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LEMS_Test_GolgiCaHVA.xml
219 lines (170 loc) · 13.3 KB
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LEMS_Test_GolgiCaHVA.xml
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<Lems>
<!-- Specify which component to run -->
<Target component="sim1"/>
<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>
<Include file="Golgi_CaHVA.channel.nml"/>
<!-- These may eventually be moved to core NeuroML definition files -->
<ComponentType name="vClampedCell" extends="baseCellMembPot" description="A 'cell' which can be clamped to a specific voltage for a certain duration to examine ion channel behaviour.">
<Parameter name="delay" dimension="time"/>
<Parameter name="duration" dimension="time"/>
<Parameter name="baseVoltage" dimension="voltage"/>
<Parameter name="targetVoltage" dimension="voltage"/>
<Parameter name="caConc" dimension="concentration"/>
<Children name="channelPopulation" type="channelPopulation"/>
<Dynamics>
<StateVariable name="v" exposure="v" dimension="voltage"/>
<OnStart>
<StateAssignment variable="v" value="baseVoltage"/>
</OnStart>
<OnCondition test="t .geq. delay .and. t .leq. duration+delay">
<StateAssignment variable="v" value="targetVoltage"/>
</OnCondition>
<OnCondition test="t .gt. duration+delay">
<StateAssignment variable="v" value="baseVoltage"/>
</OnCondition>
</Dynamics>
</ComponentType>
<ComponentType name="vClampedRampCell" extends="baseCellMembPot" description="A 'cell' which can be clamped to a steadily changing voltage for a certain duration to examine ion channel behaviour.">
<Parameter name="delay" dimension="time"/>
<Parameter name="duration" dimension="time"/>
<Parameter name="baseVoltage" dimension="voltage"/>
<Parameter name="targetVoltage0" dimension="voltage"/>
<Parameter name="targetVoltage1" dimension="voltage"/>
<Parameter name="caConc" dimension="concentration"/>
<Child name="channelPopulation" type="channelPopulation"/>
<Dynamics>
<StateVariable name="v" exposure="v" dimension="voltage"/>
<OnStart>
<StateAssignment variable="v" value="baseVoltage"/>
</OnStart>
<OnCondition test="t .geq. delay .and. t .leq. duration+delay">
<StateAssignment variable="v" value="targetVoltage0 + (targetVoltage1-targetVoltage0)*(t-delay)/(duration)"/>
</OnCondition>
<OnCondition test="t .gt. duration+delay">
<StateAssignment variable="v" value="baseVoltage"/>
</OnCondition>
</Dynamics>
</ComponentType>
<vClampedCell id="holderCell_min100" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="-100mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_min80" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="-80mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_min60" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="-60mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_min40" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="-40mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_min20" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="-20mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_0" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="0mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_20" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="20mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_40" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="40mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_60" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="60mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_80" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="80mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<vClampedCell id="holderCell_100" delay="10ms" duration="80ms" baseVoltage="-70mV" targetVoltage="100mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedCell>
