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ModelView for ModelDB: Online Presentation of Model Structure

ModelView for ModelDB: Online Presentation of Model Structure ModelDB ( modeldb.yale.edu ), a searchable repository of source code of more than 950 published computational neuroscience models, seeks to promote model reuse and reproducibility. Code sharing is a first step; however, model source code is often large and not easily understood. To aid users, we have developed ModelView, a web application for ModelDB that presents a graphical view of model structure augmented with contextual information for NEURON and NEURON-runnable (e.g. NeuroML, PyNN) models. Web presentation provides a rich, simulator-independent environment for interacting with graphs. The necessary data is generated by combining manual curation, text-mining the source code, querying ModelDB, and simulator introspection. Key features of the user interface along with the data analysis, storage, and visualization algorithms are explained. With this tool, researchers can examine and assess the structure of hundreds of models in ModelDB in a standardized presentation without installing any software, downloading the model, or reading model source code. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Neuroinformatics Springer Journals

ModelView for ModelDB: Online Presentation of Model Structure

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Publisher
Springer Journals
Copyright
Copyright © 2015 by Springer Science+Business Media New York
Subject
Biomedicine; Neurosciences; Bioinformatics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Neurology
ISSN
1539-2791
eISSN
1559-0089
DOI
10.1007/s12021-015-9269-2
pmid
25896640
Publisher site
See Article on Publisher Site

Abstract

ModelDB ( modeldb.yale.edu ), a searchable repository of source code of more than 950 published computational neuroscience models, seeks to promote model reuse and reproducibility. Code sharing is a first step; however, model source code is often large and not easily understood. To aid users, we have developed ModelView, a web application for ModelDB that presents a graphical view of model structure augmented with contextual information for NEURON and NEURON-runnable (e.g. NeuroML, PyNN) models. Web presentation provides a rich, simulator-independent environment for interacting with graphs. The necessary data is generated by combining manual curation, text-mining the source code, querying ModelDB, and simulator introspection. Key features of the user interface along with the data analysis, storage, and visualization algorithms are explained. With this tool, researchers can examine and assess the structure of hundreds of models in ModelDB in a standardized presentation without installing any software, downloading the model, or reading model source code.

Journal

NeuroinformaticsSpringer Journals

Published: Apr 21, 2015

References