CONTRIBUTING.md
LICENSE.lesser
MANIFEST.in
README.md
install_local_java.sh
pyproject.toml
setup.cfg
test-ghactions.sh
test.sh
docs/Makefile
docs/make.bat
docs/extras/Readme.md
docs/extras/pyneuroml.neuron.analysis.rst
docs/extras/pyneuroml.neuron.rst
docs/source/conf.py
docs/source/index.rst
docs/source/introduction.rst
docs/source/pyneuroml.analysis.rst
docs/source/pyneuroml.annotations.rst
docs/source/pyneuroml.archive.rst
docs/source/pyneuroml.channelml.rst
docs/source/pyneuroml.io.rst
docs/source/pyneuroml.lems.rst
docs/source/pyneuroml.modelgraphs.rst
docs/source/pyneuroml.neuron.rst
docs/source/pyneuroml.nsgr.rst
docs/source/pyneuroml.plot.rst
docs/source/pyneuroml.povray.rst
docs/source/pyneuroml.pynml.rst
docs/source/pyneuroml.rst
docs/source/pyneuroml.runners.rst
docs/source/pyneuroml.sbml.rst
docs/source/pyneuroml.swc.rst
docs/source/pyneuroml.tune.rst
docs/source/pyneuroml.utils.rst
docs/source/refs.bib
docs/source/_static/neuroml_logo.png
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examples/IM.channel.nml
examples/KConductance.channel.nml
examples/Kd.channel.nml
examples/LEMS_NML2_Ex5_DetCell.xml
examples/LEMS_NML2_Ex9_FN.xml
examples/LeakConductance.channel.nml
examples/LeakConductance.mod
examples/NML2_SingleCompHHCell.nml
examples/NaConductance.channel.nml
examples/NaConductance2.mod
examples/README.md
examples/Vm_plot.py
examples/analyseNaMod.sh
examples/analyseNaNml2.sh
examples/analyseNaNml2_iv.sh
examples/command_execute_tests.py
examples/component_evaluation.py
examples/create_new_lems_file.py
examples/dt_dependence.py
examples/export_neuroml1.py
examples/export_neuroml2.py
examples/generate_if_curve.py
examples/generate_povray.py
examples/quick_plot.py
examples/readAnnots.py
examples/record_channel_currents.py
examples/reload_data.py
examples/run_jneuroml_plot_matplotlib.py
examples/test.hoc
examples/tuneHHCell.py
examples/tuneHHCell.sh
examples/units.py
examples/results/README.md
examples/test/hinf_NaConductance.dat
examples/test/htau_NaConductance.dat
examples/test/minf_NaConductance.dat
examples/test/mtau_NaConductance.dat
examples/test/ninf_Gran_H_98.dat
examples/test/ntau_Gran_H_98.dat
examples/test_data/Ca_conc.nml
examples/test_data/Ca_pyr.channel.nml
examples/test_data/EGL-36.channel.nml
examples/test_data/HHCellNetwork.net.nml
examples/test_data/Kahp_pyr.channel.nml
examples/test_data/Kdr_bask.channel.nml
examples/test_data/Kdr_pyr.channel.nml
examples/test_data/LEMS_HH_Simulation.xml
examples/test_data/LeakConductance_bask.channel.nml
examples/test_data/LeakConductance_pyr.channel.nml
examples/test_data/NML2_FullCell.nml
examples/test_data/NML2_SimpleIonChannel.nml
examples/test_data/Na_bask.channel.nml
examples/test_data/Na_pyr.channel.nml
examples/test_data/Purk2M9s.nml
examples/test_data/TwoCell.net.nml
examples/test_data/bask.cell.nml
examples/test_data/complex_cell.cell.nml
examples/test_data/hhcell.cell.nml
examples/test_data/kChan.channel.nml
