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)

B

build_namespace() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.plot.PlotSpikes)

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_case() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.plot.PlotSpikes) 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_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

main() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.channelml) (in module pyneuroml.plot.PlotSpikes) (in module pyneuroml.povray.MakeMovie) (in module pyneuroml.povray.NeuroML2ToPOVRay) (in module pyneuroml.povray.OverlaySimulation) (in module pyneuroml.pynml) 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.generate_test_data pyneuroml.plot.Plot 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_channel() (in module pyneuroml.analysis.NML2ChannelAnalysis) 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_args() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.channelml) (in module pyneuroml.plot.PlotSpikes) (in module pyneuroml.povray.MakeMovie) (in module pyneuroml.povray.NeuroML2ToPOVRay) (in module pyneuroml.povray.OverlaySimulation) 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.generate_test_data module pyneuroml.plot.Plot 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

random() (in module pyneuroml.plot.generate_test_data) 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)