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
- property morphology¶
- property morphology_file¶
bmtk.simulator.bionet.bionetwork module¶
- class bmtk.simulator.bionet.bionetwork.BioNetwork[source]¶
Bases:
bmtk.simulator.core.simulator_network.SimNetwork
- 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.
- property gid_pool¶
- property local_gids¶
- model_type_col = 'model_type'¶
- property 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]¶
- property biophysical_gids¶
- property cell_var_output¶
- property cell_variables¶
- property celsius¶
- property dt¶
- property h¶
- property local_gids¶
- property n_steps¶
- property 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()
- property spikes_table¶
- property tstop¶
- property 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.
- property gid¶
- property group_id¶
- property hobj¶
- property netcons¶
- property network_name¶
- property node¶
- property node_id¶
- property 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.gids module¶
bmtk.simulator.bionet.iclamp module¶
bmtk.simulator.bionet.io_tools 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
- property is_virtual¶
- property source_node¶
- property 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.
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.pyfunction_cache.add_cell_model(func, directive, model_type, overwrite=True)[source]¶
- bmtk.simulator.bionet.pyfunction_cache.add_weight_function(func, name=None, overwrite=True)[source]¶
- bmtk.simulator.bionet.pyfunction_cache.cell_model(*wargs, **wkwargs)[source]¶
A decorator for registering NEURON cell loader functions.
- bmtk.simulator.bionet.pyfunction_cache.load_py_modules(cell_models=None, syn_models=None, syn_weights=None, cell_processors=None)[source]¶
- bmtk.simulator.bionet.pyfunction_cache.synapse_model(*wargs, **wkwargs)[source]¶
A decorator for registering NEURON synapse loader functions.
- bmtk.simulator.bionet.pyfunction_cache.synaptic_weight(*wargs, **wkwargs)[source]¶
A decorator for registering a function as a synaptic weight function. To use either:
@synaptic_weight def weight_function(): ...
or:
@synaptic_weight(name='name_in_edge_types') def weight_function(): ...
Once the decorator has been attached and imported the functions will automatically be added to py_modules.
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
- 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
- property morphology_file¶
- property position¶
- property rotation_angle_xaxis¶
- property rotation_angle_yaxis¶
- property rotation_angle_zaxis¶
- property rotations¶
- property rotations_quaternion¶
- class bmtk.simulator.bionet.sonata_adaptors.BioNodeAdaptor(network)[source]¶
Bases:
bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor