Index

A

add_column_to_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_line_to_display() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_selection_to_event_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_text() (in module pyneuroml.analysis.ChannelDensityPlot) allca() (in module pyneuroml.neuron)

allcells() (in module pyneuroml.neuron) allsyns() (in module pyneuroml.neuron) allv() (in module pyneuroml.neuron) analyse_spiketime_vs_dt() (in module pyneuroml.analysis) areainfo() (in module pyneuroml.neuron) assign_simulation_target() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

C

cell_info() (in module pyneuroml.pynml) cellinfo() (in module pyneuroml.neuron) cellinfohoc() (in module pyneuroml.neuron) cells_info() (in module pyneuroml.pynml) channelml2nml() (in module pyneuroml.channelml) compute_iv_curve() (in module pyneuroml.analysis.NML2ChannelAnalysis) confirm_file_exists() (in module pyneuroml.pynml)

confirm_lems_file() (in module pyneuroml.pynml) confirm_neuroml_file() (in module pyneuroml.pynml) convert_to_swc() (in module pyneuroml.swc.ExportSWC) convert_to_units() (in module pyneuroml.pynml) create_display() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) create_event_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) create_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

D

define_dummy_cell() (in module pyneuroml.povray.NeuroML2ToPOVRay)

E

evaluate_arguments() (in module pyneuroml.pynml) evaluate_component() (in module pyneuroml.pynml) evaluate_HHExpLinearRate() (in module pyneuroml.analysis.ChannelHelper) evaluate_HHExpRate() (in module pyneuroml.analysis.ChannelHelper) evaluate_HHSigmoidRate() (in module pyneuroml.analysis.ChannelHelper) execute_command_in_dir() (in module pyneuroml.pynml)

execute_command_in_dir_with_realtime_output() (in module pyneuroml.pynml) export_mod_to_neuroml2() (in module pyneuroml.neuron) export_to_neuroml1() (in module pyneuroml.neuron) export_to_neuroml2() (in module pyneuroml.neuron) extract_annotations() (in module pyneuroml.pynml) extract_lems_definition_files() (in module pyneuroml.pynml) extract_position_info() (in module pyneuroml.utils)

F

format_float() (in module pyneuroml.analysis.ChannelDensityPlot)

G

generate_channel_density_plots() (in module pyneuroml.analysis.ChannelDensityPlot) generate_current_vs_frequency_curve() (in module pyneuroml.analysis) generate_interactive_plot() (in module pyneuroml.plot.Plot) generate_lems_channel_analyser() (in module pyneuroml.analysis.NML2ChannelAnalysis) generate_lems_file_for_neuroml() (in module pyneuroml.lems) generate_lemsgraph() (in module pyneuroml.pynml) generate_nmlgraph() (in module pyneuroml.pynml) generate_plot() (in module pyneuroml.plot.Plot) generate_povray() (in module pyneuroml.povray.NeuroML2ToPOVRay) generate_volt_scale() (in module pyneuroml.povray.MakeMovie) get_channel_gates() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_channels_from_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_color_for_volts() (in module pyneuroml.povray.OverlaySimulation) get_colour_hex() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_conductance_expression() (in module pyneuroml.analysis.NML2ChannelAnalysis)

get_includes_from_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_ion_color() (in module pyneuroml.analysis.ChannelDensityPlot) (in module pyneuroml.analysis.NML2ChannelAnalysis) get_lems_model_with_units() (in module pyneuroml.pynml) get_next_hex_color() (in module pyneuroml.pynml) get_path_to_jnml_jar() (in module pyneuroml.pynml) get_pop_index() (in module pyneuroml.lems) get_rainbow_color_for_volts() (in module pyneuroml.povray.OverlaySimulation) get_seg_midpoint() (in module pyneuroml.neuron) get_standalone_lems_model() (in module pyneuroml.pynml) get_state_color() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_utils_hoc() (in module pyneuroml.neuron) get_value_in_si() (in module pyneuroml.pynml) getinfo() (in module pyneuroml.neuron) go() (pyneuroml.tune.NeuroMLSimulation.NeuroMLSimulation method) gui_string() (in module pyneuroml.pynml)

I

include_lems_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

include_neuroml2_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) include_string() (in module pyneuroml.pynml)

L

lems_info (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute) LEMSSimulation (class in pyneuroml.lems.LEMSSimulation)

list_exposures() (in module pyneuroml.pynml) list_recording_paths_for_exposures() (in module pyneuroml.pynml) load_hoc_or_python_file() (in module pyneuroml.neuron)

