PYNML-CHANNELANALYSIS(1)

NAME
pynml-channelanalysis - manual page for pynml-channelanalysis v1.3.21

DESCRIPTION
usage: pynml-channelanalysis [-h] [-v] [-minV <min v>] [-maxV <max v>]

[-temperature <temperature>]
    [-duration <duration>] [-clampDelay <clamp delay>] [-clampDuration <clamp duration>] [-clampBaseVoltage <clamp base voltage>] [-stepTargetVoltage <step target voltage>] [-erev <reversal potential>] [-scaleDt <scale dt in generated LEMS>] [-caConc <Ca2+ concentration>] [-datSuffix <dat suffix>] [-norun] [-nogui] [-html] [-md] [-ivCurve] <NeuroML 2 Channel file> [<NeuroML 2 Channel file> ...]

A script which can be run to generate a LEMS file to analyse the behaviour of channels in NeuroML 2

  positional arguments:

<NeuroML 2 Channel file>
    Name of the NeuroML 2 file(s)

  options:

-h, --help
    show this help message and exit

-v  Verbose output

-minV <min v>
    Minimum voltage to test (integer, mV), default: -100mV

-maxV <max v>
    Maximum voltage to test (integer, mV), default: 100mV

-temperature <temperature>
    Temperature (float, celsius), default: 6.3degC

-duration <duration>
    Duration of simulation in ms, default: 100ms

-clampDelay <clamp delay>
    Delay before voltage clamp is activated in ms, default: 10ms

-clampDuration <clamp duration>
    Duration of voltage clamp in ms, default: 80ms

-clampBaseVoltage <clamp base voltage>
    Clamp base (starting/finishing) voltage in mV, default: -70mV

-stepTargetVoltage <step target voltage>
    Voltage in mV through which to step voltage clamps, default: 20mV

-erev <reversal potential>
    Reversal potential of channel for currents, default: 0mV

-scaleDt <scale dt in generated LEMS>
    Scale dt in generated LEMS, default: 1

-caConc <Ca2+ concentration>
    Internal concentration of Ca2+ (float, concentration in mM), default: 5e-05mM

-datSuffix <dat suffix>
    String to add to dat file names (before .dat)

-norun
    If used, just generate the LEMS file, don't run it

-nogui
    Supress plotting of variables and only save data to file

-html
    Generate a HTML page featuring the plots for the channel

-md Generate a (GitHub flavoured) Markdown page featuring the plots for the channel

-ivCurve
    Save currents through voltage clamp at each level & plot current vs voltage for ion channel

SEE-ALSO
pynml(1), pynml-archive(1), pynml-channelanalysis(1), pynml-channelml2nml(1), pynml-modchananalysis(1), pynml-plotchan(1), pynml-plotmorph(1), pynml-plotspikes(1), pynml-plottimeseries(1), pynml-povray(1), pynml-sonata(1), pynml-summary(1), pynml-swc2nml(1), pynml-tune(1), pynml-xpp(1),

Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.

ENVIRONMENT

pyNeuroML v1.3.21 (libNeuroML v0.6.7, jNeuroML v0.14.0)