parameter name="threshold" dimension="voltage"/> |
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| 279 | <Parameter name="vscale" dimension="voltage"/> |
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| 280 | <Parameter name="C" dimension="time"/> |
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| 281 | <Parameter name="a" dimension="none"/> |
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| 282 | <Parameter name="b" dimension="none"/> |
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| 283 | <Parameter name="vs1" dimension="voltage"/> |
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| 284 | <Parameter name="vs2" dimension="voltage"/> |
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| 285 | |
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| 286 | <Requirement name="v" dimension="voltage"/> |
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| 287 | |
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| 288 | <Behavior> |
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| 289 | <StateVariable name="q" exposure="q" dimension="none"/> |
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| 290 | <DerivedVariable name="tau" dimension="time" value="C / (exp(a + v/vs1) + exp(b + v/vs2))"/> |
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| 291 | <DerivedVariable name="qinf" dimension="none" value="1 / (1 + exp((v - threshold)/vscale))"/> |
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| 292 | <TimeDerivative variable="q" value="(qinf - q) / tau"/> |
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| 293 | <DerivedVariable name="fcond" exposure="fcond" dimension="none" value="q^instances"/> |
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| 294 | </Behavior> |
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| 295 | </ComponentType>--> |
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| 296 | |
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| 297 | |
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| 298 | <!--<Component id="gtic" type="gateTauInfComplex" instances="1" C="1ms" |
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| 299 | threshold="-75mV" vscale="5.5mV" a="-14.59" vs1="16mV" b="-1.87" vs2="17mV"/>--> |
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| 300 | |
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| 301 | |
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| 302 | |
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| 303 | <!-- neater way of expressing same thing |
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| 304 | |
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| 305 | <ComponentType name="Tau_t"> |
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| 306 | <Exposure name="tau" dimension="time"/> |
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| 307 | |
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| 308 | </ComponentType> |
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| 309 | |
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| 310 | <ComponentType name="Inf_t"> |
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| 311 | <Exposure name="minf" dimension="none"/> |
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| 312 | |
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| 313 | </ComponentType> |
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| 314 | |
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| 315 | <ComponentType name="gateTauInf" extends="gate"> |
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| 316 | |
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| 317 | <Child type="Tau_t" name="Tau"/> |
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| 318 | <Child type="Inf_t" name="Inf"/> |
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| 319 | |
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| 320 | <Exposure name="minf" dimension="none"/> |
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| 321 | <Exposure name="tau" dimension="time"/> |
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| 322 | <Requirement name="v" dimension="voltage"/>--> |
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| 323 | |
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| 324 | |
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| 325 | <!-- likely need for inner types here, so the Tau and Inf type definitions could be nested in here |
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| 326 | <Behavior> |
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| 327 | <StateVariable name="m" exposure="q" dimension="none"/> |
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| 328 | <DerivedVariable name="minf" exposure="minf" dimension="none" select="Inf/minf"/> |
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| 329 | <DerivedVariable name="tau" exposure="tau" dimension="time" select="Tau/tau"/> |
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| 330 | |
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| 331 | <DerivedVariable name="fcond" exposure="fcond" dimension="none" value="m^instances"/> |
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| 332 | |
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| 333 | <TimeDerivative variable="m" value="(minf - m) / tau"/> --> |
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| 334 | |
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| 335 | |
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| 336 | <!-- note that '/' is part of a path, or a division operator depending on context |
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| 337 | |
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| 338 | </Behavior> |
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| 339 | </ComponentType>--> |
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| 340 | |
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| 341 | <!-- |
