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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.


Structure of the HDF5 file used to store the computational results of a simulation. The data tree is composed of two branches: the geometry branch stores the NeuroML representation, the results branch stores computed arrays resulting from the simulations.
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Figure 5: Structure of the HDF5 file used to store the computational results of a simulation. The data tree is composed of two branches: the geometry branch stores the NeuroML representation, the results branch stores computed arrays resulting from the simulations.

Mentions: The organization of the storage file in Neuronvisio is shown in Figure 5. The data tree comprises two branches; the geometry branch (/geometry) stores the NeuroML representation of the morphology of the model, the results branch (/results) stores computed arrays of the simulations. The HocVectors are saved in the VecRef structure. The GenericRef node acts as placeholder for data structure customization, highlighting the extensibility of the design. The BaseRef class can be used to store any custom arrays not expressed as NEURON HocVectors. Every BaseRef object is contained in a group, which is specified by the group_id attribute. This attribute is automatically set to the name of the class, MyRef in this example. It is used in the selection interface presented to the user to assign the independent variable against which computed values should be plotted.


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

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

Structure of the HDF5 file used to store the computational results of a simulation. The data tree is composed of two branches: the geometry branch stores the NeuroML representation, the results branch stores computed arrays resulting from the simulations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Structure of the HDF5 file used to store the computational results of a simulation. The data tree is composed of two branches: the geometry branch stores the NeuroML representation, the results branch stores computed arrays resulting from the simulations.
Mentions: The organization of the storage file in Neuronvisio is shown in Figure 5. The data tree comprises two branches; the geometry branch (/geometry) stores the NeuroML representation of the morphology of the model, the results branch (/results) stores computed arrays of the simulations. The HocVectors are saved in the VecRef structure. The GenericRef node acts as placeholder for data structure customization, highlighting the extensibility of the design. The BaseRef class can be used to store any custom arrays not expressed as NEURON HocVectors. Every BaseRef object is contained in a group, which is specified by the group_id attribute. This attribute is automatically set to the name of the class, MyRef in this example. It is used in the selection interface presented to the user to assign the independent variable against which computed values should be plotted.

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.