Databases and Data Repositories in Computational Neuroscience: Overview
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.
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...
- 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):e1000815PubMedCentralPubMedGoogle Scholar
- 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
- Laird AR, Lancaster JL, Fox PT (2004) Brainmap: the social evolution of a functional neuroimaging database. Neuroinformatics 3:65–78Google Scholar
- Larson SD, Martone ME (2009) Ontologies for neuroscience: what are they and what are they good for? Front Neurosci 3:1Google Scholar
- 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 4:92PubMedCentralPubMedGoogle Scholar
- 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 80:202–219PubMedGoogle Scholar
- 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):375–379Google Scholar
- 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):220–231Google Scholar
- 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
- Vijayalakshmi C, Laibe C, Le Novere N (2013) Biomodels database: a repository of mathematical models of biological processes. Methods Mol Biol 1021:189–199Google Scholar