Encyclopedia of Computational Neuroscience

Living Edition
| Editors: Dieter Jaeger, Ranu Jung

Databases and Data Repositories in Computational Neuroscience: Overview

  • Richard C. GerkinEmail author
  • Shreejoy J. Tripathy
  • Sharon Crook
  • Jeanette Kotaleski
Living reference work entry

Latest version View entry history

DOI: https://doi.org/10.1007/978-1-4614-7320-6_780-2


Computational neuroscience research often produces models that help explain empirical data and provide predictions about the biological systems that produce the data. Empirical and theoretical researchers can benefit from resources that facilitate model publication and exchange and provide neuroscience data that informs and contains these existing and future models.

Detailed Description

Databases of Computational Models

One category of databases in computational neuroscience is those that focus on computational models. The BioModels database (Li et al. 2010; Vijayalakshmi et al. 2013) is a general repository of computational models of biological processes that includes some models from neuroscience. The SenseLab database, ModelDB, (Migliore et al. 2003) provides a resource for published neuroscience models in a variety of formats. Many of these were developed specifically for simulating the electrophysiological and neurochemical properties of single neurons and networks of...

This is a preview of subscription content, log in to check access.


  1. Ascoli GA, Donohue DE, Halavi M (2007) Neuromorpho.org: a central resource for neuronal morphologies. J Neurosci 27(35):9247–9251CrossRefPubMedGoogle Scholar
  2. Bakker R, Wachtler T, Diesmann M (2012) Cocomac 2.0 and the future of tract-tracing databases. Front Neuroinform 6:30PubMedCentralCrossRefPubMedGoogle Scholar
  3. Bota M, Dong H-W, Swanson L (2005) Brain architecture management system. Neuroinformatics 3(1):15–48CrossRefPubMedGoogle Scholar
  4. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME (2008) The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 6(3):175–194PubMedCentralCrossRefPubMedGoogle Scholar
  5. Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung K-H, Lai PC, Bahl G, Masiar P, Lam HYK, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM (2007) SenseLab: new developments in disseminating neuroscience information. Brief Bioinform 8(3):150–162PubMedCentralCrossRefPubMedGoogle Scholar
  6. Gardner D et al (2008) The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics 6(3):149–165PubMedCentralCrossRefPubMedGoogle Scholar
  7. Glaser JR, Glaser EM (1990) Neuron imaging with neurolucida – a PC-based system for image combining microscopy. Comput Med Imaging Graph 14(5):307–317CrossRefPubMedGoogle Scholar
  8. Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010a) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6(6):e1000815PubMedCentralCrossRefPubMedGoogle Scholar
  9. Gleeson P, Piasini E, Crook S, Cannon R, Steuber V, Jaeger D, Solinas S, DAngelo E, Silver RA (2010b) The open source brain initiative: enabling collaborative modelling in computational neuroscience. BMC Neurosci 13(1):1–2Google Scholar
  10. Hamilton DJ, Shepherd GM, Martone ME, Ascoli GA (2012) An ontological approach to describing neurons and their relationships. Front Neuroinform 6:15PubMedCentralCrossRefPubMedGoogle Scholar
  11. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117(4):500–544PubMedCentralCrossRefPubMedGoogle Scholar
  12. Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME (2012) Development and use of ontologies inside the neuroscience information framework: a practical approach. Front Genet 3:111PubMedCentralCrossRefPubMedGoogle Scholar
  13. Laird AR, Lancaster JL, Fox PT (2004) Brainmap: the social evolution of a functional neuroimaging database. Neuroinformatics 3:65–78CrossRefGoogle Scholar
  14. Larson SD, Martone ME (2009) Ontologies for neuroscience: what are they and what are they good for? Front Neurosci 3:1CrossRefGoogle Scholar
  15. Larson SD, Martone ME (2013) NeuroLex.org: an online framework for neuroscience knowledge. Front Neuroinform 7:18PubMedCentralCrossRefPubMedGoogle Scholar
  16. Lein ES et al (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445(7124):168–176CrossRefPubMedGoogle Scholar
  17. Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C (2010) BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92PubMedCentralCrossRefPubMedGoogle Scholar
  18. Marcus DS, Harms MP, Snyder AZ, Jenkinson M, Wilson JA, Glasser MF, Barch DM, Archie KA, Burgess GC, Ramaratnam M, Hodge M, Horton W, Herrick R, Olsen T, McKay M, House M, Hileman M, Reid E, Harwell J, Coalson T, Schindler T, Elam JS, Curtiss SW, WU-Minn HCP Consortium, Van Essen DC (2013) Human connectome project informatics: quality control, database services, and data visualization. Neuroimage 80:202–219CrossRefPubMedGoogle Scholar
  19. Markram H (2006) The blue brain project. Nat Rev Neurosci 7(2):153–160CrossRefPubMedGoogle Scholar
  20. Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S, Ellisman MH (2003) The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1(4):375–379CrossRefGoogle Scholar
  21. Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson SD, Lamont SP, Gupta A, Ellisman MH (2009) Cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol 161(3):220–231CrossRefGoogle Scholar
  22. Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, Hines M (2003) ModelDB. Neuroinformatics 1(1):135–139PubMedCentralCrossRefPubMedGoogle Scholar
  23. Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schrmann F, Markram H (2011) Channelpedia: an integrative and interactive database for ion channels. Front Neuroinform 5:36PubMedCentralCrossRefPubMedGoogle Scholar
  24. Stephan KE, Kamper L, Bozkurt A, Burns GA, Young MP, Ktter R (2001) Advanced database methodology for the collation of connectivity data on the macaque brain (CoCoMac). Philos Trans R Soc Lond B Biol Sci 356(1412):1159–1186PubMedCentralCrossRefPubMedGoogle Scholar
  25. Tripathy SJ, Savitskaya J, Burton SD, Urban NN, Gerkin RC (2014) NeuroElectro: a window to the world’s Neuron electrophysiology data. Frontiers in Neuroinformatics 8:40Google Scholar
  26. Vijayalakshmi C, Laibe C, Le Novere N (2013) Biomodels database: a repository of mathematical models of biological processes. Methods Mol Biol 1021:189–199CrossRefGoogle Scholar
  27. Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terk-ildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM (2011) The physiome model repository 2. Bioinformatics 27(5):743–744CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Richard C. Gerkin
    • 1
    Email author
  • Shreejoy J. Tripathy
    • 2
  • Sharon Crook
    • 3
  • Jeanette Kotaleski
    • 4
  1. 1.School of Life SciencesArizona State UniversityTempeUSA
  2. 2.Department of BiologyCarnegie Mellon UniversityPittsburghUSA
  3. 3.School of Mathematical and Statistical Sciences and School of Life SciencesArizona State UniversityTempeUSA
  4. 4.School of Computer Science and CommunicationRoyal Institute of TechnologyStockholmSweden