<!-- Using twice duration & scaled up max_target_voltage to avoid problem at t = delay+duration -->
<vClampedRampCell id="rampCell0" delay="0ms" duration="200ms" baseVoltage="-100mV" targetVoltage0="-100mV" targetVoltage1="300mV" caConc="5e-05mM">
<channelPopulation id="test" ionChannel="GolgiCaHVA" number="1" erev="0mV"/>
</vClampedRampCell>
<network id="net1" type="networkWithTemperature" temperature = "6.3 degC">
<population id="holderCellPop_min100" component="holderCell_min100" size="1"/>
<population id="holderCellPop_min80" component="holderCell_min80" size="1"/>
<population id="holderCellPop_min60" component="holderCell_min60" size="1"/>
<population id="holderCellPop_min40" component="holderCell_min40" size="1"/>
<population id="holderCellPop_min20" component="holderCell_min20" size="1"/>
<population id="holderCellPop_0" component="holderCell_0" size="1"/>
<population id="holderCellPop_20" component="holderCell_20" size="1"/>
<population id="holderCellPop_40" component="holderCell_40" size="1"/>
<population id="holderCellPop_60" component="holderCell_60" size="1"/>
<population id="holderCellPop_80" component="holderCell_80" size="1"/>
<population id="holderCellPop_100" component="holderCell_100" size="1"/>
<population id="rampCellPop0" component="rampCell0" size="1"/>
</network>
<Simulation id="sim1" length="100ms" step="0.0025ms" target="net1">
<Display id="d0" title="GolgiCaHVA: Clamp voltages (mV)" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-120.0" ymax="120.0">
<Line id="-100mV" quantity="holderCellPop_min100[0]/v" scale="1mV" color="#ffff00" timeScale="1ms"/>
<Line id="-80mV" quantity="holderCellPop_min80[0]/v" scale="1mV" color="#ffe500" timeScale="1ms"/>
<Line id="-60mV" quantity="holderCellPop_min60[0]/v" scale="1mV" color="#ffcc00" timeScale="1ms"/>
<Line id="-40mV" quantity="holderCellPop_min40[0]/v" scale="1mV" color="#ffb200" timeScale="1ms"/>
<Line id="-20mV" quantity="holderCellPop_min20[0]/v" scale="1mV" color="#ff9900" timeScale="1ms"/>
<Line id="0mV" quantity="holderCellPop_0[0]/v" scale="1mV" color="#ff7f00" timeScale="1ms"/>
<Line id="20mV" quantity="holderCellPop_20[0]/v" scale="1mV" color="#ff6600" timeScale="1ms"/>
<Line id="40mV" quantity="holderCellPop_40[0]/v" scale="1mV" color="#ff4c00" timeScale="1ms"/>
<Line id="60mV" quantity="holderCellPop_60[0]/v" scale="1mV" color="#ff3300" timeScale="1ms"/>
<Line id="80mV" quantity="holderCellPop_80[0]/v" scale="1mV" color="#ff1900" timeScale="1ms"/>
<Line id="100mV" quantity="holderCellPop_100[0]/v" scale="1mV" color="#ff0000" timeScale="1ms"/>
</Display>
<Display id="d1" title="GolgiCaHVA: Fractional conductance at 6.3 degC" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-0.1" ymax="1.1">
<Line id="-100mV" quantity="holderCellPop_min100[0]/test/GolgiCaHVA/fopen" scale="1" color="#ffff00" timeScale="1ms"/>
<Line id="-80mV" quantity="holderCellPop_min80[0]/test/GolgiCaHVA/fopen" scale="1" color="#ffe500" timeScale="1ms"/>
<Line id="-60mV" quantity="holderCellPop_min60[0]/test/GolgiCaHVA/fopen" scale="1" color="#ffcc00" timeScale="1ms"/>
<Line id="-40mV" quantity="holderCellPop_min40[0]/test/GolgiCaHVA/fopen" scale="1" color="#ffb200" timeScale="1ms"/>
<Line id="-20mV" quantity="holderCellPop_min20[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff9900" timeScale="1ms"/>
<Line id="0mV" quantity="holderCellPop_0[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff7f00" timeScale="1ms"/>
<Line id="20mV" quantity="holderCellPop_20[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff6600" timeScale="1ms"/>
