bmtk.simulator.bionet package¶
Subpackages¶
- bmtk.simulator.bionet.default_setters package
- bmtk.simulator.bionet.modules package
- Submodules
- bmtk.simulator.bionet.modules.ecp module
- bmtk.simulator.bionet.modules.record_cellvars module
- bmtk.simulator.bionet.modules.record_clamp module
- bmtk.simulator.bionet.modules.record_netcons module
- bmtk.simulator.bionet.modules.record_spikes module
- bmtk.simulator.bionet.modules.save_synapses module
- bmtk.simulator.bionet.modules.sim_module module
- bmtk.simulator.bionet.modules.xstim module
- bmtk.simulator.bionet.modules.xstim_waveforms module
- Module contents
Submodules¶
bmtk.simulator.bionet.biocell module¶
-
class
bmtk.simulator.bionet.biocell.
BioCell
(node, population_name, bionetwork)[source]¶ Bases:
bmtk.simulator.bionet.cell.Cell
Implemntation of a morphologically and biophysically detailed type cell.
-
calc_seg_coords
(morph_seg_coords)[source]¶ Update the segment coordinates (after rotations) for individual cells
-
morphology
¶
-
morphology_file
¶
-
-
class
bmtk.simulator.bionet.biocell.
BioCellSpontSyn
(node, population_name, bionetwork)[source]¶ Bases:
bmtk.simulator.bionet.biocell.BioCell
Special class that allows certain synapses to spontaneously fire (without spiking) at a specific time.
bmtk.simulator.bionet.bionetwork module¶
-
class
bmtk.simulator.bionet.bionetwork.
BioNetwork
[source]¶ Bases:
bmtk.simulator.core.simulator_network.SimNetwork
-
build_disconnected_inputs
(spike_trains, edges_path, edge_types_path, source_node_set, target_node_set)[source]¶
-
get_gj_id
(network, src_nid, trg_nid, source_gap)[source]¶ Returns the gap junction id for the given nodes on a given network.
Parameters: source_gap – whether to return the id of the gap junction on the source node or the target node.
-
gid_pool
¶
-
local_gids
¶
-
model_type_col
= 'model_type'¶
-
py_function_caches
¶
-
bmtk.simulator.bionet.biosimulator module¶
-
class
bmtk.simulator.bionet.biosimulator.
BioSimulator
(network, dt, tstop, v_init, celsius, nsteps_block, start_from_state=False)[source]¶ Bases:
bmtk.simulator.core.simulator.Simulator
Includes methods to run and control the simulation
-
attach_current_clamp
(amplitude, delay, duration, gids=None, section_name='soma', section_index=0, section_dist=0.5)[source]¶
-
biophysical_gids
¶
-
cell_var_output
¶
-
cell_variables
¶
-
celsius
¶
-
dt
¶
-
h
¶
-
local_gids
¶
-
n_steps
¶
-
nsteps_block
¶
-
post_fadvance
()[source]¶ Runs after every execution of fadvance (see advance.hoc) Called after every time step to perform computation and save data to memory block or to disk. The initial condition tstep=0 is not being saved
-
run
()[source]¶ Run the simulation: if beginning from a blank state, then will use h.run(), if continuing from the saved state, then will use h.continuerun()
-
spikes_table
¶
-
tstop
¶
-
v_init
¶
-
bmtk.simulator.bionet.cell module¶
-
class
bmtk.simulator.bionet.cell.
Cell
(node, population_name, network=None)[source]¶ Bases:
object
A abstract base class for any cell object.
A base class for implementation of a cell-type objects like biophysical cells, LIF cells, etc. Do not instantiate a Cell object directly. Cell classes act as wrapper around HOC cell object with extra functionality for setting positions, synapses, and other parameters depending on the desired cell class.