examples/test_data/naChan.channel.nml
examples/test_data/passiveChan.channel.nml
examples/test_data/pyr_4_sym.cell.nml
examples/test_data/realtime.py
examples/test_data/simple_cell.cell.nml
examples/test_data/simplenet.nml
examples/test_data/simplenet.py
examples/test_data/snooze.py
examples/test_data/snooze.sh
examples/test_data/valid_doc.sbml
examples/test_data/valid_doc_sedml.sbml
examples/test_data/valid_doc_sedml.sedml
examples/test_data/ca1/LEMS_SimTestOLMChannels.xml
examples/test_data/ca1/TestOLMChannels.net.nml
examples/test_data/ca1/TestOLMNet.net.nml
examples/test_data/ca1/cells/olm.cell.nml
examples/test_data/ca1/channels/HCNolm.channel.nml
examples/test_data/ca1/channels/Kdrfast.channel.nml
examples/test_data/ca1/channels/KvAolm.channel.nml
examples/test_data/ca1/channels/Nav.channel.nml
examples/test_data/ca1/channels/leak_chan.channel.nml
examples/test_data/xppaut/fhn.ode
examples/test_data/xppaut/nca.ode
examples/test_data/xppaut/wc.ode
examples/tune/Ca_conc.nml
examples/tune/Ca_pyr.channel.nml
examples/tune/Kahp_pyr.channel.nml
examples/tune/Kdr_pyr.channel.nml
examples/tune/LEMS_OnePyr.xml
examples/tune/LeakConductance_pyr.channel.nml
examples/tune/Na_pyr.channel.nml
examples/tune/OnePyr.net.nml
examples/tune/README.md
examples/tune/Selection_817.jpg
examples/tune/pyr_4_sym.cell.nml
examples/tune/tunePyr.py
examples/tune/temp/README.md
man/man1/README.md
man/man1/common.h2m
man/man1/generate-man-pages.sh
man/man1/pynml-archive.1
man/man1/pynml-channelanalysis.1
man/man1/pynml-channelml2nml.1
man/man1/pynml-modchananalysis.1
man/man1/pynml-plotchan.1
man/man1/pynml-plotmorph.1
man/man1/pynml-plotspikes.1
man/man1/pynml-plottimeseries.1
man/man1/pynml-povray.1
man/man1/pynml-sonata.1
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man/man1/pynml-swc2nml.1
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man/man1/pynml-xpp.1
man/man1/pynml.1
man/man1/version.h2m
pyNeuroML.egg-info/PKG-INFO
pyNeuroML.egg-info/SOURCES.txt
pyNeuroML.egg-info/dependency_links.txt
pyNeuroML.egg-info/entry_points.txt
pyNeuroML.egg-info/requires.txt
pyNeuroML.egg-info/top_level.txt
pyneuroml/__init__.py
pyneuroml/annotations.py
pyneuroml/biosimulations.py
pyneuroml/errors.py
pyneuroml/io.py
pyneuroml/modelgraphs.py
pyneuroml/nsgr.py
pyneuroml/pynml.py
pyneuroml/runners.py
pyneuroml/validators.py
pyneuroml/analysis/ChannelDensityPlot.py
pyneuroml/analysis/ChannelHelper.py
pyneuroml/analysis/ChannelInfo_TEMPLATE.html
pyneuroml/analysis/ChannelInfo_TEMPLATE.md
pyneuroml/analysis/LEMS_Test_TEMPLATE.xml
pyneuroml/analysis/NML2ChannelAnalysis.py
pyneuroml/analysis/__init__.py
pyneuroml/archive/__init__.py
pyneuroml/channelml/ChannelML2NeuroML2.xsl
pyneuroml/channelml/ChannelML2NeuroML2beta.xsl
pyneuroml/channelml/__init__.py
pyneuroml/lems/LEMSSimulation.py
pyneuroml/lems/LEMS_TEMPLATE.xml
pyneuroml/lems/__init__.py
pyneuroml/lib/jNeuroML-0.14.0-jar-with-dependencies.jar
pyneuroml/neuron/TEMPLATE.channel.nml
pyneuroml/neuron/__init__.py