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| 342 | <ComponentType name="hillTau" extends="Tau_t"> |
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| 343 | <Parameter name="C" dimension="time"/> |
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| 344 | <Parameter name="a" dimension="none"/> |
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| 345 | <Parameter name="b" dimension="none"/> |
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| 346 | <Parameter name="vs1" dimension="voltage"/> |
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| 347 | <Parameter name="vs2" dimension="voltage"/> |
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| 348 | <Requirement name="v" dimension="voltage"/> |
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| 349 | <Behavior> |
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| 350 | <DerivedVariable name="tau" exposure="tau" dimension="time" value="C / (exp(a + v/vs1) + exp(b + v/vs2))"/> |
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| 351 | </Behavior> |
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| 352 | </ComponentType> |
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| 353 | |
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| 354 | <ComponentType name="hillInf" extends="Inf_t"> |
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| 355 | <Parameter name="threshold" dimension="voltage"/> |
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| 356 | <Parameter name="vscale" dimension="voltage"/> |
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| 357 | <Requirement name="v" dimension="voltage"/> |
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| 358 | |
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| 359 | <Behavior> |
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| 360 | <DerivedVariable name="inf" exposure="minf" dimension="none" value="1 / (1 + exp((v - threshold)/vscale))"/> |
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| 361 | </Behavior> |
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| 362 | </ComponentType>--> |
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| 363 | |
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| 364 | |
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| 365 | |
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| 366 | |
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| 367 | <ComponentType name="baseIonChannel" |
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| 368 | description="Base for all ion channel ComponentTypes"> |
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| 369 | <Parameter name="conductance" dimension="conductance"/> |
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| 370 | <Exposure name="g" dimension="conductance"/> |
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| 371 | <Exposure name="fopen" dimension="none"/> |
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| 372 | <Requirement name="v" dimension="voltage"/> |
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| 373 | |
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| 374 | </ComponentType> |
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| 375 | |
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| 376 | <ComponentType name="ionChannel" |
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| 377 | extends="baseIonChannel" |
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| 378 | description="Temporary ComponentTypes extending _baseIonChannel_. This is needed since many existing examples use the name ionChannel. Should be removed."> |
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| 379 | |
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| 380 | </ComponentType> |
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| 381 | |
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| 382 | <ComponentType name="ionChannelPassive" |
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| 383 | extends="ionChannel" |
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| 384 | description="Simple passive ion channel where the constant conductance through the channel is equal to _conductance"> |
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| 385 | <Child name="notes" type="notes"/> |
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| 386 | <Text name="neuroLexId"/> |
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| 387 | |
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| 388 | <Behavior> |
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| 389 | <DerivedVariable name="fopen" exposure="fopen" value="1" dimension="none"/> |
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| 390 | <DerivedVariable name="g" exposure="g" value="conductance" dimension="conductance"/> |
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| 391 | </Behavior> |
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| 392 | </ComponentType> |
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| 393 | |
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| 394 | <!--<ComponentType name="parameter"> |
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| 395 | <Parameter name="value" dimension="none"/> |
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| 396 | </ComponentType>--> |
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| 397 | |
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| 398 | <ComponentType name="ionChannelHH" |
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| 399 | extends="ionChannel" |
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| 400 | description="Ion channel according to the Hodgkin Huxley formalism, with a number of gates (of type _gateHH_)"> |
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| 401 | <Child name="notes" type="notes"/> |
