Index

A

acc_label() (bluepyopt.ephys.locations.ArbBranchLocation method) (bluepyopt.ephys.locations.ArbBranchRelLocation method) (bluepyopt.ephys.locations.ArbLocsetLocation method) (bluepyopt.ephys.locations.ArbRegionLocation method) (bluepyopt.ephys.locations.ArbSegmentLocation method) (bluepyopt.ephys.locations.ArbSegmentRelLocation method) (bluepyopt.ephys.locations.NrnPointProcessLocation method) (bluepyopt.ephys.locations.NrnSeclistCompLocation method) (bluepyopt.ephys.locations.NrnSeclistLocation method) (bluepyopt.ephys.locations.NrnSeclistSecLocation method) (bluepyopt.ephys.locations.NrnSecSomaDistanceCompLocation method) (bluepyopt.ephys.locations.NrnSectionCompLocation method) (bluepyopt.ephys.locations.NrnSomaDistanceCompLocation method) (bluepyopt.ephys.locations.NrnTrunkSomaDistanceCompLocation method)

adjust_stochasticity() (bluepyopt.ephys.protocols.SweepProtocol method) ArbBranchLocation (class in bluepyopt.ephys.locations) ArbBranchRelLocation (class in bluepyopt.ephys.locations) ArbFileMorphology (class in bluepyopt.ephys.morphologies) ArbLocation (class in bluepyopt.ephys.locations) ArbLocsetLocation (class in bluepyopt.ephys.locations) ArbRegionLocation (class in bluepyopt.ephys.locations) ArbSegmentLocation (class in bluepyopt.ephys.locations) ArbSegmentRelLocation (class in bluepyopt.ephys.locations) ArbSweepProtocol (class in bluepyopt.ephys.protocols) ArbSweepProtocolException

B

bluepyopt.deapext.optimisations module bluepyopt.ephys.efeatures module bluepyopt.ephys.evaluators module bluepyopt.ephys.locations module bluepyopt.ephys.mechanisms module bluepyopt.ephys.models module bluepyopt.ephys.morphologies module bluepyopt.ephys.objectives module bluepyopt.ephys.objectivescalculators module bluepyopt.ephys.parameters module

bluepyopt.ephys.parameterscalers module bluepyopt.ephys.protocols module bluepyopt.ephys.recordings module bluepyopt.ephys.responses module bluepyopt.ephys.stimuli module bluepyopt.evaluators module bluepyopt.objectives module bluepyopt.optimisations module bluepyopt.parameters module

C

calculate_feature() (bluepyopt.ephys.efeatures.eFELFeature method) calculate_feature_scores() (bluepyopt.ephys.objectives.EFeatureObjective method) calculate_feature_values() (bluepyopt.ephys.objectives.EFeatureObjective method) calculate_score() (bluepyopt.ephys.efeatures.eFELFeature method) (bluepyopt.ephys.efeatures.extraFELFeature method) (bluepyopt.ephys.objectives.MaxObjective method) (bluepyopt.ephys.objectives.SingletonObjective method) (bluepyopt.ephys.objectives.SingletonWeightObjective method) (bluepyopt.ephys.objectives.WeightedSumObjective method) calculate_scores() (bluepyopt.ephys.objectivescalculators.ObjectivesCalculator method) calculate_value() (bluepyopt.ephys.objectives.SingletonObjective method) calculate_values() (bluepyopt.ephys.objectivescalculators.ObjectivesCalculator method) CellEvaluator (class in bluepyopt.ephys.evaluators) CellModel (class in bluepyopt.ephys.models)

check_bounds() (bluepyopt.parameters.MetaListEqualParameter method) (bluepyopt.parameters.Parameter method) check_name() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.LFPyCellModel method) check_nonfrozen_params() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method) CompRecording (class in bluepyopt.ephys.recordings) create_acc() (bluepyopt.ephys.models.CellModel method) create_empty_cell() (bluepyopt.ephys.models.CellModel static method) (bluepyopt.ephys.models.LFPyCellModel static method) create_empty_template() (bluepyopt.ephys.models.CellModel static method) (bluepyopt.ephys.models.LFPyCellModel static method) create_hoc() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.LFPyCellModel method)

