Software ecosystem

Below is a list of packages that build on Brian, either from us, colleagues we’ve worked with, or entirely separate groups. If you have written a package using Brian and it’s not listed here, let us know!

Brian team

• brian2cuda

  Brian 2 device that generates CUDA code for simulations on GPUs. Supports all features that are supported by the C++ standalone device, and can accelerate simulations by orders of magnitudes (Brian2CUDA paper).

• brian2genn

  Brian 2 frontend to the GPU-enhanced neural network simulator (GeNN). Allows you to run Brian models on GPU up to 400x faster (Brian2GeNN paper).

• brian2modelfitting

  Model Fitting Toolbox for Brian 2 simulator, to allow the user to find the best fit of the parameters for recorded traces and spike trains.

• brian2hears

  Brian hears is an auditory modelling library for Python.

• brian2tools

  The brian2tools package is a collection of useful tools for the Brian 2 simulator.

Third party packages

• Dendrify

  Dendrify, through simple commands, automatically generates reduced compartmental neuron models for Brian 2, with simplified yet biologically relevant dendritic and synaptic integrative properties (paper).

• Neuronal Dynamics Exercises

  This repository contains python exercises accompanying the book Neuronal Dynamics by Wulfram Gerstner, Werner M. Kistler, Richard Naud and Liam Paninski.

• PyRhO

  A virtual optogenetics laboratory (paper).

• CxSystem2

  CxSystem2 is a simulation framework for cortical networks, which operates on personal computers. It is implemented in Python on top of the popular Brian2 simulator, and runs on Linux, Windows and MacOS. There is also a web-based version available via the Human Brain Project Brain Simulation Platform (BSP).

• SNN toolbox

  The SNN conversion toolbox contains functions to transform rate-based artificial neural networks into spiking neural networks, and to simulate them.

• NeuroRobot

  A neurorobot is a robot controlled by a computer simulation of a biological brain. At Backyard Brains we use neurorobots to teach computational neuroscience in high schools. This repository contains all the Matlab and Arduino code needed to run our neurorobots. If you haven’t got a neurorobot yet, you can still run the neurorobot app using only your computer and webcamera.

Older software (Brian version 1 only)

Packages

• CLONES. Closed-Loop Neural Simulations. An open-source interface between Brian and Sofa, a physics engine for biomedical simulation. clones allows you to model animal behaviour through the interaction of neurons, muscles and the environment. The video (click for full screen) demonstrates the clones implementation of Jordan Boyle’s C. Elegans locomotion model (Boyle, JH. C. elegans locomotion: an integrated approach. PhD thesis, university of Leeds, 2009).
• DANA. Distributed, Asynchronous, Numerical and Adaptive computing framework. A project designed for rate based models, complementing Brian’s focus on spiking models. Partly inspired by and aiming at full integration with Brian.
• PyNN. A simulator-independent package for building neuronal network models. Allows you to write code for a model once using the PyNN API, and then run it without modification on any simulator that PyNN supports (currently Neuron, NEST, PCSIM and Brian).

Distributions

• Debian. A GNU/Linux distribution with an extensive coverage of scientific software. Brian in Debian is maintained by NeuroDebian project, which also provides up-to-date releases of neuroscience-related software for recent Debian and Ubuntu releases.
• Python(x,y). A distribution of Python oriented towards scientific computation, including Brian as a plugin.
• Sage. A free open-source mathematics software system based on Python, including Brian as an optional extension.