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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.


ModelDB Explorer tab. The ModelDB Explorer tab retrieves the list of NEURON models available in ModelDB. The two tabs in the lower panel provide a “Model Overview” and “README” information. Models can be selected in this panel. The Load Model button downloads, extracts, and compiles the selected model, loading it into the current session.
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Figure 2: ModelDB Explorer tab. The ModelDB Explorer tab retrieves the list of NEURON models available in ModelDB. The two tabs in the lower panel provide a “Model Overview” and “README” information. Models can be selected in this panel. The Load Model button downloads, extracts, and compiles the selected model, loading it into the current session.

Mentions: A listing of all NEURON models available on ModelDB is available in XML format, recording model characteristics and properties. An updated list is released with every new version of Neuronvisio. Between releases, it can be automatically updated by the user, through a script provided with the Neuronvisio source code. The XML file is parsed at run time and the content is loaded in a Qt tree widget, available in the ModelDB explorer tab, as shown in Figure 2. It is possible to browse models by year of publication, author, title, or a unique id number. Additionally, columns can be ordered alphabetically, and to assist in model selection, a keywords-based search is also provided.


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

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

ModelDB Explorer tab. The ModelDB Explorer tab retrieves the list of NEURON models available in ModelDB. The two tabs in the lower panel provide a “Model Overview” and “README” information. Models can be selected in this panel. The Load Model button downloads, extracts, and compiles the selected model, loading it into the current session.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: ModelDB Explorer tab. The ModelDB Explorer tab retrieves the list of NEURON models available in ModelDB. The two tabs in the lower panel provide a “Model Overview” and “README” information. Models can be selected in this panel. The Load Model button downloads, extracts, and compiles the selected model, loading it into the current session.
Mentions: A listing of all NEURON models available on ModelDB is available in XML format, recording model characteristics and properties. An updated list is released with every new version of Neuronvisio. Between releases, it can be automatically updated by the user, through a script provided with the Neuronvisio source code. The XML file is parsed at run time and the content is loaded in a Qt tree widget, available in the ModelDB explorer tab, as shown in Figure 2. It is possible to browse models by year of publication, author, title, or a unique id number. Additionally, columns can be ordered alphabetically, and to assist in model selection, a keywords-based search is also provided.

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.