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Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

Mattioni M, Cohen U, Le Novère N - Front Neuroinform (2012)

Bottom Line: The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results.Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results.The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus Cambridge, UK.

ABSTRACT
The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

No MeSH data available.


Neuronvisio Controls main interface. From this interface it is possible to initialize and launch simulations, or to start the 3D viewer. The “Model” tab allows simulation duration (tstop), numerical integration interval (dt), and resting potential values (mV) to be assigned.
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Figure 1: Neuronvisio Controls main interface. From this interface it is possible to initialize and launch simulations, or to start the 3D viewer. The “Model” tab allows simulation duration (tstop), numerical integration interval (dt), and resting potential values (mV) to be assigned.

Mentions: The main window of Neuronvisio will be ready to accept inputs as shown in Figure 1.


Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

Mattioni M, Cohen U, Le Novère N - Front Neuroinform (2012)

Neuronvisio Controls main interface. From this interface it is possible to initialize and launch simulations, or to start the 3D viewer. The “Model” tab allows simulation duration (tstop), numerical integration interval (dt), and resting potential values (mV) to be assigned.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368231&req=5

Figure 1: Neuronvisio Controls main interface. From this interface it is possible to initialize and launch simulations, or to start the 3D viewer. The “Model” tab allows simulation duration (tstop), numerical integration interval (dt), and resting potential values (mV) to be assigned.
Mentions: The main window of Neuronvisio will be ready to accept inputs as shown in Figure 1.

Bottom Line: The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results.Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results.The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus Cambridge, UK.

ABSTRACT
The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

No MeSH data available.