NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF

Neuroinformatics
Maryam HalaviGiorgio A Ascoli

Abstract

Neuronal morphology affects network connectivity, plasticity, and information processing. Uncovering the design principles and functional consequences of dendritic and axonal shape necessitates quantitative analysis and computational modeling of detailed experimental data. Digital reconstructions provide the required neuromorphological descriptions in a parsimonious, comprehensive, and reliable numerical format. NeuroMorpho.Org is the largest web-accessible repository service for digitally reconstructed neurons and one of the integrated resources in the Neuroscience Information Framework (NIF). Here we describe the NeuroMorpho.Org approach as an exemplary experience in designing, creating, populating, and curating a neuroscience digital resource. The simple three-tier architecture of NeuroMorpho.Org (web client, web server, and relational database) encompasses all necessary elements to support a large-scale, integrate-able repository. The data content, while heterogeneous in scientific scope and experimental origin, is unified in format and presentation by an in house standardization protocol. The server application (MRALD) is secure, customizable, and developer-friendly. Centralized processing and expert annotation yields a co...Continue Reading

References

Jan 28, 2009·Journal of Computational Neuroscience·Anthony R KellemsSteven J Cox
Mar 20, 2010·Journal of Computational Neuroscience·Anthony R KellemsSteven J Cox
Jul 29, 2009·Neuroinformatics·Todd A Gillette, John J Grefenstette
May 23, 2012·Neuroinformatics·Krissia ZawadzkiLuciano da Fontoura Costa
Oct 19, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Kerry M BrownGiorgio A Ascoli
Oct 24, 2008·Neuroinformatics·Daniel GardnerRobert W Williams
Feb 1, 2011·The Journal of Comparative Neurology·Kazunori ShinomiyaKei Ito
Jun 29, 2010·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Erik Meijering
Mar 9, 2011·IEEE Transactions on Visualization and Computer Graphics·Sébastien LasserreHenry Markram
Mar 1, 2015·Journal of Neuroscience Methods·Henrique Ferraz de ArrudaLuciano da Fontoura Costa
Jun 29, 2014·The Neuroscientist : a Review Journal Bringing Neurobiology, Neurology and Psychiatry·Ruchi Parekh, Giorgio A Ascoli
Oct 9, 2015·PLoS Biology·Giorgio A Ascoli
Feb 1, 2017·Nature Methods·Giorgio A AscoliRubén Armañanzas
Aug 19, 2016·Journal of Neurophysiology·Mara Almog, Alon Korngreen
Jul 12, 2013·Journal of Neurophysiology·R C EvansK T Blackwell
Apr 15, 2020·ELife·Alexander S BatesGregory Sxe Jefferis
Jul 24, 2018·Computational Intelligence and Neuroscience·Maryamossadat Aghili, Ruogu Fang
Feb 28, 2018·Scientific Data·Masood A AkramGiorgio A Ascoli
Jan 24, 2018·Scientific Data·Sumit NandaGiorgio A Ascoli
Nov 17, 2016·Frontiers in Neuroanatomy·Xavier VasquesLaura Cif
Aug 24, 2019·Frontiers in Neuroinformatics·Raghu Sesha IyengarMohan Raghavan

Citations

Jul 25, 1996·Nature·Z F Mainen, Terrence J Sejnowski
Jun 1, 1997·Current Opinion in Neurobiology·J Eilers, A Konnerth
Nov 20, 1998·Journal of Neuroscience Methods·R C CannonH V Wheal
May 24, 2000·Progress in Neurobiology·M Tissot, R F Stocker
Oct 29, 2000·Science·Idan Segev, Michael London
Feb 13, 2001·Journal of Neurophysiology·P VetterMichael Häusser
Aug 6, 2002·Journal of Structural Biology·Maryann E MartoneMark H Ellisman
Feb 8, 2005·Genome Biology·Jonathan BardMichael Ashburner
May 11, 2005·Journal of Neurobiology·Allan T GulledgeGreg J Stuart
Jul 22, 2005·Annual Review of Neuroscience·Michael London, Michael Häusser
Jan 21, 2006·Current Opinion in Neurobiology·Anirvan Ghosh, Christine E Holt
Mar 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Beth L ChenDmitri B Chklovskii
Mar 23, 2006·Nature Reviews. Neuroscience·Giorgio A Ascoli
Sep 1, 2006·Neuroinformatics·Giorgio A Ascoli
Dec 21, 2006·The Journal of Comparative Neurology·Mihail Bota, Larry W Swanson
Apr 13, 2007·Journal of Neurophysiology·Klaus M Stiefel, Terrence J Sejnowski
Jun 15, 2007·Theoretical Biology & Medical Modelling·Hermann CuntzIdan Segev
Jun 22, 2007·Brain Research Reviews·Mihail Bota, Larry W Swanson
Aug 31, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Giorgio A AscoliMaryam Halavi
Jan 11, 2008·Journal of Neurophysiology·Dan Bar-Yehuda, Alon Korngreen
Feb 29, 2008·Journal of Neurophysiology·Quan Wen, Dmitri B Chklovskii
Oct 24, 2008·Neuroinformatics·Daniel GardnerRobert W Williams
Nov 1, 2008·Frontiers in Neuroinformatics·Stephen D LarsonMaryann E Martone
Nov 1, 2008·Neuroinformatics·William J BugMaryann E Martone

Related Concepts

Twitter Messaging
Complement System Proteins
Meta Analysis (Statistical Procedure)
Science of Morphology
Neurons
Neuroanatomy
Computer Programs and Programming
Neuronal
Dendrites
Information Extraction

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.