"NetPyNE implementation and scaling of the Potjans-Diesmann cortical microcircuit model"
Cecilia Romaro, Fernando Araujo Najman, William W Lytton, Antonio C Roque, Salvador Dura-Bernal
Abstract: The Potjans-Diesmann cortical microcircuit model is a widely used model originally implemented in NEST. Here, we re-implemented the model using NetPyNE, a high-level Python interface to the NEURON simulator, and reproduced the findings of the original publication. We also implemented a method for scaling the network size which preserves first and second order statistics, building on existing work on network theory. Our new implementation enabled the use of more detailed neuron models with multicompartmental morphologies and multiple biophysically-realistic ion channels.
This opens the model to new research, including the study of dendritic processing, the influence of individual channel parameters, the relation to local field potentials, and other multiscale interactions. The scaling method we used provides flexibility to increase or decrease the network size as needed when running these CPU-intensive detailed simulations. Finally, NetPyNE facilitates modifying or extending the model using its declarative language; optimizing model parameters; running efficient large-scale parallelized simulations; and analyzing the model through built-in methods, including local field potential calculation and information flow measures.