ModelView for ModelDB: Online Presentation of Model Structure

Robert A McDougalGordon M Shepherd


ModelDB ( ), 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.


Aug 11, 2001·The Neuroscientist : a Review Journal Bringing Neurobiology, Neurology and Psychiatry·M L Hines, N T Carnevale
Nov 19, 2003·Neural Networks : the Official Journal of the International Neural Network Society·Shiro Usui
Apr 2, 2004·Neuroinformatics·Michele MiglioreMichael L Hines
Apr 20, 2007·Neuron·Padraig GleesonR Angus Silver
Mar 28, 2008·Methods in Molecular Biology·Michael L HinesN T Carnevale
Feb 6, 2009·Frontiers in Neuroinformatics·Andrew P DavisonPierre Yger
Dec 4, 2013·Frontiers in Neuroinformatics·Robert A McDougalWilliam W Lytton

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Apr 6, 2016·IEEE Transactions on Bio-medical Engineering·Robert A McDougalWilliam W Lytton
Nov 3, 2016·Journal of Neurophysiology·Mara Almog, Alon Korngreen
Oct 9, 2019·PharmacoEconomics·Eric Q WuPraveen Thokala
Sep 16, 2016·Journal of Computational Neuroscience·Robert A McDougalMichael L Hines
Apr 27, 2019·ELife·Salvador Dura-BernalWilliam W Lytton

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