rerun_db¶

simrun.rerun_db.rerun_db(db, outdir, tStop=None, neuron_param_modify_functions=[], network_param_modify_functions=[], synapse_activation_modify_functions=[], stis=None, silent=False, additional_network_params=[], child_process=False)¶

Recreate and resimulate a network-embedded neuron simulation from a simrun-initialized database.

This method recreates the network-embedded neuron simulation from the parameter files in the simrun-initialized database. It allows to adapt the cell parameters, network parameters, and the synaptic activation patterns with modification functions. The results are stored in the specified directory, relative to the original unmodified simulation results.

Attention

This function uses the exact same synapse activations as already present in the database, except if synapse_activation_modify_functions is given. In other words, adapting release probabilities of synapses with network_param_modify_functions will have no effect, as the synapse activations are not regenerated.

Parameters:¶

db : DataBase¶: A simrun-initialized database to resimulate.
stis : list¶: List of simulation trial indices to be resimulated.
outdir : str¶: Directory where the simulation results are stored, relative to the current working directory. Preferably, use an absolute path.
tStop : float¶: Time in ms at which the simulation should stop.
neuron_param_modify_functions : list¶: List of functions which take NTParameterSet neuron parameters and may return it changed.
network_param_modify_functions : list¶: List of functions which take NTParameterSet network parameters and may return it changed.
synapse_activation_modify_functions : list¶: List of functions which take a Synapse activation dataframe and may return it changed.
additional_network_params : list¶: List of additional Network parameters files to be used in the simulation.
silent : bool¶: If True, suppresses output from the simulation.
child_process : bool¶: If True, runs the simulation in a child process.

Returns:¶

A list of dask delayed objects. When computed with a dask scheduler, it writes the simulation results to the specified directory.

Return type:¶

list