PSICS - the Parallel Stochastic Ion Channel Simulator
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Input formats

Models and control parameters are read from a set of linked XML files. Each file covers a particular aspect of the model so that each file can be used in a range of different contexts and common modifications to the model often only involve switching one file for another.

The Model specification section of the user guide explains the structure of PSICS XML files, the various parameter types and how to set up complete models. This reference introduces each component type and tabulates all the allowed attributes (parameters) and elements (sub-objects).

Contents

Element Index

All XML tags that can be used in PSICS models.

About

Access

Activity

AfferentEvents

AlphaTimecourse

BiExponentialTimecourse

Branch

CellEnvironment

CellLocation

CellMorphology

CellProperties

CellRegion

ChannelDiscretization

ChannelPopulation

ChannelSet

ChannelStochThreshold

ClosedState

CommandSet

Comparison

ConductanceClamp

ConductanceNoise

ConductanceProfile

ConductancePulse

ConductanceStep

CurrentClamp

CurrentNoise

CurrentProfile

CurrentPulse

CurrentStep

DensityAdjustment

DistributionRule

EventSequence

Exclusion

ExpLinearTransition

ExpTransition

ExponentialTimecourse

FixedRateTransition

IaFCell

Ion

KSChannel

KSComplex

Line

LineGraph

LineSet

LogNormalWeights

LogUniformWeights

MeanVariance

ModelFolder

NormalWeights

OpenState

PSICSRun

PassiveProperties

Point

PoissonGenerator

PowerSpectrum

ProfileTimecourse

RegionMask

RunSet

SigmoidTransition

SingleSynapse

SmartRecorder

Stats

StructureDiscretization

Synapse

SynapsePopulation

SynapseSet

TauInfCodedTransition

TauInfTransition

ThresholdSensor

TimeSeries

UniformGenerator

UniformWeights

VHalfTransition

VRateTransition

View

ViewConfig

VoltageClamp

VoltageNoise

VoltageProfile

VoltagePulse

VoltageRecorder

VoltageStep

XAxis

YAxis

Attribute Index

All attribute names and the elements on which they occur.

