Simulation software

Note: a more complete list of software applications for computational neuroscience and neuroinformatics is available from the INCF Software Centre

  • BRIAN Brian is a simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.

  • DANA Dana is a python framework for distributed, asynchronous, distributed and adaptive computing.

  • Emergent Emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world.

  • GENESIS GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.

  • LFPy LFPy is a Python package for calculation of extracellular potentials from multicompartment neuron models. It relies on the NEURON simulator and uses the Python interface it provides. LFPy provides a set of easy-to-use Python classes for setting up your model, running your simulations and calculating the extracellular potentials arising from activity in your model neuron. If you have a model working in NEURON already, it is likely that it can be adapted to work with LFPy.

  • MCell - A Monte Carlo Simulator of Cellular Microphysiology MCell is a modeling tool for realistic simulation of cellular signaling in the complex 3-D subcellular microenvironment in and around living cells

  • MOOSE MOOSE is a Multiscale Object Oriented Simulation Environment for modeling and simulation in Neuroscience and Systems Biology. It is a general purpose simulator that can be used to create models and run simulations in computational biology.

  • MvaSpike Mvaspike is a general purpose tool aimed at modeling and simulating large, complex networks of biological neural networks. It is based on an event-based modeling and simulation strategy, targetting mainly pulse-coupled, spiking neural networks (e.g. integrate-and-fire neurons, other spiking point neurons).

  • NANS: Neuron And Network Simulator NANS is a suite of four interactive graphical simulators for the modelling and display of neurons and networks of neurons. The fundamental building blocks are segments of neuronal membrane, which are used to construct compartmentally-modelled neurons. Any number of neurons can be connected with synapses to define complex networks.

  • NEST NEST is a simulation software for large-scale neuronal network simulations. It supports parallel simulation using threads as well as MPI communication.

  • Neuron Simulation environment for empirically-based simulations of neurons and networks of neurons.

  • Openworm A simulation platform to build digital in-silico living system.

  • PSICS - the Parallel Stochastic Ion Channel Simulator PSICS computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It supports representation of ion channels as kinetic schemes inviolving one or more serial gating complexes.

  • PyDSTool PyDSTool is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems).

  • STEPS - STochastic Engine for Pathway Simulation STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh.

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