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Neuroinformatics. 2015 Oct;13(4):459-70. doi: 10.1007/s12021-015-9269-2.

ModelView for ModelDB: Online Presentation of Model Structure.

Author information

1
Department of Neurobiology, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA. robert.mcdougal@yale.edu.
2
Department of Neurobiology, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA.

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.

KEYWORDS:

Code analysis; ModelDB; Repository; Visualization

PMID:
25896640
PMCID:
PMC4618280
DOI:
10.1007/s12021-015-9269-2
[Indexed for MEDLINE]
Free PMC Article
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