D

DEAPOptimisation (class in bluepyopt.deapext.optimisations) destroy() (bluepyopt.ephys.mechanisms.NrnMODMechanism method) (bluepyopt.ephys.mechanisms.NrnMODPointProcessMechanism method) (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method) (bluepyopt.ephys.models.Model method) (bluepyopt.ephys.morphologies.NrnFileMorphology method) (bluepyopt.ephys.parameters.NrnMetaListEqualParameter method) (bluepyopt.ephys.parameters.NrnParameter method) (bluepyopt.ephys.protocols.SweepProtocol method) (bluepyopt.ephys.recordings.CompRecording method) (bluepyopt.ephys.recordings.LFPRecording method) (bluepyopt.ephys.stimuli.LFPySquarePulse method) (bluepyopt.ephys.stimuli.NrnCurrentPlayStimulus method) (bluepyopt.ephys.stimuli.NrnNetStimStimulus method) (bluepyopt.ephys.stimuli.NrnRampPulse method) (bluepyopt.ephys.stimuli.NrnSquarePulse method)

E

EFeature (class in bluepyopt.ephys.efeatures) EFeatureObjective (class in bluepyopt.ephys.objectives) eFELFeature (class in bluepyopt.ephys.efeatures) envelope() (bluepyopt.ephys.stimuli.NrnCurrentPlayStimulus method) (bluepyopt.ephys.stimuli.NrnRampPulse method) (bluepyopt.ephys.stimuli.NrnSquarePulse method) EPhysLocAccException EPhysLocInstantiateException

evaluate() (bluepyopt.ephys.evaluators.CellEvaluator method) evaluate_with_dicts() (bluepyopt.ephys.evaluators.CellEvaluator method) (bluepyopt.evaluators.Evaluator method) evaluate_with_lists() (bluepyopt.ephys.evaluators.CellEvaluator method) (bluepyopt.evaluators.Evaluator method) Evaluator (class in bluepyopt.evaluators) extract_nrn_seclists() (bluepyopt.ephys.morphologies.ArbFileMorphology static method) extraFELFeature (class in bluepyopt.ephys.efeatures)

F

find_icomp() (bluepyopt.ephys.locations.NrnSomaDistanceCompLocation method) freeze() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method) (bluepyopt.parameters.MetaListEqualParameter method) (bluepyopt.parameters.Parameter method)

G

generate_reinitrng_hoc_block() (bluepyopt.ephys.mechanisms.NrnMODMechanism method)

get_template_name() (bluepyopt.ephys.models.HocCellModel static method)

H

hash_hoc() (bluepyopt.ephys.mechanisms.NrnMODMechanism static method) hash_py() (bluepyopt.ephys.mechanisms.NrnMODMechanism static method)

HocCellModel (class in bluepyopt.ephys.models) HocMorphology (class in bluepyopt.ephys.models)

I

IBEADEAPOptimisation (class in bluepyopt.deapext.optimisations) init_simulator_and_evaluate_with_lists() (bluepyopt.ephys.evaluators.CellEvaluator method) instantiate() (bluepyopt.ephys.locations.ArbLocation method) (bluepyopt.ephys.locations.NrnPointProcessLocation method) (bluepyopt.ephys.locations.NrnSeclistCompLocation method) (bluepyopt.ephys.locations.NrnSeclistLocation method) (bluepyopt.ephys.locations.NrnSeclistSecLocation method) (bluepyopt.ephys.locations.NrnSecSomaDistanceCompLocation method) (bluepyopt.ephys.locations.NrnSectionCompLocation method) (bluepyopt.ephys.locations.NrnSomaDistanceCompLocation method) (bluepyopt.ephys.mechanisms.NrnMODMechanism method) (bluepyopt.ephys.mechanisms.NrnMODPointProcessMechanism method) (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method) (bluepyopt.ephys.models.Model method) (bluepyopt.ephys.morphologies.NrnFileMorphology method) (bluepyopt.ephys.parameters.NrnGlobalParameter method) (bluepyopt.ephys.parameters.NrnMetaListEqualParameter method) (bluepyopt.ephys.parameters.NrnParameter method) (bluepyopt.ephys.parameters.NrnPointProcessParameter method) (bluepyopt.ephys.parameters.NrnRangeParameter method) (bluepyopt.ephys.parameters.NrnSectionParameter method) (bluepyopt.ephys.protocols.SweepProtocol method) (bluepyopt.ephys.recordings.CompRecording method) (bluepyopt.ephys.stimuli.LFPStimulus method) (bluepyopt.ephys.stimuli.LFPySquarePulse method) (bluepyopt.ephys.stimuli.NrnCurrentPlayStimulus method) (bluepyopt.ephys.stimuli.NrnNetStimStimulus method) (bluepyopt.ephys.stimuli.NrnRampPulse method) (bluepyopt.ephys.stimuli.NrnSquarePulse method)

