EI-clustered circuit model¶
This is PyNEST implementation of the EI-clustered circuit model described by Rostami et al. [1].
Citing this code¶
If you use this code, we ask you to cite the paper by Rostami et al. [1] and the NEST release on Zenodo.
File structure¶
run_simulation.py: an example script to try out the EI-clustered circuit model
network.py: the main
Network
class with functions to build and simulate the networkhelper.py: helper functions for calculation of synaptic weights and currents and plot function for raster plots
network_params.py: network and neuron parameters
stimulus_params.py: parameters for optional external stimulation
sim_params.py: simulation parameters
Running the simulation¶
python run_simulation.py
A raster plot of the network activity is saved as clustered_ei_raster.png
.
The code can be parallelized by using multiple threads during the NEST simulation.
This can be done by setting the parameter n_vp
in the run_simulation.py
script.
Contributions to this PyNEST model implementation¶
2023: initial version of code and documentation by Felix J. Schmitt, Vahid Rostami and Martin Nawrot.
Acknowledgments¶
Funding for the study by Rostami et al. [1]: This work was supported by the German Research Foundation (DFG), in parts through the Collaborative Research Center ’Motor Control in Health and Disease’ (DFG-SFB 1451, Project-ID 431549029) and under the Institutional Strategy of the University of Cologne within the German Excellence Initiative (DFG-ZUK 81/1) and in parts through the DFG graduate school ’Neural Circuit Analysis’ (DFG-RTG 1960, ID 365082554) and through the European Union’s Horizon 2020 Framework Programme for Research and Innovation under grant agreement number 945539 (Human Brain Project SGA3). The figure is created with BioRender.com.
Other implementations of the EI-clustered model¶
A GeNN version by Felix J. Schmitt, Vahid Rostami and Martin Nawrot [2].
References¶
PyNEST EI-clustered network: Simulation Parameters
PyNEST EI-clustered network: Stimulus Parameters
PyNEST EI-clustered network: Run Simulation
PyNEST EI-clustered network: Network Parameters
PyNEST EI-clustered network: Helper Functions
PyNEST EI-clustered network: Network Class