ModelDB statistics

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Protocols

ModelDB specifications

Information


Unique identifier OMICS_14850
Name ModelDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Michael Hines
  • person_outline Tom Morse
  • person_outline Robert McDougal

Additional information


https://senselab.med.yale.edu/ModelDB/DwnldGuide.html https://senselab.med.yale.edu/modeldb/guide2.cshtml

Publications for ModelDB

ModelDB citations

 (32)
library_books

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

2018
Front Neuroinform
PMCID: 5938413
PMID: 29765315
DOI: 10.3389/fninf.2018.00020

[…] implementation of the model and data-analysis method in a public and widely adopted simulation tool or programming language (e.g., Python) in some of the available model repositories, for example in ModelDB and BioModels database (Le Novère et al., ), is a must. Regardless of all the available formats and tools, many authors do not publish their models in a format that is easily exchangeable betw […]

library_books

Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience

2018
Front Neuroinform
PMCID: 5911506
PMID: 29713272
DOI: 10.3389/fninf.2018.00018

[…] uman Brain Project, the Allen Brain Institute, the International Neuroinformatics Coordinating Facility, and others. Other databases include the NeuroMorpho.Org database of neuronal morphologies, the ModelDB database of computational neuroscience models (see this issue) in a variety of simulation packages and languages, and the Open Source Brain database for collaborative research (, ; Gleeson et […]

library_books

Gap junction plasticity as a mechanism to regulate network wide oscillations

2018
PLoS Comput Biol
PMCID: 5864095
PMID: 29529034
DOI: 10.1371/journal.pcbi.1006025

[…] ap junction plasticity on information transfer. The model is written in Python and takes advantage of the tensorflow library that leverages GPU parallel processing capabilities []. It is available on ModelDB (http://modeldb.yale.edu/230324). […]

call_split

A hippocampo cerebellar centred network for the learning and execution of sequence based navigation

2017
Sci Rep
PMCID: 5736633
PMID: 29259243
DOI: 10.1038/s41598-017-18004-7
call_split See protocol

[…] The models were programmed in Python using the numpy library. The code is available on ModelDB and github (https://github.com/gviejo/Fos). […]

library_books

Pleiotropic effects of schizophrenia associated genetic variants in neuron firing and cardiac pacemaking revealed by computational modeling

2017
PMCID: 5802468
DOI: 10.1038/s41398-017-0007-4

[…] r FEniCS. For details on the spatial distribution of parameters in the 2D simulations, see ref.. Scripts for running L5PC and 0D SANC simulations are publicly available (https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=187615). […]

library_books

Predictive Place Cell Sequences for Goal Finding Emerge from Goal Memory and the Cognitive Map: A Computational Model

2017
Front Comput Neurosci
PMCID: 5643423
PMID: 29075187
DOI: 10.3389/fncom.2017.00084

[…] omparing different network parameter settings, the sequence generation component of the model was implemented using the ANNarchy simulator, version 4.5 (Vitay et al., ). Code will be published in the ModelDB database following publication (http://senselab.med.yale.edu/ModelDB/). […]

Citations

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ModelDB institution(s)
Department of Neuroscience, Yale University, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Center for Medical Informatics, Yale University, New Haven, CT, USA; Department of Anesthesiology, Yale University, New Haven, CT, USA; Institute of Biophysics, National Research Council, Palermo, Italy
ModelDB funding source(s)
Supported by the National Institutes of Health (NIH) grants R01 DC009977 from the National Institute on Deafness and Other Communication Disorders (NIDCD) and T15 LM007056 from the National Library of Medicine (NLM).

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