emodel_generalisation.bluecellulab_evaluator

Compute the threshold and holding current using bluecellulab, adapted from BluePyThresh.

Functions

binsearch_threshold_current(cell, config, ...)	Binary search for threshold currents
calculate_holding_current(cell, config)	Calculate holding current.
calculate_rmp_and_rin(cell, config)	Calculate rmp and input resistance from rmp.
calculate_threshold_current(cell, config, ...)	Calculate threshold current
evaluate_currents(morphs_combos_df, ...[, ...])	Compute the threshold and holding currents using bluecellulab.
run_spike_sim(cell, config, holding_current, ...)	Run simulation on a cell and compute number of spikes.
set_cell_deterministic(cell, deterministic)	Disable stochasticity in ion channels

emodel_generalisation.bluecellulab_evaluator.binsearch_threshold_current(cell, config, holding_current, min_current, max_current)

Binary search for threshold currents

emodel_generalisation.bluecellulab_evaluator.calculate_holding_current(cell, config)

Calculate holding current.

adapted from: bluecellulab.tools.holding_current_subprocess,

emodel_generalisation.bluecellulab_evaluator.calculate_rmp_and_rin(cell, config)

Calculate rmp and input resistance from rmp.

emodel_generalisation.bluecellulab_evaluator.calculate_threshold_current(cell, config, holding_current)

Calculate threshold current

emodel_generalisation.bluecellulab_evaluator.evaluate_currents(morphs_combos_df, protocol_config, emodels_hoc_dir, morphology_path='path', resume=False, db_url='eval_db.sql', parallel_factory=None, template_format='v6', timeout=1000, only_rin=False)

Compute the threshold and holding currents using bluecellulab.

emodel_generalisation.bluecellulab_evaluator.run_spike_sim(cell, config, holding_current, step_current)

Run simulation on a cell and compute number of spikes.

emodel_generalisation.bluecellulab_evaluator.set_cell_deterministic(cell, deterministic)

Disable stochasticity in ion channels