Database of NEURON, PYTHON and MATLAB codes, demos and tutorials

Schematic diagram of the kinetic schemes used for modeling ion channels and synaptic transmission. Different processes essential for modeling neuronal behavior can be described by similar type of equations. Voltage dependence, transmitter release, binding and gating of receptors, second messenger action, and neuromodulation can be all described by the same kinetic formalism (see Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism, Journal of Computational Neuroscience 1: 195-230, 1994).


NEURON demos

The first part of this database is a series of NEURON demo programs related to various cellular and network models that were developed in the laboratory. Each demo reproduces figures of articles published in the literature, in which the models are described in detail, as well as the biological background. Some of these models also appear in the ModelDB database at Yale University.

Note: the models described below were simulated using the NEURON simulator written by Michael Hines. The simulations will run straightforwardly provided the Interviews version of NEURON is installed properly. NEURON is publically available on internet via (see the NEURON home page). For more informations about how to get NEURON and how to install it, please refer to the NEURON home page, or to Michael Hines directly.

These demos can be used by anyone interested - the only condition we ask is to give appropriate citation to the original paper(s).


PYTHON demos

The second part of this database consists of PYTHON demos of some of the analysis procedures developed in the laboratory. PYTHON is a publically-available package in the standard LINUX distribution and is also available for Windows and Mac.

These demos can be used by anyone interested - the only condition we ask is to give appropriate citation to the original paper(s).


MATLAB demos

The third part of this database consists of MATLAB demos of some of the analysis procedures developed in the laboratory. MATLAB is a commercial software produced by Mathworks and which is available for LINUX, Windows and Mac.

These demos can be used by anyone interested - the only condition we ask is to give appropriate citation to the original paper(s).


Various Utilities

The third part of this database is a series of utilities of general interest, some of which were developed in the laboratory.

  • Generation of MPEG, AVI or GIF animations from NEURON (zip format)

    The package illustrates how to create animations from NEURON. The example taken generates MPEG or GIF animations of the spatial distribution of membrane potential during bursting in a model of thalamic reticular neuron, relative to the paper:

    Destexhe, A., Contreras, D., Steriade, M., Sejnowski, T.J. and Huguenard, J.R.
    In vivo, in vitro and computational analysis of dendritic calcium currents in thalamic reticular neurons.
    Journal of Neuroscience 16: 169-185, 1996

    in which all biological/modeling details are given. The demo is for LINUX (works with Ubuntu 12.4), and requires several packages to be installed. The principle is to generate a series of GIF frames, and then build a movie file from these frames. Please see the README file for a description of the procedure.

  • Utility to collapse a dendritic tree into three equivalent compartments using NEURON (zip format)

    This demo program illustrates how to create a reduced model of a complex morphology using NEURON. The program uses a principle of conservation of the axial resistance. The collapse is made such as the collapsed dendritic structure preserves the axial resistance of the original structure. The algorithm works by merging successive pairs of dendritic branches into an equivalent branch (a branch that preserves the axial resistance of the two original branches). This merging of branches can be done according to different methods selectable in the present code (see README for details). This program has been used in the following article:

    Destexhe, A., Neubig, M., Ulrich, D. and Huguenard, J.R.
    Dendritic low-threshold calcium currents in thalamic relay cells.
    Journal of Neuroscience 18: 3574-3588, 1998

    in which details of the method are given. More instructions are provided in a README file.

  • NTSCABLE

    This program translates digitized morphological descriptions of a neuron into files which can be used directly by NEURON. NTSCABLE was originally written by J.C. Wathey at the Salk Institute, and was intended to convert data files in the syntax of the Neuron Tracing System (Eutectic Electronics) into CABLE format, the predecessor of NEURON (hence the name "ntscable"). The program is now compatible with NEURON and can convert data files generated by various digitizing systems, including EUTECTIC, Douglas (2D and 3D), Nevin and NEUROLUCDIA (Microbrightfield) format for the last version (NTSCABLE 2.01).

    This program is public domain, works straightforwardly on UNIX or LINUX workstations and there is a relatively detailed documentation available. To access the documentation on NTSCABLE, click here and to get the last version of this package including code sources, click here .

  • SCoP MANUAL

    SCoP is a general tool for solving different types of mathematical problems and is the heart of the NEURON simulator. The NMODL language is based on SCoP, and all SCoP functions and features can be used within NMODL. SCoP features include the ability to solve differential equations, kinetic equations (or diagrams), partial differential equations, algebraic equations and more. There are many utility functions such as curve fitting, probability functions, random number generation, etc. The inclusion of SCoP is one of the features that make NEURON particularly powerful -- it can solve problems that go beyond the strict framework of membrane equations (for example diffusion of compounds, etc).

    Description of the SCoP language (language description, all utility functions are described here)

    NMODL Language (1991) (please see the NEURON web site for more recent versions)

    Unit checking utility for NMODL (please see the NEURON web site for more recent versions)


For more information, please contact:

Unité de Neurosciences, Information & Complexité (UNIC)
CNRS
UPR-3293, Bat 33,
1 Avenue de la Terrasse,
91198 Gif-sur-Yvette, France.

Tel: 33-1-69-82-34-35
Fax: 33-1-69-82-34-27


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