accessPSICSRun
actionRegionMask
activityPSICSRun
allocationChannelPopulation, SynapsePopulation
amplitudeVoltageNoise, CurrentNoise, ConductanceNoise
atSingleSynapse, CurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
baseConductanceSynapse
baseElementSizeStructureDiscretization
baseTemperatureFixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransition, ExpTransition, SigmoidTransition, TauInfCodedTransition, TauInfTransition
beyondPoint, Branch
binSizeMeanVariance
capacitanceIaFCell
channelChannelPopulation, ChannelSet, ChannelStochThreshold, SmartRecorder
colorChannelPopulation, SynapsePopulation, Line, LineSet, PowerSpectrum, MeanVariance
columnTimeSeries
comparisonMeanVariance, MeanVariance
covaluesRunSet
covaryRunSet
cytoplasmResistivityCellProperties, PassiveProperties
deltaVChannelDiscretization
densityFactorChannelPopulation, SynapsePopulation
distanceCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
distributionChannelPopulation, SynapsePopulation
durationVoltagePulse, CurrentPulse, ConductancePulse
environmentPSICSRun
evsourceAfferentEvents, AfferentEvents
fileEventSequence, TimeSeries, Line, LineSet, PowerSpectrum, MeanVariance
filepatternRunSet
forwardFixedRateTransition, VRateTransition
frequencyUniformGenerator, PoissonGenerator
fromFixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransition, ExpTransition, SigmoidTransition, TauInfCodedTransition, TauInfTransition, CurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
functionLine, LineSet, PowerSpectrum, MeanVariance
gRelOpenState
gSingleKSChannel
gammaVHalfTransition, VRateTransition
heightLineGraph
holdCurrentClamp, VoltageClamp, ConductanceClamp
iSingleComparison
infoPSICSRun
infvarTauInfCodedTransition
instancesKSComplex
labelPoint, Branch, CurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder, XAxis, YAxis, Line, LineSet, PowerSpectrum, MeanVariance
leak_timescaleIaFCell
lengthBranch
lineColorCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
lineStyleCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
lineWidthCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
locationCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
loglogPowerSpectrum
loserExclusion
maintainDensityAdjustment
matchCellRegion
maxUniformWeights, NormalWeights, LogUniformWeights, LogNormalWeights, XAxis, YAxis
maxDensityChannelPopulation, SynapsePopulation
maxPointsPSICSRun
maxshowLine, LineSet, PowerSpectrum, MeanVariance
meanVoltageNoise, CurrentNoise, ConductanceNoise
membraneCapacitanceCellProperties, PassiveProperties
mergeStructureDiscretization, RunSet
methodPSICSRun
midpointExpLinearTransition, ExpTransition, SigmoidTransition
minUniformWeights, NormalWeights, LogUniformWeights, LogNormalWeights, XAxis, YAxis
minorPoint, Branch
morphologyPSICSRun, ViewConfig
morphologyDataViewConfig
nChannelComparison
nameIon
numberChannelSet, SynapseSet
offsetBranch
onSurfacePoint, Branch
oneByOnePSICSRun
parentPoint, Branch
partofPoint, Branch
pathCellLocation
pathFractionCellLocation
permeantIonKSChannel, Synapse
potentialConductanceClamp
profileCurrentClamp, VoltageClamp, ConductanceClamp
propertiesPSICSRun
q10FixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransition, ExpTransition, SigmoidTransition, TauInfCodedTransition, TauInfTransition
quickChannelsPSICSRun
rPoint, Branch
rangeSmartRecorder
rankByCellLocation
rateExpLinearTransition, ExpTransition, SigmoidTransition
recordCurrentClamp, VoltageClamp, ConductanceClamp, SmartRecorder
recordClampsAccess
refractory_periodIaFCell
regionPassiveProperties
relativeToChannelPopulation, SynapsePopulation
repeatAfterVoltagePulse, VoltageStep, VoltageNoise, CurrentPulse, CurrentStep, CurrentNoise, ConductancePulse, ConductanceStep, ConductanceNoise
repeatsPSICSRun
rescaleLine, LineSet, PowerSpectrum, MeanVariance
reset_potentialIaFCell
reversalPotentialIon
reverseFixedRateTransition, VRateTransition
riseBiExponentialTimecourse
runTimePSICSRun
saveIntervalAccess
scaleExpLinearTransition, ExpTransition, SigmoidTransition
scaleFactorTimeSeries
sdNormalWeights, LogNormalWeights
seedPoissonGenerator, VoltageNoise, CurrentNoise, ConductanceNoise
separateFilesAccess
separateFilesExtensionAccess
sequenceFractionCellLocation
sequenceIndexCellLocation
showLine, LineSet, PowerSpectrum, MeanVariance
squareCapsPSICSRun, CellMorphology
startVoltageProfile, VoltagePulse, VoltageStep, VoltageNoise, CurrentProfile, CurrentPulse, CurrentStep, CurrentNoise, ConductanceProfile, ConductancePulse, ConductanceStep, ConductanceNoise
startPotentialPSICSRun
stepValueCurrentClamp, VoltageClamp, ConductanceClamp
stochThresholdPSICSRun
synapseSingleSynapse, SynapsePopulation, SynapseSet
tauVHalfTransition, ExponentialTimecourse, BiExponentialTimecourse, AlphaTimecourse
tauMinVHalfTransition, VRateTransition
tauMinFwdVHalfTransition
tauMinRevVHalfTransition
tauvarTauInfCodedTransition
tdWeightingPSICSRun
temperatureCellEnvironment
thresholdThresholdSensor, IaFCell, ChannelStochThreshold
timeScaleVoltageNoise, CurrentNoise, ConductanceNoise
timeSeriesCurrentClamp, CurrentClamp, VoltageClamp, VoltageClamp, ConductanceClamp, ConductanceClamp
timeStepPSICSRun
timeUnitTimeSeries
tmaxMeanVariance
tminMeanVariance
toFixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransition, ExpTransition, SigmoidTransition, TauInfCodedTransition, TauInfTransition, VoltagePulse, VoltageStep, CurrentPulse, CurrentStep, ConductancePulse, ConductanceStep
totalNumberChannelPopulation, SynapsePopulation
towardsCurrentClamp, VoltageClamp, ConductanceClamp, VoltageRecorder, SmartRecorder
vHalfVHalfTransition
vMaxChannelDiscretization
vMinChannelDiscretization
valueUnitTimeSeries
valuesRunSet, CommandSet
varyDensityAdjustment, RunSet, CommandSet
widthLineGraph, Line, LineSet, PowerSpectrum, MeanVariance
winnerExclusion
xClosedState, OpenState, Point, Branch
xaxisLineGraph, LineGraph
xmaxView, Stats
xminView, Stats
yClosedState, OpenState, Point, Branch
yaxisLineGraph, LineGraph
ymaxView
yminView
zVHalfTransition, VRateTransition, Point, Branch
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