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| 402 | <Child name="conductanceScaling" type="baseConductanceScaling"/> |
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| 403 | <!--<Children name="parameters" type="parameter"/>--> |
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| 404 | <Children name="gates" type="gateHH"/> |
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| 405 | <Requirement name="temperature" dimension="temperature"/> |
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| 406 | <Text name="neuroLexId"/> |
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| 407 | <Text name="species"/> |
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| 408 | |
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| 409 | <Behavior> |
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| 410 | <DerivedVariable name="conductanceScale" dimension="none" select="conductanceScaling/factor" onAbsent="1"/> |
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| 411 | <DerivedVariable name="fopenUnscaled" dimension="none" select="gates[*]/fcond" reduce="multiply"/> |
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| 412 | <DerivedVariable name="fopen" exposure="fopen" dimension="none" value="conductanceScale * fopenUnscaled"/> |
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| 413 | <DerivedVariable name="g" exposure="g" value="conductance * fopen" dimension="conductance"/> |
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| 414 | </Behavior> |
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| 415 | </ComponentType> |
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| 416 | |
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| 417 | |
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| 418 | |
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| 419 | <ComponentType name="KSState" |
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| 420 | description="One of the states in which a _gateKS_ can be. The rates of transitions between these states are given by _KSTransition_s"> |
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| 421 | <Parameter name="relativeConductance" dimension="none"/> |
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| 422 | <Child name="notes" type="notes"/> |
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| 423 | <Exposure name="occupancy" dimension="none"/> |
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| 424 | <Exposure name="q" dimension="none"/> |
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| 425 | |
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| 426 | <Behavior> |
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| 427 | <StateVariable name="occupancy" exposure="occupancy" dimension="none"/> |
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| 428 | <DerivedVariable name="q" dimension="none" exposure="q" value="relativeConductance * occupancy"/> |
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| 429 | </Behavior> |
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| 430 | </ComponentType> |
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| 431 | |
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| 432 | <ComponentType name="closedState" |
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| 433 | extends="KSState" |
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| 434 | description="A _KSState_ with _relativeConductance of 0"> |
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| 435 | <Fixed parameter="relativeConductance" value="0"/> |
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| 436 | </ComponentType> |
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| 437 | |
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| 438 | |
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| 439 | <ComponentType name="openState" |
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| 440 | extends="KSState" |
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| 441 | description="A _KSState_ with _relativeConductance of 1"> |
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| 442 | <Fixed parameter="relativeConductance" value="1"/> |
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| 443 | </ComponentType> |
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| 444 | |
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| 445 | |
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| 446 | <ComponentType name="ionChannelKS" |
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| 447 | extends="ionChannel" |
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| 448 | description="A kinetic scheme based ion channel with multiple _gateKS_s, each of which consists of multiple _KSState_s and _KSTransition_s giving the rates of transition between them"> |
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| 449 | <Parameter name="conductance" dimension="conductance"/> |
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| 450 | <Children name="gates" type="gateKS"/> |
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| 451 | |
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| 452 | <Text name="species"/> |
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| 453 | |
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| 454 | <Behavior> |
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| 455 | <DerivedVariable name="fopen" exposure="fopen" dimension="none" select="gates[*]/fcond" reduce="multiply"/> |
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| 456 | <DerivedVariable name="g" exposure="g" dimension="conductance" value="fopen * conductance"/> |
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| 457 | |
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| 458 | </Behavior> |
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| 459 | </ComponentType> |
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| 460 | |
