Python Package: SER model
Dear Computational Neuroscience Community, I would like to point you to a potentially useful Python Package that might be of interest for your research, especially in the realm dynamical models and spreading dynamics on networks. "ser": S(usceptible)E(xcited)R(efractory) model on graphs, a dynamical model of spreading excitations. Code Repository: https://github.com/fabridamicelli/ser As of today, a few people already trust it and the package registers >11K total downloads, ~500/month (pypi.org) and has been used already in a few research projects. A few interesting features: - It is light-weight and fast (`numba` accelerated), i.e. many experiments can be simply run on a laptop - Installation and getting started is easy: `pip install ser` - Example notebooks: https://github.com/fabridamicelli/ser/blob/main/examples The SER model is a classical cellular automaton model used to study all sorts of complex systems, ranging from forest fire dynamics to self-organized criticality in the brain. Despite of the simplicity of its setup, it is capable of generating complex emergent dynamics with absolutely non-trivial higher-order statistical properties. To learn more about the SER model and its applications, you might want to check out these references: - Messe et al. (2018). Toward a theory of coactivation patterns in excitable neural networks. doi.org/10.1371/journal.pcbi.1006084 - Haimovici et al. (2013). Brain Organization into Resting State Networks Emerges at Criticality on a Model of the Human Connectome. doi.org/10.1103/PhysRevLett.110.178101 - Damicelli et al. (2019). Topological reinforcement as a principle of modularity emergence in brain networks. doi.org/10.1162/netn_a_00085 Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/ser/issues). All the best, Fabrizio Damicelli
Dear Computational Neuroscience Community, I would like to point you to a potentially useful Python Package that might be of interest for your research, especially in the realm dynamical models and synchronization phenomena. The Kuramoto model is used to study a wide range of systems (for a review on its usage in the Neuroscience, see Breakspear et al. 2010, Generative models of cortical oscillations: neurobiological implications of the Kuramoto model) "kuramoto": Python implementation of the Kuramoto model. * Code Repository: https://github.com/fabridamicelli/kuramoto * Easy install with `pip install kuramoto` * Example notebooks: https://github.com/fabridamicelli/kuramoto/tree/master/examples * A super concise intro to the model and its behaviour and further references can be found here: https://github.com/fabridamicelli/kuramoto#kuramoto-model-101 As of today, a few people already trust it and the package registers >10K total downloads, ~500/month (pypi.org). Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/kuramoto/issues) All the best, Fabrizio Damicelli
Dear Computational Neuroscience Community, I would like to point you to a potentially useful Python Package,especially in the realm dynamical models and synchronization phenomena. The Kuramoto model is used to study a wide range of systems (for a review on its usage in the Neuroscience, see Breakspear et al. 2010, Generative models of cortical oscillations: neurobiological implications of the Kuramoto model) "kuramoto": Python implementation of the Kuramoto model. [https://opengraph.githubassets.com/676ee08440b553afd4448323a4a8244abc846110f69d0f0519e97be914fd298c/fabridamicelli/kuramoto]<https://github.com/fabridamicelli/kuramoto> GitHub - fabridamicelli/kuramoto: Python implementation of the Kuramoto model<https://github.com/fabridamicelli/kuramoto> Python implementation of the Kuramoto model. Contribute to fabridamicelli/kuramoto development by creating an account on GitHub. github.com * Code: (https://github.com/fabridamicelli/kuramoto) * Easy install with `pip install kuramoto` * Example notebooks: https://github.com/fabridamicelli/kuramoto/tree/master/examples * A super concise intro to the model and its behaviour and further references can be found here: https://github.com/fabridamicelli/kuramoto#kuramoto-model-101 As of today, a few people already trust it and the package registers >27K total downloads, ~900/month (pypi.org). Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/kuramoto/issues) All the best, Fabrizio Damicelli
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Fabrizio Damicelli