synapses (run.xml)
Simple cell with distributions of synapses and event generators to activate them
Total CPU time 1.950 seconds; at 10:36:15 Thu 24 Sep 2009
Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | time/ms | timeStep | CPU Time / s |
85 | 0 / 0 | 0 / 0 | 62864 / 85 | 500.0 | 0.01 | 1.14 |
85 | 0 / 0 | 0 / 0 | 62864 / 85 | 500.0 | 0.02 | 0.580 |
85 | 0 / 0 | 0 / 0 | 62864 / 85 | 500.0 | 0.05 | 0.230 |
Morphology: cell
Predefined views
whole
enlarged
All files
Model | Preprocessed | Outupt data | Reference data etc |
run.xml cell.xml membrane.xml environment.xml recording.xml activity.xml leak.xml syn1.xml syn2.xml |
out-0.01.ppp out-0.02.ppp out-0.05.ppp |
log.txt out-0.01.sum out-0.02.sum out-0.05.sum out-0.01.dat out-0.01.txt out-0.02.dat out-0.02.txt out-0.05.dat out-0.05.txt |
stim1.txt NM1.swc |
Model
Archive file of the complete model: synapses.jarrun.xml
<PSICSRun timeStep="0.01ms" runTime="500ms" startPotential="-65mV" environment="environment" properties="membrane" access="recording" activity="activity" morphology="cell" stochThreshold="0"> <StructureDiscretization baseElementSize="12um"/> <RunSet vary="timeStep" values="[0.01, 0.02, 0.05]ms" filepattern="out-$"/> <info>Simple cell with distributions of synapses and event generators to activate them</info> <ViewConfig> <LineGraph width="500" height="400"> <XAxis min="0" max="250" label="time / ms"/> <YAxis min="-80" max="60" label="potential / mV"/> <LineSet file="out-0.01.txt" color="red"/> <LineSet file="out-0.02.txt" color="green"/> <LineSet file="out-0.05.txt" color="blue"/> <View id="whole" xmin="-10." xmax="500." ymin="-100." ymax="80."/> <View id="enlarged" xmin="-10." xmax="50." ymin="-70." ymax="0."/> </LineGraph> </ViewConfig> </PSICSRun>
cell.xml
<CellMorphology id="cell"> <Point id="p0" x="0" y="0" z="0" r="0.5"/> <Point parent="p0" id="p1" x="10" y="0" z = "0" r="0.5"/> <Point parent="p1" id="p2" x="20" y="0" z = "0" r="0.5"/> <Point parent="p2" id="p3" x="1000" y="5" z = "0" r="0.5"/> <!-- <Point parent="p0" id="p3" x="200" y="200" z = "0" r="0.5"/> --> </CellMorphology>
membrane.xml
<CellProperties id="membrane" cytoplasmResistivity="1000ohm_cm" membraneCapacitance="1uF_per_cm2"> <ChannelPopulation id="population_1" channel="leak" density="20per_um2"/> <SynapsePopulation id="sypop1" synapse="syn1" density="0.1per_um2" seed="1010"> <LogUniformWeights min="0.1" max="3"/> </SynapsePopulation> <SynapsePopulation id="sypop2" synapse="syn1" density="0.01per_um2"> <!-- <NormalWeights min="0.1" max="3" sd="0.5"/> <UniformWeights min="0.1" max="3"/> <LogUniformWeights min="0.1" max="3"/> --> <LogNormalWeights min="0.1" max="3" sd="0.5"/> </SynapsePopulation> <SingleSynapse id="sy3" synapse="syn2" at="p0"/> <SingleSynapse id="sy4" synapse="syn2" at="p1"/> <SingleSynapse id="sy5" synapse="syn1" at="p2"/> </CellProperties>
environment.xml
<CellEnvironment id="environment"> <Ion id="Na" name="Sodium" reversalPotential="40mV"/> <Ion id="K" name="Potassium" reversalPotential="-80mV"/> </CellEnvironment>
recording.xml
<Access id="recording" recordClamps="true"> <CellLocation id="pA" path="10" rankBy="radius" sequenceFraction="1."/> <CellLocation id="pB" path="50" rankBy="radius" sequenceFraction="1."/> <CellLocation id="pC" path="120" rankBy="radius" sequenceIndex="1."/> <VoltageRecorder location="pA" lineColor="blue"/> <VoltageRecorder location="pB" lineColor="blue"/> <VoltageRecorder location="pC" lineColor="blue"/> <VoltageRecorder at="p3" lineColor="blue"/> </Access>
activity.xml
<Activity id="activity"> <AfferentEvents population="sypop1"> <UniformGenerator frequency="0.001Hz"/> <!-- <EventSequence file="stim1"/> --> </AfferentEvents> <AfferentEvents population="sypop2"> <PoissonGenerator frequency="2Hz" seed="101"/> <!-- <UniformGenerator frequency="20Hz"/> <GammaGenerator theta="5ms" k="4"/> --> </AfferentEvents> <AfferentEvents population="sypop1"> <ThresholdSensor threshold="-50mV"/> <!-- This delivers an event to every synapse in population "sypop1" when the potential in the first compartment (fixed for now - could allow sensors to be moved in future) passes -50 mV from below. --> </AfferentEvents> </Activity>
leak.xml
<KSChannel id="leak" gSingle="0.01pS" permeantIon="K"> <OpenState id="o1"/> </KSChannel>
syn1.xml
<Synapse id="syn1" permeantIon="Na" baseConductance="400pS"> <ExponentialTimecourse tau="4ms"/> <!-- <BiExponentialTimecourse rise="2ms" tau="12ms"/> <AlphaTimecourse tau="4ms"/> <ProfileTimecourse file="stim1.txt" timeUnit="1ms"/> --> </Synapse>
syn2.xml
<Synapse id="syn2" permeantIon="K" baseConductance="100pS"> <BiExponentialTimecourse rise="1ms" tau="5ms"/> <!-- <BiExponentialTimecourse rise="2ms" tau="12ms"/> <AlphaTimecourse tau="4ms"/> <ProfileTimecourse file="stim1.txt" timeUnit="1ms"/> --> </Synapse>