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NEURON

NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane, and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. It evolved from a long collaboration between Michael Hines at the Department of Computer Science, Yale University School of Medicine, and John W. Moore at the Department of Neurobiology, Duke University Medical Center. Their express goal was to create a tool designed specifically for solving the equations that describe nerve cells. NEURON allows users to focus on the important anatomical and biophysical features of the model, without being distracted by computational issues such as compartmental size. It does this in part through the notion of continuous cable ‘sections’ which are connected together to form any kind of branched architecture and which are endowed with properties that can vary continuously with position along the section. User-defined properties of membrane and cytoplasm are expressed in terms of kinetic schemes and sets of simultaneous equations. Membrane voltage and states are computed efficiently by compiling these model descriptions and using an implicit integration method optimised for branched structures. Variable-order variable-stepsize integration can be chosen to achieve increased accuracy and/or speed. NEURON realises a tremendous degree of flexibility by using an object-oriented interpreter to set up the anatomical and biophysical properties of the model, define the appearance of the graphical interface, control simulations, and plot results. Two recent additions to the graphical user interface deserve special mention: the ‘CellBuilder’ enables users to create new models from scratch and modify existing models without writing any code; and the ‘Multiple Run Fitter’ greatly facilitates optimisation of models that have high-dimensional parameter spaces

Medium: Downloadable from: http://www.neuron.yale.edu/neuron/install/install.html
System requirements: Initially developed in the UNIX/Linux environment, NEURON was subsequently ported to Windows (all versions) and Mac OS. It is the only neural simulator that runs on all popular hardware platforms, from sub-US$1,000 microcomputers to supercomputers, bringing the ability to perform research-quality simulations within reach of neuroscientists around the world
Price: Freeware