bmtk.tests.simulator.bionet package
Submodules
bmtk.tests.simulator.bionet.bionet_virtual_files module
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class
bmtk.tests.simulator.bionet.bionet_virtual_files.EdgeRow[source]
Bases: object
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property
with_dynamics_params
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class
bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile(target_nodes, source_nodes)[source]
Bases: object
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edges_itr(target_gid)[source]
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load(edges_file, edge_types_file)[source]
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property
source_network
Name of network containing the source gids
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property
target_network
Name of network containing the target gids
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class
bmtk.tests.simulator.bionet.bionet_virtual_files.NodeRow[source]
Bases: object
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property
with_dynamics_params
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class
bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile(N)[source]
Bases: object
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get_node(gid, cache=False)[source]
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property
gids
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load(nodes_file, node_types_file)[source]
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property
name
name of network containing these nodes
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next()[source]
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property
node_types_table
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property
version
bmtk.tests.simulator.bionet.conftest module
bmtk.tests.simulator.bionet.set_cell_params module
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bmtk.tests.simulator.bionet.set_cell_params.Biophys1(cell_prop)[source]
Set parameters for cells from the Allen Cell Types database
Prior to setting parameters will replace the axon with the stub
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bmtk.tests.simulator.bionet.set_cell_params.IntFire1(cell_prop)[source]
Set parameters for the IntFire1 cell models.
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bmtk.tests.simulator.bionet.set_cell_params.fix_axon(hobj)[source]
Replace reconstructed axon with a stub
- Parameters
- hobj: instance of a Biophysical template
NEURON’s cell object
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bmtk.tests.simulator.bionet.set_cell_params.set_params_peri(hobj, params_file_name)[source]
Set biophysical parameters for the cell
- Parameters
- hobj: instance of a Biophysical template
NEURON’s cell object
- params_file_name: string
name of json file containing biophysical parameters for cell’s model which determine spiking behavior
bmtk.tests.simulator.bionet.set_syn_params module
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bmtk.tests.simulator.bionet.set_syn_params.exp2syn(syn_params, xs, secs)[source]
Create a list of exp2syn synapses
- Parameters
- syn_params: dict
parameters of a synapse
- xs: float
normalized distance along the section
- secs: hoc object
target section
- Returns
- syns: synapse objects
bmtk.tests.simulator.bionet.set_weights module
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bmtk.tests.simulator.bionet.set_weights.gaussianLL(tar_prop, src_prop, con_prop)[source]
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bmtk.tests.simulator.bionet.set_weights.wmax(tar_prop, src_prop, con_prop)[source]
bmtk.tests.simulator.bionet.test_biograph module
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bmtk.tests.simulator.bionet.test_biograph.test_add_edges()[source]
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bmtk.tests.simulator.bionet.test_biograph.test_add_nodes()[source]
bmtk.tests.simulator.bionet.test_gids module
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bmtk.tests.simulator.bionet.test_gids.test_gid_pool()[source]
bmtk.tests.simulator.bionet.test_nrn module
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bmtk.tests.simulator.bionet.test_nrn.test_cell_model()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_cell_model_decorator()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_load_py_modules()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_synapse_model()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_synapse_model_decorator()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_weight()[source]
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bmtk.tests.simulator.bionet.test_nrn.test_weight_decorator()[source]
Module contents