pyneuroml/neuron/mview_neuroml1.hoc
pyneuroml/neuron/mview_neuroml2.hoc
pyneuroml/neuron/nrn_export_utils.py
pyneuroml/neuron/utils.hoc
pyneuroml/neuron/analysis/HHanalyse.py
pyneuroml/neuron/analysis/__init__.py
pyneuroml/plot/Plot.py
pyneuroml/plot/PlotMorphology.py
pyneuroml/plot/PlotMorphologyPlotly.py
pyneuroml/plot/PlotMorphologyVispy.py
pyneuroml/plot/PlotSpikes.py
pyneuroml/plot/PlotTimeSeries.py
pyneuroml/plot/__init__.py
pyneuroml/povray/MakeMovie.py
pyneuroml/povray/NeuroML2ToPOVRay.py
pyneuroml/povray/OverlaySimulation.py
pyneuroml/povray/__init__.py
pyneuroml/sbml/__init__.py
pyneuroml/sedml/__init__.py
pyneuroml/swc/ExportNML.py
pyneuroml/swc/ExportSWC.py
pyneuroml/swc/LoadSWC.py
pyneuroml/swc/__init__.py
pyneuroml/tellurium/__init__.py
pyneuroml/tune/NeuroMLController.py
pyneuroml/tune/NeuroMLSimulation.py
pyneuroml/tune/NeuroMLTuner.py
pyneuroml/tune/__init__.py
pyneuroml/utils/__init__.py
pyneuroml/utils/cli.py
pyneuroml/utils/components.py
pyneuroml/utils/info.py
pyneuroml/utils/jnmlwrapper.py
pyneuroml/utils/misc.py
pyneuroml/utils/moose.py
pyneuroml/utils/plot.py
pyneuroml/utils/units.py
pyneuroml/utils/xml.py
pyneuroml/xppaut/__init__.py
tests/HH_example_cell.nml
tests/HH_example_k_channel.nml
tests/HH_example_leak_channel.nml
tests/HH_example_na_channel.nml
tests/HH_example_net.nml
tests/__init__.py
tests/izhikevich_test_file.nml
tests/test_annotations.py
tests/test_biosimulations.py
tests/test_io.py
tests/test_nsgr.py
tests/test_pynml.py
tests/test_runners.py
tests/analysis/__init__.py
tests/analysis/test_cell_analysis.py
tests/analysis/test_channel_analysis.py
tests/analysis/test_channel_density_plots.py
tests/archive/__init__.py
tests/archive/test_archive.py
tests/channelml/CaPool.xml
tests/channelml/DoubExpSyn.xml
tests/channelml/NMDA.xml
tests/channelml/NaChannel_HH.xml
tests/channelml/SingleExpSyn.xml
tests/channelml/__init__.py
tests/channelml/test_channelml.py
tests/lems/__init__.py
tests/lems/test_lems.py
tests/lems/test_lemssimulation.py
tests/neuron/__init__.py
tests/neuron/test_neuron_utils.py
tests/neuron/test_data/olm.hoc
tests/neuron/test_data/mods/HCNolm.mod
tests/neuron/test_data/mods/Kdrfast.mod
tests/neuron/test_data/mods/KvAolm.mod
tests/neuron/test_data/mods/Nav.mod
tests/neuron/test_data/mods/leak_chan.mod
tests/plot/CaDynamics.nml
tests/plot/CaDynamics_all.nml
tests/plot/Ca_HVA.channel.nml
tests/plot/Ca_LVA.channel.nml
tests/plot/Cell_497232312.cell.nml
tests/plot/Ih.channel.nml
tests/plot/Im.channel.nml
tests/plot/Im_v2.channel.nml
tests/plot/Izh2007Cells.net.nml
tests/plot/K_P.channel.nml
tests/plot/K_T.channel.nml
tests/plot/Kd.channel.nml
tests/plot/Kv2like.channel.nml
tests/plot/Kv3_1.channel.nml
tests/plot/NaTa.channel.nml
tests/plot/NaTs.channel.nml
tests/plot/NaV.channel.nml
tests/plot/Nap.channel.nml
tests/plot/SK.channel.nml
tests/plot/__init__.py
tests/plot/pas.channel.nml
tests/plot/test-spherical-soma.cell.nml
tests/plot/test.cell.nml