instantiate_determinism() (bluepyopt.ephys.mechanisms.NrnMODMechanism method) instantiate_iclamp_stimuli() (bluepyopt.ephys.protocols.ArbSweepProtocol method) instantiate_locations() (bluepyopt.ephys.protocols.ArbSweepProtocol method) instantiate_morphology() (bluepyopt.ephys.models.CellModel method) instantiate_morphology_3d() (bluepyopt.ephys.models.CellModel method) instantiate_recordings() (bluepyopt.ephys.protocols.ArbSweepProtocol method) instantiate_synaptic_stimuli() (bluepyopt.ephys.protocols.ArbSweepProtocol method)

L

LFPRecording (class in bluepyopt.ephys.recordings) LFPStimulus (class in bluepyopt.ephys.stimuli) LFPyCellModel (class in bluepyopt.ephys.models) LFPySquarePulse (class in bluepyopt.ephys.stimuli)

load() (bluepyopt.ephys.morphologies.ArbFileMorphology static method) load_hoc_template() (bluepyopt.ephys.models.HocCellModel static method) Location (class in bluepyopt.ephys.locations) lower_bound (bluepyopt.parameters.Parameter property)

M

MaxObjective (class in bluepyopt.ephys.objectives) Mechanism (class in bluepyopt.ephys.mechanisms) MetaListEqualParameter (class in bluepyopt.parameters) MetaParameter (class in bluepyopt.ephys.parameters) Model (class in bluepyopt.ephys.models) module bluepyopt.deapext.optimisations bluepyopt.ephys.efeatures bluepyopt.ephys.evaluators bluepyopt.ephys.locations bluepyopt.ephys.mechanisms bluepyopt.ephys.models bluepyopt.ephys.morphologies bluepyopt.ephys.objectives bluepyopt.ephys.objectivescalculators bluepyopt.ephys.parameters bluepyopt.ephys.parameterscalers bluepyopt.ephys.protocols bluepyopt.ephys.recordings bluepyopt.ephys.responses bluepyopt.ephys.stimuli bluepyopt.evaluators bluepyopt.objectives bluepyopt.optimisations bluepyopt.parameters

Morphology (class in bluepyopt.ephys.morphologies)

N

NrnCurrentPlayStimulus (class in bluepyopt.ephys.stimuli) NrnFileMorphology (class in bluepyopt.ephys.morphologies) NrnGlobalParameter (class in bluepyopt.ephys.parameters) NrnMetaListEqualParameter (class in bluepyopt.ephys.parameters) NrnMODMechanism (class in bluepyopt.ephys.mechanisms) NrnMODPointProcessMechanism (class in bluepyopt.ephys.mechanisms) NrnNetStimStimulus (class in bluepyopt.ephys.stimuli) NrnParameter (class in bluepyopt.ephys.parameters) NrnPointProcessLocation (class in bluepyopt.ephys.locations) NrnPointProcessParameter (class in bluepyopt.ephys.parameters)

NrnRampPulse (class in bluepyopt.ephys.stimuli) NrnRangeParameter (class in bluepyopt.ephys.parameters) NrnSeclistCompLocation (class in bluepyopt.ephys.locations) NrnSeclistLocation (class in bluepyopt.ephys.locations) NrnSeclistSecLocation (class in bluepyopt.ephys.locations) NrnSecSomaDistanceCompLocation (class in bluepyopt.ephys.locations) NrnSectionCompLocation (class in bluepyopt.ephys.locations) NrnSectionParameter (class in bluepyopt.ephys.parameters) NrnSomaDistanceCompLocation (class in bluepyopt.ephys.locations) NrnSquarePulse (class in bluepyopt.ephys.stimuli) NrnTrunkSomaDistanceCompLocation (class in bluepyopt.ephys.locations)

