bmtk.simulator.bionet.default_setters package

Submodules

bmtk.simulator.bionet.default_setters.cell_models module

bmtk.simulator.bionet.default_setters.cell_models.Biophys1(cell, template_name, dynamic_params)

Loads a biophysical NEURON hoc object using Cell-Types database objects.

bmtk.simulator.bionet.default_setters.cell_models.Biophys1_dict(cell)

Set parameters for cells from the Allen Cell Types database Prior to setting parameters will replace the axon with the stub

bmtk.simulator.bionet.default_setters.cell_models.Biophys1_nml(json_file)

bmtk.simulator.bionet.default_setters.cell_models.IntFire1(cell, template_name, dynamics_params)

Loads a point integrate and fire neuron

bmtk.simulator.bionet.default_setters.cell_models.NMLLoad(cell, template_name, dynamic_params)

Convert a NEUROML file to a NEURON hoc cell object.

Current limitations: * Ignores nml morphology section. You must pass in a swc file * Only for biophysically detailed cell biophysical components. All properties must be assigned to a segment group.

Parameters:

• cell –

• template_name –

• dynamic_params –

Returns:

bmtk.simulator.bionet.default_setters.cell_models.aibs_allactive(hobj, cell, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.aibs_allactive_directed(hobj, cell, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.aibs_perisomatic(hobj, cell, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.aibs_perisomatic_directed(hobj, cell, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.fix_axon_allactive(hobj)

Replace reconstructed axon with a stub

Parameters:

hobj: instance of a Biophysical template

NEURON’s cell object

bmtk.simulator.bionet.default_setters.cell_models.fix_axon_allactive_directed(hobj)

bmtk.simulator.bionet.default_setters.cell_models.fix_axon_peri(hobj)

Replace reconstructed axon with a stub

Parameters:

hobj – hoc object

bmtk.simulator.bionet.default_setters.cell_models.fix_axon_perisomatic_directed(hobj)

bmtk.simulator.bionet.default_setters.cell_models.get_axon_direction(hobj)

bmtk.simulator.bionet.default_setters.cell_models.loadHOC(cell, template_name, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.set_extracellular(hobj, cell, dynamics_params)

bmtk.simulator.bionet.default_setters.cell_models.set_params_allactive(hobj, params_dict)

bmtk.simulator.bionet.default_setters.cell_models.set_params_peri(hobj, biophys_params)

Set biophysical parameters for the cell

Parameters:

• hobj – NEURON’s cell object

• biophys_params – name of json file with biophys params for cell’s model which determine spiking behavior

Returns:

bmtk.simulator.bionet.default_setters.synapse_models module

bmtk.simulator.bionet.default_setters.synapse_models.Exp2Syn(syn_params, sec_x, sec_id)

Create a list of exp2syn synapses

Parameters:

• syn_params – parameters of a synapse

• sec_x – normalized distance along the section

• sec_id – target section

Returns:

NEURON synapse object

bmtk.simulator.bionet.default_setters.synapse_models.exp1isyn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.exp1syn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.exp2syn(syn_params, xs, secs)

Create a list of exp2syn synapses

Parameters:

• syn_params – parameters of a synapse

• xs – list of normalized distances along the section

• secs – target sections

Returns:

list of NEURON synpase objects

bmtk.simulator.bionet.default_setters.synapse_models.expsyn(syn_params, x, sec)

Create a list of expsyn synapses

Parameters:

• syn_params – parameters of a synapse (dict)

• x – normalized distance along the section (float)

• sec – target section (hoc object)

Returns:

synapse objects

bmtk.simulator.bionet.default_setters.synapse_models.stp1syn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.stp2syn(syn_params, x, sec)

bmtk.simulator.bionet.default_setters.synapse_models.stp3syn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.stp4syn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.stp5isyn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synapse_models.stp5syn(syn_params, x, sec)

bmtk.simulator.bionet.default_setters.synapse_models.tmgsyn(syn_params, xs, secs)

bmtk.simulator.bionet.default_setters.synaptic_weights module

bmtk.simulator.bionet.default_setters.synaptic_weights.default_weight_fnc(edge_props, src_props, trg_props)

bmtk.simulator.bionet.default_setters.synaptic_weights.gaussianLL(edge_props, src_props, trg_props)

bmtk.simulator.bionet.default_setters.synaptic_weights.wmax(edge_props, src_props, trg_props)

Module contents