tests/plot/test_PlotSpikes.py
tests/plot/test_morphology_plot.py
tests/plot/test_plot.py
tests/plot/test_plot_time_series.py
tests/plot/L23-example/CaDynamics_E2_NML2.nml
tests/plot/L23-example/HL23PV.cell.nml
tests/plot/L23-example/HL23PYR.cell.nml
tests/plot/L23-example/HL23SST.cell.nml
tests/plot/L23-example/HL23VIP.cell.nml
tests/plot/L23-example/HL23VIP.morph.cell.nml
tests/plot/L23-example/TestNetwork.net.nml
tests/plot/L23-example/channels/Ca_HVA.channel.nml
tests/plot/L23-example/channels/Ca_LVA.channel.nml
tests/plot/L23-example/channels/Ih.channel.nml
tests/plot/L23-example/channels/Im.channel.nml
tests/plot/L23-example/channels/K_P.channel.nml
tests/plot/L23-example/channels/K_T.channel.nml
tests/plot/L23-example/channels/Kv3_1.channel.nml
tests/plot/L23-example/channels/Nap.channel.nml
tests/plot/L23-example/channels/SK.channel.nml
tests/plot/L23-example/channels/pas.channel.nml
tests/plot/L23-example/channels/NaTg/NaTg.channel.nml
tests/plot/L23-example/synapses/AMPA_syn.synapse.nml
tests/plot/olm-example/HCNolm.channel.nml
tests/plot/olm-example/Kdrfast.channel.nml
tests/plot/olm-example/KvAolm.channel.nml
tests/plot/olm-example/Nav.channel.nml
tests/plot/olm-example/leak_chan.channel.nml
tests/sbml/__init__.py
tests/sbml/test_sbml.py
tests/sbml/test_data/inconsistent_units_doc.sbml
tests/sbml/test_data/invalid_doc00.sbml
tests/sbml/test_data/invalid_doc01.sbml
tests/sbml/test_data/invalid_doc02.sbml
tests/sbml/test_data/no_read_access.sbml
tests/sbml/test_data/valid_doc.sbml
tests/sedml/__init__.py
tests/sedml/test_sedml.py
tests/sedml/test_data/invalid_doc01.sedml
tests/sedml/test_data/invalid_doc02.sedml
tests/sedml/test_data/missing_model_source.sedml
tests/sedml/test_data/no_read_access.sedml
tests/sedml/test_data/valid_doc.sbml
tests/sedml/test_data/valid_doc.sedml
tests/swc/Case1_new.swc
tests/swc/Case1_new_cvapp.morph.nml
tests/swc/Case2_new.swc
tests/swc/Case2_new_cvapp.morph.nml
tests/swc/Case3_new.swc
tests/swc/Case3_new_cvapp.morph.nml
tests/swc/Case4_new.swc
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tests/swc/Case5_new.swc
tests/swc/Case5_new_cvapp.morph.nml
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tests/swc/dCH-cobalt.CNG.swc
tests/swc/dCH-cobalt.CNG_cvapp.morph.nml
tests/swc/dCH-cobalt.CNG_small.swc
tests/swc/dCH-cobalt.CNG_small_cvapp.morph.nml
tests/swc/l22.swc
tests/swc/l22_cvapp.morph.nml
tests/swc/l22_cylsoma.swc
tests/swc/l22_cylsoma_cvapp.morph.nml
tests/swc/l22_small.swc
tests/swc/l22_small_cvapp.morph.nml
tests/swc/l22_sphersoma.swc
tests/swc/l22_sphersoma_cvapp.morph.nml
tests/swc/test_ExportNML.py
tests/swc/test_LoadSWC.py
tests/tellurium/__init__.py
tests/tellurium/do_test_tellurium.py
tests/tellurium/test_data/LEMS_NML2_Ex9_FN.sbml
tests/tellurium/test_data/LEMS_NML2_Ex9_FN.sedml
tests/tellurium/test_data/LEMS_Regular_HindmarshRose.sbml
tests/tellurium/test_data/LEMS_Regular_HindmarshRose.sedml
tests/utils/__init__.py
tests/utils/test_utils.py