<Line id="40mV" quantity="holderCellPop_40[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff4c00" timeScale="1ms"/>
<Line id="60mV" quantity="holderCellPop_60[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff3300" timeScale="1ms"/>
<Line id="80mV" quantity="holderCellPop_80[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff1900" timeScale="1ms"/>
<Line id="100mV" quantity="holderCellPop_100[0]/test/GolgiCaHVA/fopen" scale="1" color="#ff0000" timeScale="1ms"/>
</Display>
<Display id="d7" title="GolgiCaHVA: Currents (nA) at different clamped potentials; 6.3 degC; rev potential: 0 mV" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-0.002" ymax="0.0014">
<Line id="-100mV" quantity="holderCellPop_min100[0]/test/i" scale="1nA" color="#ffff00" timeScale="1ms"/>
<Line id="-80mV" quantity="holderCellPop_min80[0]/test/i" scale="1nA" color="#ffe500" timeScale="1ms"/>
<Line id="-60mV" quantity="holderCellPop_min60[0]/test/i" scale="1nA" color="#ffcc00" timeScale="1ms"/>
<Line id="-40mV" quantity="holderCellPop_min40[0]/test/i" scale="1nA" color="#ffb200" timeScale="1ms"/>
<Line id="-20mV" quantity="holderCellPop_min20[0]/test/i" scale="1nA" color="#ff9900" timeScale="1ms"/>
<Line id="0mV" quantity="holderCellPop_0[0]/test/i" scale="1nA" color="#ff7f00" timeScale="1ms"/>
<Line id="20mV" quantity="holderCellPop_20[0]/test/i" scale="1nA" color="#ff6600" timeScale="1ms"/>
<Line id="40mV" quantity="holderCellPop_40[0]/test/i" scale="1nA" color="#ff4c00" timeScale="1ms"/>
<Line id="60mV" quantity="holderCellPop_60[0]/test/i" scale="1nA" color="#ff3300" timeScale="1ms"/>
<Line id="80mV" quantity="holderCellPop_80[0]/test/i" scale="1nA" color="#ff1900" timeScale="1ms"/>
<Line id="100mV" quantity="holderCellPop_100[0]/test/i" scale="1nA" color="#ff0000" timeScale="1ms"/>
</Display>
<Display id="s_inf" title="GolgiCaHVA: Gate s steady state, s_inf" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-0.1" ymax="1.1">
<Line id="s_inf (x axis: -100mV to 100mV)" quantity="rampCellPop0[0]/test/GolgiCaHVA/s/inf" scale="1" color="#000000" timeScale="1ms"/>
</Display>
<Display id="s_tau" title="GolgiCaHVA: Gate s time course, s_tau (ms) at 6.3 degC" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-10" ymax="110">
<Line id="s_tau (x axis: -100mV to 100mV)" quantity="rampCellPop0[0]/test/GolgiCaHVA/s/tau" scale="1ms" color="#000000" timeScale="1ms"/>
</Display>
<Display id="u_inf" title="GolgiCaHVA: Gate u steady state, u_inf" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-0.1" ymax="1.1">
<Line id="u_inf (x axis: -100mV to 100mV)" quantity="rampCellPop0[0]/test/GolgiCaHVA/u/inf" scale="1" color="#000000" timeScale="1ms"/>
</Display>
<Display id="u_tau" title="GolgiCaHVA: Gate u time course, u_tau (ms) at 6.3 degC" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-10" ymax="110">
<Line id="u_tau (x axis: -100mV to 100mV)" quantity="rampCellPop0[0]/test/GolgiCaHVA/u/tau" scale="1ms" color="#000000" timeScale="1ms"/>
</Display>
<OutputFile id="s_inf_of1" fileName="GolgiCaHVA.s.inf.lems.dat">
<OutputColumn id="s" quantity="rampCellPop0[0]/test/GolgiCaHVA/s/inf"/>
</OutputFile>
<OutputFile id="s_tau_of1" fileName="GolgiCaHVA.s.tau.lems.dat">
<OutputColumn id="s" quantity="rampCellPop0[0]/test/GolgiCaHVA/s/tau"/>
</OutputFile>
<OutputFile id="u_inf_of1" fileName="GolgiCaHVA.u.inf.lems.dat">
<OutputColumn id="u" quantity="rampCellPop0[0]/test/GolgiCaHVA/u/inf"/>
</OutputFile>
<OutputFile id="u_tau_of1" fileName="GolgiCaHVA.u.tau.lems.dat">
<OutputColumn id="u" quantity="rampCellPop0[0]/test/GolgiCaHVA/u/tau"/>
</OutputFile>
<OutputFile id="rampCellV" fileName="GolgiCaHVA.rampV.lems.dat">
<OutputColumn id="v" quantity="rampCellPop0[0]/v"/>
</OutputFile>
</Simulation>
</Lems>