-
gid
¶
-
group_id
¶
-
hobj
¶
-
netcons
¶
-
network_name
¶
-
node
¶
-
node_id
¶
-
soma_position
¶
-
bmtk.simulator.bionet.config module¶
-
class
bmtk.simulator.bionet.config.
Config
(*args, **kwargs)[source]¶ Bases:
bmtk.simulator.core.simulation_config.SimulationConfig
bmtk.simulator.bionet.iclamp module¶
bmtk.simulator.bionet.morphology module¶
bmtk.simulator.bionet.nml_reader module¶
-
class
bmtk.simulator.bionet.nml_reader.
NMLTree
(nml_path)[source]¶ Bases:
object
-
element_registry
= {'{http://www.neuroml.org/schema/neuroml2}channelDensity': <class 'bmtk.simulator.bionet.nml_reader.ChannelDensity'>, '{http://www.neuroml.org/schema/neuroml2}channelDensityNernst': <class 'bmtk.simulator.bionet.nml_reader.ChannelDensityNernst'>, '{http://www.neuroml.org/schema/neuroml2}concentrationModel': <class 'bmtk.simulator.bionet.nml_reader.ConcentrationModel'>, '{http://www.neuroml.org/schema/neuroml2}resistivity': <class 'bmtk.simulator.bionet.nml_reader.Resistivity'>, '{http://www.neuroml.org/schema/neuroml2}specificCapacitance': <class 'bmtk.simulator.bionet.nml_reader.SpecificCapacitance'>}¶
-
nml_ns
= '{http://www.neuroml.org/schema/neuroml2}'¶
-
bmtk.simulator.bionet.nrn module¶
-
bmtk.simulator.bionet.nrn.
load_neuron_modules
(mechanisms_dir, templates_dir, default_templates=True)[source]¶ Parameters: - mechanisms_dir –
- templates_dir –
- default_templates –
bmtk.simulator.bionet.pointprocesscell module¶
-
class
bmtk.simulator.bionet.pointprocesscell.
ConnectionStruct
(edge_prop, src_node, nc, is_virtual=False)[source]¶ Bases:
object
-
is_virtual
¶
-
source_node
¶
-
syn_weight
¶
-
-
class
bmtk.simulator.bionet.pointprocesscell.
PointProcessCell
(node, population_name, bionetwork)[source]¶ Bases:
bmtk.simulator.bionet.cell.Cell
Implimentation of a Leaky Integrate-and-file neuron type cell.
-
class
bmtk.simulator.bionet.pointprocesscell.
PointProcessCellSpontSyns
(node, population_name, bionetwork)[source]¶ Bases:
bmtk.simulator.bionet.pointprocesscell.PointProcessCell
Special class that allows certain synapses to spontaneously fire (without spiking) at a specific time.
bmtk.simulator.bionet.pointsomacell module¶
-
class
bmtk.simulator.bionet.pointsomacell.
PointSomaCell
[source]¶ Bases:
bmtk.simulator.bionet.cell.Cell
Used to represent single compartment cells with neural mechanisms
bmtk.simulator.bionet.pyfunction_cache module¶
bmtk.simulator.bionet.seclamp module¶
bmtk.simulator.bionet.sonata_adaptors module¶
-
class
bmtk.simulator.bionet.sonata_adaptors.
BioEdge
(sonata_edge, edge_adaptor)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge
-
afferent_section_id
¶
-
afferent_section_pos
¶
-
-
class
bmtk.simulator.bionet.sonata_adaptors.
BioEdgeAdaptor
(network)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor
-
class
bmtk.simulator.bionet.sonata_adaptors.
BioNode
(node, prop_adaptor)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode
-
morphology_file
¶
-
position
¶
-
rotation_angle_xaxis
¶
-
rotation_angle_yaxis
¶
-
rotation_angle_zaxis
¶
-
rotations
¶
-
rotations_quaternion
¶
-
-
class
bmtk.simulator.bionet.sonata_adaptors.
BioNodeAdaptor
(network)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor