NEURON

From HP-SEE Wiki

Contents 1 Authors/Maintainers 2 Summary 3 Features 4 Architectural/Functional Overview 5 Usage Overview 6 Dependencies 7 HP-SEE Applications 8 Resource Centers 9 Usage by Other Projects and Communities 10 Recommendations for Configuration and Usage

• Web site: http://www.neuron.yale.edu/neuron/
• Described version: 7.1
• Licensing: e.g. GPL 2
• User documentation: http://www.neuron.yale.edu/neuron/
• Download: link
• Source code: http://www.neuron.yale.edu/neuron/

Authors/Maintainers

• Ted Hines, N. Carnevale

Summary

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties

Features

NEURON's computational engine employs special algorithms that achieve high efficiency by exploiting the structure of the equations that describe neuronal properties. It has functions that are tailored for conveniently controlling simulations, and presenting the results of real neurophysiological problems graphically in ways that are quickly and intuitively grasped. Instead of forcing users to reformulate their conceptual models to fit the requirements of a general purpose simulator, NEURON is designed to let them deal directly with familiar neuroscience concepts. Consequently, users can think in terms of the biophysical properties of membrane and cytoplasm, the branched architecture of neurons, and the effects of synaptic communication between cells.

• Domain-specific programming and configuration language (HOC)
• Parallel processing support through MPI
• Modular architecture using DL libraries to implement ionic equation kinetics
• High resolution differential equation solver (CVODE)

Architectural/Functional Overview

• Separates biology from purely computational concerns
• Integrator-independent model specification
• Efficient spatial and temporal discretization
• Graphical user interface
• User-extendable library of biophysical mechanisms
• Customizable initialization and simulation flow control

Usage Overview

• http://www.neuron.yale.edu/neuron/what_is_neuron

Dependencies

• Interviews Graphics Library (bundled in source)

HP-SEE Applications

• CMSLTM

Resource Centers

Usage by Other Projects and Communities

Recommendations for Configuration and Usage

Please change MPI environment to openMPI before compiling.

Install neuron from source following the instructions in http://www.neuron.yale.edu/neuron/download/compile_linux

Configure with --with-nrnpara option