Encyclopedia of Computational Neuroscience

Living Edition
| Editors: Dieter Jaeger, Ranu Jung

ModelDB

  • Robert A. McDougal
  • Rixin Wang
  • Thomas M. Morse
  • Michele Migliore
  • Luis Marenco
  • Ted Carnevale
  • Michael Hines
  • Gordon M. Shepherd
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-7320-6_158-1

Definition

ModelDB is a database that supports the development of the field of computational neuroscience by storing and making available the computer code for publications that contain biophysical models of neurons and microcircuits. The focus is on models of biologically realistic neurons and circuits, but the spatial scales also range from molecules (ion channels and receptors) through behavior (dynamical systems, including an organism and its environment). The complexity of these mathematical models makes it challenging to recreate the simulations described in the papers from scratch, due to incomplete or ambiguous information in the paper or to errors introduced in attempting to recreate the model. Having the author’s original code or a third-party contribution available for download is invaluable for recreating a model for verification, extending the model, and reusing the model as a template or building block for new research projects.

Detailed Description

ModelDB began in the...

Keywords

Suffix Hines 
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Notes

Acknowledgments

We gratefully acknowledge funding from NIH grant DC009977.

References

  1. Hines ML, Carnevale NT (2013) NEURON Simulation Environment. In: Kotaleski JH, Crook S, (eds) Encyclopedia of computational neuroscience. SpringerGoogle Scholar
  2. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500–544PubMedCentralPubMedGoogle Scholar
  3. McDougal RA, Morse TM, Marenco L, Wang R, Carnevale NT, Hines ML, Shepherd GM (2013) ModelView for ModelDB: exploring model properties in a web browser. In: Society for Neuroscience Abstract, Poster 101.04Google Scholar
  4. Pechura CM, Martin JB (1991) Mapping the brain and its functions: integrating enabling technologies into neuroscience research. National Academy Press, Washington, DCGoogle Scholar
  5. Peterson BE, Healy MD, Nadkarni PM, Miller PL, Shepherd GM (1996) ModelDB: an environment for running and storing computational models and their results applied to neuroscience. J Am Med Inform Assoc 3:389–398PubMedCentralPubMedCrossRefGoogle Scholar
  6. Rall W, Shepherd GM (1968) Theoretical reconstruction of field potentials and dendrodendritic synaptic interactions in olfactory bulb. J Neurophysiol 31:884–915PubMedGoogle Scholar
  7. Shepherd GM, Grillner S (2010) Handbook of brain microcircuits. Oxford University Press, New YorkCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Robert A. McDougal
    • 1
  • Rixin Wang
    • 2
  • Thomas M. Morse
    • 1
  • Michele Migliore
    • 1
    • 3
  • Luis Marenco
    • 2
  • Ted Carnevale
    • 1
  • Michael Hines
    • 1
  • Gordon M. Shepherd
    • 1
  1. 1.Department of NeurobiologyYale University School of MedicineNew HavenUSA
  2. 2.Center for Medical InformaticsYale University School of MedicineNew HavenUSA
  3. 3.Institute of Biophysics, National Research CouncilPalermoItaly