Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)

 Download zip file 
Help downloading and running models
Accession:266872
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 rescaling the network size which preserves first and second order statistics, building on existing work on network theory. The new implementation enables using more detailed neuron models with multicompartment morphologies and multiple biophysically realistic channels. This opens the model to new research, including the study of dendritic processing, the influence of individual channel parameters, and generally multiscale interactions in the network. The rescaling method provides flexibility to increase or decrease the network size if required when running these more realistic 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.
Reference:
1 . Romaro C, Najman FA, Lytton WW, Roque AC, Dura-Bernal S (2021) NetPyNE Implementation and Scaling of the Potjans-Diesmann Cortical Microcircuit Model Neural Computation 33(7):1993-2032 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Connectionist Network;
Brain Region(s)/Organism: Auditory cortex; Olfactory cortex;
Cell Type(s): Abstract integrate-and-fire leaky neuron; Abstract integrate-and-fire neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Python; NEURON; NetPyNE;
Model Concept(s): Detailed Neuronal Models; Simplified Models;
Implementer(s): Dura-Bernal, Salvador [salvadordura at gmail.com]; Romaro, Cecilia [ceciliaromaro at gmail.com]; 
MIT License

Copyright (c) 2019 ceciliaromaro

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Loading data, please wait...