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| 461 | |
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| 462 | |
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| 463 | <ComponentType name="KSTransition" description="Specified the forward and reverse rates of transition between two _KSState_s in a _gateKS_"> |
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| 464 | <Link name="from" type="KSState"/> |
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| 465 | <Link name="to" type="KSState"/> |
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| 466 | <Exposure name="rf" dimension="per_time"/> |
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| 467 | <Exposure name="rr" dimension="per_time"/> |
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| 468 | |
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| 469 | </ComponentType> |
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| 470 | |
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| 471 | |
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| 472 | <ComponentType name="forwardTransition" |
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| 473 | extends="KSTransition" |
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| 474 | description="A forward only _KSTransition_ for a _gateKS_ which specifies a _rate (type _baseHHRate_) which follows one of the standard Hodgkin Huxley forms (e.g. _HHExpRate_, _HHSigmoidRate_, _HHExpLinearRate_"> |
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| 475 | |
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| 476 | <Child name="rate" type="baseHHRate"/> |
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| 477 | |
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| 478 | <Behavior> |
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| 479 | <DerivedVariable name="rf0" dimension="per_time" select="rate/r"/> |
|---|
| 480 | <DerivedVariable name="rf" exposure="rf" dimension="per_time" value="rf0"/> |
|---|
| 481 | <DerivedVariable name="rr" exposure="rr" dimension="per_time" value="0"/> |
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| 482 | </Behavior> |
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| 483 | |
|---|
| 484 | </ComponentType> |
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| 485 | |
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| 486 | <ComponentType name="reverseTransition" |
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| 487 | extends="KSTransition" |
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| 488 | description="A reverse only _KSTransition_ for a _gateKS_ which specifies a _rate (type _baseHHRate_) which follows one of the standard Hodgkin Huxley forms (e.g. _HHExpRate_, _HHSigmoidRate_, _HHExpLinearRate_"> |
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| 489 | |
|---|
| 490 | <Child name="rate" type="baseHHRate"/> |
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| 491 | |
|---|
| 492 | <Behavior> |
|---|
| 493 | <DerivedVariable name="rr0" dimension="per_time" select="rate/r"/> |
|---|
| 494 | <DerivedVariable name="rr" exposure="rr" dimension="per_time" value="rr0"/> |
|---|
| 495 | <DerivedVariable name="rf" exposure="rf" dimension="per_time" value="0"/> |
|---|
| 496 | </Behavior> |
|---|
| 497 | </ComponentType> |
|---|
| 498 | |
|---|
| 499 | |
|---|
| 500 | <ComponentType name="vHalfTransition" |
|---|
| 501 | extends="KSTransition" |
|---|
| 502 | description="Transition which specifies both the forward and reverse rates of transition"> |
|---|
| 503 | <Parameter name="vHalf" dimension="voltage"/> |
|---|
| 504 | <Parameter name="z" dimension="none"/> |
|---|
| 505 | <Parameter name="gamma" dimension="none"/> |
|---|
| 506 | <Parameter name="tau" dimension="time"/> |
|---|
| 507 | <Parameter name="tauMin" dimension="time"/> |
|---|
| 508 | <Constant name="kte" dimension="voltage" value="25.3mV"/> |
|---|
| 509 | <Requirement name="v" dimension="voltage"/> |
|---|
| 510 | |
|---|
| 511 | <Behavior> |
|---|
| 512 | |
|---|
| 513 | <DerivedVariable name="rf0" dimension="per_time" value="exp(z * gamma * (v - vHalf) / kte) / tau"/> |
|---|
| 514 | <DerivedVariable name="rr0" dimension="per_time" value="exp(-z * (1 - gamma) * (v - vHalf) / kte) / tau"/> |
|---|
| 515 | <DerivedVariable name="rf" exposure="rf" dimension="per_time" value="1 / (1/rf0 + tauMin)"/> |
|---|
| 516 | <DerivedVariable name="rr" exposure="rr" dimension="per_time" value="1 / (1/rr0 + tauMin)"/> |
|---|
| 517 | </Behavior> |
|---|
| 518 | </ComponentType> |
|---|
| 519 | |
|---|
| 520 | |
|---|
| 521 | |
|---|
| 522 | <ComponentType name="gateKS" |
|---|
| 523 | extends="baseGate" |
|---|
| 524 | description="A gate which consists of multiple _KSState_s and _KSTransition_s giving the rates of transition between them"> |
|---|
| 525 | <Parameter name="deltaV" dimension="voltage"/> |
|---|
| 526 | <Children name="states" type="KSState"/> |
|---|
| 527 | <Children name="transitions" type="KSTransition"/> |
|---|
| 528 | <Exposure name="qq" dimension="none"/> |
|---|
| 529 | |
|---|
| 530 | <Behavior> |
|---|
| 531 | |
|---|
| 532 | <DerivedVariable name="q" exposure="q" dimension="none" select="states[*]/q" reduce="add"/> |
|---|
| 533 | <DerivedVariable name="fopen" exposure="fcond" dimension="none" value="q^instances"/> |
|---|
| 534 | <DerivedVariable name="qq" exposure="qq" dimension="none" value="q"/> |
|---|
| 535 | |
|---|
| 536 | <KineticScheme name="ks"> |
|---|
| 537 | <Nodes children="states" variable="occupancy"/> |
|---|
| 538 | <Edges children="transitions" sourceNodeName="from" targetNodeName="to" forwardRate="rf" reverseRate="rr"/> |
|---|
| 539 | <Tabulable variable="v" increment="deltaV"/> |
|---|
| 540 | </KineticScheme> |
|---|
| 541 | |
|---|
| 542 | </Behavior> |
|---|
| 543 | |
|---|
| 544 | </ComponentType> |
|---|
| 545 | |
|---|
| 546 | |
|---|
| 547 | |
|---|
| 548 | </Lems> |
|---|
| 549 | |
|---|
