Model files in the NetPyNE simulation environment for the paper:
Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit
by Adam Ponzi, Salvador Dura-Bernal, and Michele Migliore
Download the files.
Compile the mod files on the command line with 'nrnivmodl mechanisms'.
Install the NetPyNE simulation environment (http://netpyne.org/install.html)
To run the code using mpi-exec: (1) Remove or rename the directory t42_data (which is subsequently recreated when the code is run). (2) Set the numcores parameter in t42_batch.py to the required number of cores. (3) On the command line : 'nrniv -python t42_batch.py' (4) On completion, in the file maketrace.py set asBatch = True. Run maketrace.py.
To run the code directly: (1) On the command line: 'nrniv -python t42_init.py'. In this case no new directories are created. (2) On completion, in the file maketrace.py set asBatch = False. Run maketrace.py.
Questions on how to use this model should be directed to email@example.com