We strongly support open access science. These programs are all provided as free software and you are welcome to re-use this code (see the individual files for license information). If the code is useful we do appreciate a citation of the relevant paper. The code hosted here has been beta tested and we appreciate your feedback and any suggestions to improve it. Please feel free to contact us if you're interested in particular methods that are not listed here. We also support the Wikiproject Neuroscience and try to keep relevant Wikipedia articles up to date. See for instance Neural oscillation. |

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code | description | citation |
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Consistency-based thresholding | Threshold a group of networks by the consistency of edge weights across the group. | Roberts JA, Perry A, Roberts G, Mitchell PB, Breakspear M (2017). Consistency-based thresholding of the human connectome. NeuroImage 145:118-129. |

distob | Distributed computing made easier, using automatic remote objects in python. | TBA 2015 |

Diversity SIRS model | Susceptible-infected-refractory-susceptible model with diversity in the excitability parameter. | Gollo LL, Copelli M, & Roberts JA (2016). Diversity improves performance in excitable networks. PeerJ, 4, e1912. |

Geometric surrogate networks | Generate random surrogate weighted networks that preserve the effect of distance on the weights. | Roberts JA, Perry A, Lord AR, Roberts G, Mitchell PB, Smith RE, Calamante F, Breakspear M (2016). The contribution of geometry to the human connectome. NeuroImage 124: 379-393. |

Metastable brain waves | Simulate metastable brain waves, and analysis tools to quantify the dynamics. | Roberts JA, Gollo LL, Abeysuriya R, Roberts G, Mitchell PB, Woolrich MW, Breakspear M (2019). Metastable brain waves. Nature Communications 10: 1056 |

Neurodynamics | Simulate the dynamics of any of the >100,000 neurons, whose digital reconstructions are available at the NeuroMorpho.org website | Kirch, Christoph, and Leonardo L. Gollo. "Spatially resolved dendritic integration: Towards a functional classification of neurons." bioRxiv (2019): 657403. |

NormalForm | Mathematica package: find a smooth transformation that maps a complicated dynamical system to a simple one | Aburn, Holmes, Daffertshofer and Breakspear "Normal form transformations explain effect of noise near Hopf bifurcations" in prep. |

nsim | Simulate systems from ODEs or SDEs, analyze EEG or other timeseries, all done in parallel on a cluster or multiple CPUs. | Aburn, Holmes, Daffertshofer and Breakspear "Normal form transformations explain effect of noise near Hopf bifurcations" in prep. |

Partially-randomized surrogate networks | Generate partially-randomized surrogate networks that preserve the effect of distance on the weights. | Gollo LL, Roberts JA, Cropley VL, Di Biase MA, Pantelis C, Zalesky A, Breakspear M (2018). Fragility and volatility of structural hubs in the human connectome. Nature Neuroscience 21:1107-1116. |

PruneNeuron | Prune neuronal dendritic tree and simulate its dynamics | Kirch C, & Gollo LL (2020). Dynamical effects of dendritic pruning implicated in aging and neurodegeneration: Towards a measure of neuronal reserve. |

Rank-shift index | Compare the ranking of nodes between two networks | Kale P, Zalesky A, & Gollo LL (2018). Estimating the impact of structural directionality: How reliable are undirected connectomes?. Network Neuroscience, 2(02), 259-284. |

sdeint | Numerical integration of Ito or Stratonovich SDEs. Includes Euler-Maruyama, Stratonovich Heun and Stochastic Runge-Kutta methods | TBA 2015 |

SDE integration tools | Integrate scalar or vector Stochastic Differential Equations (SDE) in Stratonovich form using the Heun algorithm. Includes example code simulating generalized Ornstein-Uhlenbeck processes (with multiplicative and additive noise) and a simple cortical model (Jansen-Rit). | Aburn, Holmes, Roberts, Boonstra and Breakspear (2012) "Critical Fluctuations in Cortical Models Near Instability", Front. Physio. 3:331. doi:10.3389/fphys.2012.00331 |

SDMs examples | Examples (Morris-Lecar neuron, Breakspear-Terry-Friston neural mass model, and bistable Hopf oscillator) from SDMs paper | Roberts JA, Friston KJ, Breakspear M (2016). Clinical Applications of Stochastic Dynamic Models of the Brain, Part I: A Primer. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2: 216-224. |

time-frequency coherency | computes the complex-valued time-frequency coherency between two signal vectors | Mehrkanoon S, Breakspear M, Daffertshofer A, Boonstra TW (2013). Non-identical smoothing operators for estimating time-frequency interdependence in electrophysiological recordings. EURASIP Journal on Advances in Signal Processing 2013, 2013:73. doi:10.1186/1687-6180-2013-73 |

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