M

make_html_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_iv_curve_fig() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_lems_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_md_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_overview_dir() (in module pyneuroml.analysis.NML2ChannelAnalysis) merge_with_template() (in module pyneuroml.analysis.NML2ChannelAnalysis) module pyneuroml pyneuroml.analysis pyneuroml.analysis.ChannelDensityPlot pyneuroml.analysis.ChannelHelper pyneuroml.analysis.NML2ChannelAnalysis pyneuroml.channelml pyneuroml.lems pyneuroml.lems.LEMSSimulation pyneuroml.neuron pyneuroml.neuron.analysis pyneuroml.plot pyneuroml.plot.Plot pyneuroml.plot.PlotMorphology pyneuroml.plot.PlotSpikes pyneuroml.povray pyneuroml.povray.MakeMovie pyneuroml.povray.NeuroML2ToPOVRay pyneuroml.povray.OverlaySimulation pyneuroml.pynml pyneuroml.swc pyneuroml.swc.ExportSWC pyneuroml.tune pyneuroml.tune.NeuroMLController pyneuroml.tune.NeuroMLSimulation pyneuroml.tune.NeuroMLTuner pyneuroml.utils

morphinfo() (in module pyneuroml.neuron) morphinfohoc() (in module pyneuroml.neuron) my_random (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute)

N

NeuroMLController (class in pyneuroml.tune.NeuroMLController) NeuroMLSimulation (class in pyneuroml.tune.NeuroMLSimulation)

nml2_to_png() (in module pyneuroml.pynml) nml2_to_svg() (in module pyneuroml.pynml)

P

parse_arguments() (in module pyneuroml.pynml) plot_2D() (in module pyneuroml.plot.PlotMorphology) plot_channel() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_interactive_3D() (in module pyneuroml.plot.PlotMorphology) plot_iv_curve() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_iv_curve_vm() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_iv_curves() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_kinetics() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_steady_state() (in module pyneuroml.analysis.NML2ChannelAnalysis) print_v() (in module pyneuroml) process_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) pyneuroml module pyneuroml.analysis module pyneuroml.analysis.ChannelDensityPlot module pyneuroml.analysis.ChannelHelper module pyneuroml.analysis.NML2ChannelAnalysis module pyneuroml.channelml module pyneuroml.lems module pyneuroml.lems.LEMSSimulation module pyneuroml.neuron module pyneuroml.neuron.analysis module

pyneuroml.plot module pyneuroml.plot.Plot module pyneuroml.plot.PlotMorphology module pyneuroml.plot.PlotSpikes module pyneuroml.povray module pyneuroml.povray.MakeMovie module pyneuroml.povray.NeuroML2ToPOVRay module pyneuroml.povray.OverlaySimulation module pyneuroml.pynml module pyneuroml.swc module pyneuroml.swc.ExportSWC module pyneuroml.tune module pyneuroml.tune.NeuroMLController module pyneuroml.tune.NeuroMLSimulation module pyneuroml.tune.NeuroMLTuner module pyneuroml.utils module

Q

quick_summary() (in module pyneuroml.pynml)

R

read_lems_file() (in module pyneuroml.pynml) read_neuroml2_file() (in module pyneuroml.pynml) read_sonata_spikes_hdf5_file() (in module pyneuroml.plot.PlotSpikes) reload_saved_data() (in module pyneuroml.pynml) reload_standard_dat_file() (in module pyneuroml.pynml) replace_brackets() (in module pyneuroml.neuron) rm_NML_str() (in module pyneuroml.neuron) run() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.plot.PlotSpikes) (pyneuroml.tune.NeuroMLController.NeuroMLController method) run_2stage_optimization() (in module pyneuroml.tune.NeuroMLTuner)

run_individual() (in module pyneuroml.tune.NeuroMLController) (pyneuroml.tune.NeuroMLController.NeuroMLController method) run_jneuroml() (in module pyneuroml.pynml) run_jneuroml_with_realtime_output() (in module pyneuroml.pynml) run_lems_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) run_lems_with_eden() (in module pyneuroml.pynml) run_lems_with_jneuroml() (in module pyneuroml.pynml) run_lems_with_jneuroml_brian2() (in module pyneuroml.pynml) run_lems_with_jneuroml_netpyne() (in module pyneuroml.pynml) run_lems_with_jneuroml_neuron() (in module pyneuroml.pynml) run_optimisation() (in module pyneuroml.tune.NeuroMLTuner)

S

safe_variable() (in module pyneuroml.lems) save_fig() (in module pyneuroml.analysis.NML2ChannelAnalysis) save_to_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) secinfo() (in module pyneuroml.neuron)

secinfohoc() (in module pyneuroml.neuron) set_report_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) show() (pyneuroml.tune.NeuroMLSimulation.NeuroMLSimulation method) split_nml2_quantity() (in module pyneuroml.pynml) summary() (in module pyneuroml.pynml)

T

TEMPLATE_FILE (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute)

to_xml() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

V

validate_neuroml1() (in module pyneuroml.pynml)

validate_neuroml2() (in module pyneuroml.pynml) validate_neuroml2_lems_file() (in module pyneuroml.pynml)

W

write_lems_file() (in module pyneuroml.pynml)

write_neuroml2_file() (in module pyneuroml.pynml)