ring

Parallelized ring network of ball and stick cells.

AUTHORS: - THOMAS MCTAVISH (2010-11-04): initial version. Modified version of the

project by Hines and Carnevale. (Hines M.L. and Carnevale N.T, Translating network models to parallel hardware in NEURON, Journal of Neuroscience Methods 169 (2008) 425-455).

class ring.Ring(N=5, stim_w=0.004, stim_spike_num=1, syn_w=0.01, syn_delay=5, playlist=[])

A network of N ball-and-stick cells where cell n makes an excitatory synapse onto cell n + 1 and the last, Nth cell in the network projects to the first cell.

connect_cells()

Connect cell n to cell n + 1.

connect_stim()

Connect a spike generator on the first cell in the network.

create_cells()

Create cell objects on this host and set their location.

get_spikes()

Get the spikes as a list of lists.

set_gids()

Set the gidlist on this host.

set_numcells(N, radius=50)

Create, layout, and connect N cells.

write_spikes(file_name='out.spk')

Append the spike output file with spikes on this host. The output format is the timestamp followed by a tab then the gid of the source followed by a newline.

Parameters:file_name – is the full or relative path to a spike output file.

Note

When parallelized, each process will write to the same file so it is opened in append mode. The order in which the processes write is arbitrary so while the spikes within the process may be ordered by time, the output file will be unsorted. A quick way to sort a file is with the bash command sort, which can be called after all processes have written the file with the following format:

exec_cmd = 'sort -k 1n,1n -k 2n,2n ' + file_name +                         ' > ' + 'sorted_' + file_name
os.system(exec_cmd)