PYNML-TUNE(1)

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

DESCRIPTION
usage: pynml-tune [-h] [-simTime <simTime>] [-dt <dt>]

    [-analysisStartTime <analysisStartTime>] [-populationSize <populationSize>] [-maxEvaluations <maxEvaluations>] [-numSelected <numSelected>] [-numOffspring <numOffspring>] [-mutationRate <mutationRate>] [-numElites <numElites>] [-numParallelEvaluations <numParallelEvaluations>] [-seed <seed>] [-simulator <simulator>] [-knownTargetValues <knownTargetValues>] [-nogui] [-showPlotAlready] [-saveToFile] [-saveToFileScatter] [-saveToFileHist] [-saveToFileOutput] [-verbose] [-dryRun] [-extraReportInfo <extraReportInfo>] [-cleanup] <prefix> <neuromlFile> <target> <parameters> <max_constraints> <min_constraints> <targetData> <weights>

A script to tune a NeuroML 2 model against a number of target properties. This corresponds to the pyneuroml.tune.NeuroMLTuner.run_optimisation function in the Python API

  positional arguments:

<prefix>
    Prefix for optimisation run

<neuromlFile>
    NeuroML2 file containing model

<target>
    Target in NeuroML2 model

<parameters>
    List of parameter to adjust

<max_constraints>
    Max values for parameters

<min_constraints>
    Min values for parameters

<targetData>
    List of name/value pairs for properties extracted from data to judge fitness against

<weights>
    Weights to assign to each target name/value pair

  options:

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

-simTime <simTime>
    Simulation duration

-dt <dt>
    Simulation timestep

-analysisStartTime <analysisStartTime>
    Analysis start time

-populationSize <populationSize>
    Population size

-maxEvaluations <maxEvaluations>
    Maximum evaluations

-numSelected <numSelected>
    Number selected

-numOffspring <numOffspring>
    Number offspring

-mutationRate <mutationRate>
    Mutation rate

-numElites <numElites>
    Number of elites

-numParallelEvaluations <numParallelEvaluations>
    Number of evaluations to run in parallel

-seed <seed>
    Seed for optimiser

-simulator <simulator>
    Simulator to run (options: 'jNeuroML', 'jNeuroML_NEURON')

-knownTargetValues <knownTargetValues>
    List of name/value pairs which represent the known values of the target parameters

-nogui
    Should GUI elements be supressed?

-showPlotAlready
    Should generated plots be suppressed until show() called?

-saveToFile
    Name of file to save generated fitness plot to, default: skip.

-saveToFileScatter
    Name of file to save generated scatter plot to, default: skip.

-saveToFileHist
    Name of file to save generated histogram plot to, default: skip.

-saveToFileOutput
    Name of file to save generated output plot to, default: skip.

-verbose
    Verbose mode

-dryRun
    Dry run; just print setup information

-extraReportInfo <extraReportInfo>
    Extra tag/value pairs can be put into the report.json: -extraReportInfo=["tag":"value"]

-cleanup
    Should (some) generated files, e.g. *.dat, be deleted as optimisation progresses?

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)