Welcome to the PyRates documentation!

PyRates is a Python 3 tool for building rate-based neural models and performing numerical simulations of their dynamic behavior.

Among its core features are:

  • Models can be configured via YAML files or Python dictionaries
  • You can choose between _numpy and _tensorflow as your backend for simulations
  • Every network comes with a _networkx graph representation
  • Output are easily visualized via _seaborn and _mnepython
  • Functionalities for multi-dimensional parameter sweeps on single machines and clusters are provided

Installation

PyRates requires an installation of Python >=3.6.1. We recommend to install PyRates into a separate virtual environment. If using Anaconda, such a virtual environment can be set up via the command line:

conda create -n pyrates python>=3.6.1

And activated by calling:

conda activate pyrates

PyRates can either be installed via pip:

pip install pyrates

Or via the setup.py provided on GitHub <https://github.com/pyrates-neuroscience/PyRates>:

python setup.py install

This installation contains merely the minimum of required Python packages to build and run models in PyRates. Additional packages that may be installed include:

  • matplotlib (for visualization)
  • seaborn (for visualization)
  • mne (for visualization and post-processing)
  • tensorflow2.0 (for an alternative backend with GPU support)
  • paramiko and h5py (for cluster computation support)
  • numba (for CPU parallelization and just-in-time compilation of simulations via the NumPy backend)

All of these packages are available at PyPI and can thus be installed via:

pip install <name>

HowTo

Here, we provide examples of how to use the major user interfaces and links to instructive jupyter notebooks on our github repository.

Indices and tables