TCTX

tctx is a Python library containing the code for the manuscript:

Sequential propagation and routing of activity in a cortical network

Juan Luis Riquelme, Mike Hemberger, Gilles Laurent, Julijana Gjorgjieva

Installation

Use the package manager pip to install tctx.

pip install tctx

Usage

Simulations must be set up, run, post-processed.

Simulation setup

Setup will instantiate networks and create a registry of simulations to be run, specifying all parameters. Networks and simulation batches are saved as HDF5 files. All setup code can be accessed via tctx/simsetup.oy following the steps in tctx/notebooks/sims.ipynb.

Simulation run

Simulations are run with Nest simulator using the script tctx/seqexp.py. For example:

nohup python tctx/experiments/seqexp.py registry.h5 -l info --redirect &> nohup_$HOSTNAME.log &

Simulation results post-processing

Post-processing extracts properties from the simulation results such as detecting followers from trigger neurons. Post-processing results are saved as HDF5 next to the simulation batch. All post-processing code can be accessed via tctx/postpro.py and following the steps in tctx/notebooks/sims.ipynb.