This software simulates a cortical microcircuit based on the Potjans-Diesmann model. It is implemented in different languages, Python, Julia, C and NEST. The C code represents an improved implementation of the original simulation code in the repository mesopopdyn_gif.
There are the following implementations:
- Microscopic simulation (my custom C code)
- Microscopic simulation (NEST)
- Mesoscopic simulation (my custom C code)
- Mesoscopic simulation (NEST)
- Mesoscopic simulation (Python with Numba)
- Mesoscopic simulation (Python without Numba)
- Mesoscopic simulation (Julia)
For the C and NEST simulations you need to run PDmodel_C-code-tilo_NEST.py. For the Python simulations you need to run PDmodel_mesopython.py. For the Julia simulation you need to run PDmodel_mesojulia.jl
There are three folders:
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single_run/: simulations of a single trial of the PD model as in Fig.1 and Fig. 8 of Schwalger et al. PLoS Comput Biol (2017) but without adaptation
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benchmarking/: simulations of 10s of biological time to measure execution times
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mesopopdyngif_C_v18_py3/: contains the C code for micro- and mesoscopic simulations as well as the python modules that provide a Python interface. You need to build the C libraries with make (and ignore warnings).