O

Objective (class in bluepyopt.objectives) objective_dict() (bluepyopt.ephys.evaluators.CellEvaluator method)

objective_list() (bluepyopt.ephys.evaluators.CellEvaluator method) ObjectivesCalculator (class in bluepyopt.ephys.objectivescalculators) Optimisation (class in bluepyopt.optimisations)

P

param_dict() (bluepyopt.ephys.evaluators.CellEvaluator method) Parameter (class in bluepyopt.parameters) params_by_names() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method)

plot() (bluepyopt.ephys.responses.TimeLFPResponse method) (bluepyopt.ephys.responses.TimeVoltageResponse method) prefix (bluepyopt.ephys.mechanisms.NrnMODMechanism property) Protocol (class in bluepyopt.ephys.protocols)

R

read_csv() (bluepyopt.ephys.responses.TimeVoltageResponse method) Recording (class in bluepyopt.ephys.recordings) replace_axon() (bluepyopt.ephys.morphologies.ArbFileMorphology static method) (bluepyopt.ephys.morphologies.NrnFileMorphology static method) response (bluepyopt.ephys.recordings.CompRecording property) (bluepyopt.ephys.recordings.LFPRecording property)

Response (class in bluepyopt.ephys.responses) run() (bluepyopt.deapext.optimisations.DEAPOptimisation method) (bluepyopt.ephys.protocols.ArbSweepProtocol method) (bluepyopt.ephys.protocols.SequenceProtocol method) (bluepyopt.ephys.protocols.SweepProtocol method) run_protocol() (bluepyopt.ephys.evaluators.CellEvaluator method) run_protocols() (bluepyopt.ephys.evaluators.CellEvaluator method)

S

seed_from_param_dict() (bluepyopt.ephys.evaluators.CellEvaluator static method) SequenceProtocol (class in bluepyopt.ephys.protocols) set_nseg() (bluepyopt.ephys.morphologies.NrnFileMorphology method) set_sec_index() (bluepyopt.ephys.locations.NrnTrunkSomaDistanceCompLocation method) setup_deap() (bluepyopt.deapext.optimisations.DEAPOptimisation method) SingletonObjective (class in bluepyopt.ephys.objectives) SingletonWeightObjective (class in bluepyopt.ephys.objectives) step_delay (bluepyopt.ephys.protocols.StepProtocol property) step_duration (bluepyopt.ephys.protocols.StepProtocol property)

StepProtocol (class in bluepyopt.ephys.protocols) Stimulus (class in bluepyopt.ephys.stimuli) subprotocols() (bluepyopt.ephys.protocols.ArbSweepProtocol method) (bluepyopt.ephys.protocols.SequenceProtocol method) (bluepyopt.ephys.protocols.SweepProtocol method) sum (bluepyopt.deapext.optimisations.WeightedSumFitness property) SweepProtocol (class in bluepyopt.ephys.protocols) SweepProtocolException SynapticStimulus (class in bluepyopt.ephys.stimuli)

T

TimeLFPResponse (class in bluepyopt.ephys.responses) TimeVoltageResponse (class in bluepyopt.ephys.responses)

to_csv() (bluepyopt.ephys.responses.TimeVoltageResponse method) total_duration (bluepyopt.ephys.protocols.ArbSweepProtocol property) (bluepyopt.ephys.protocols.SweepProtocol property)

U

unfreeze() (bluepyopt.ephys.models.CellModel method) (bluepyopt.ephys.models.HocCellModel method) (bluepyopt.ephys.models.LFPyCellModel method) (bluepyopt.parameters.MetaListEqualParameter method) (bluepyopt.parameters.Parameter method)

upper_bound (bluepyopt.parameters.Parameter property)

V

value (bluepyopt.ephys.parameters.MetaParameter property) (bluepyopt.parameters.MetaListEqualParameter property) (bluepyopt.parameters.Parameter property)

W

weighted_sum (bluepyopt.deapext.optimisations.WeightedSumFitness property) WeightedSumFitness (class in bluepyopt.deapext.optimisations)

WeightedSumObjective (class in bluepyopt.ephys.objectives) write_acc() (bluepyopt.ephys.models.CellModel method) WSListIndividual (class in bluepyopt.deapext.optimisations)