Literature DB >> 33472826

Highlights from the Era of Open Source Web-Based Tools.

Kristin R Anderson1,2,3,4,5, Julie A Harris6, Lydia Ng6, Pjotr Prins7, Sara Memar8, Bengt Ljungquist9, Daniel Fürth10, Robert W Williams7, Giorgio A Ascoli9, Dani Dumitriu11,2,3,4,5.   

Abstract

High digital connectivity and a focus on reproducibility are contributing to an open science revolution in neuroscience. Repositories and platforms have emerged across the whole spectrum of subdisciplines, paving the way for a paradigm shift in the way we share, analyze, and reuse vast amounts of data collected across many laboratories. Here, we describe how open access web-based tools are changing the landscape and culture of neuroscience, highlighting six free resources that span subdisciplines from behavior to whole-brain mapping, circuits, neurons, and gene variants.
Copyright © 2021 the authors.

Keywords:  neuroscience; online repositories; open access; open science; open source; web-based tools

Year:  2021        PMID: 33472826      PMCID: PMC7880282          DOI: 10.1523/JNEUROSCI.1657-20.2020

Source DB:  PubMed          Journal:  J Neurosci        ISSN: 0270-6474            Impact factor:   6.167


  93 in total

1.  The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

Authors:  Luis Marenco; Giorgio A Ascoli; Maryann E Martone; Gordon M Shepherd; Perry L Miller
Journal:  Neuroinformatics       Date:  2008-10-31

2.  Diverse Central Projection Patterns of Retinal Ganglion Cells.

Authors:  Emily M Martersteck; Karla E Hirokawa; Mariah Evarts; Amy Bernard; Xin Duan; Yang Li; Lydia Ng; Seung W Oh; Benjamin Ouellette; Joshua J Royall; Michelle Stoecklin; Quanxin Wang; Hongkui Zeng; Joshua R Sanes; Julie A Harris
Journal:  Cell Rep       Date:  2017-02-21       Impact factor: 9.423

3.  GeneNetwork: A Toolbox for Systems Genetics.

Authors:  Megan K Mulligan; Khyobeni Mozhui; Pjotr Prins; Robert W Williams
Journal:  Methods Mol Biol       Date:  2017

Review 4.  Quantitative investigations of axonal and dendritic arbors: development, structure, function, and pathology.

Authors:  Ruchi Parekh; Giorgio A Ascoli
Journal:  Neuroscientist       Date:  2014-06-27       Impact factor: 7.519

5.  The touchscreen operant platform for assessing executive function in rats and mice.

Authors:  Adam C Mar; Alexa E Horner; Simon R O Nilsson; Johan Alsiö; Brianne A Kent; Chi Hun Kim; Andrew Holmes; Lisa M Saksida; Timothy J Bussey
Journal:  Nat Protoc       Date:  2013-09-19       Impact factor: 13.491

6.  Conserved properties of dendritic trees in four cortical interneuron subtypes.

Authors:  Yoshiyuki Kubota; Fuyuki Karube; Masaki Nomura; Allan T Gulledge; Atsushi Mochizuki; Andreas Schertel; Yasuo Kawaguchi
Journal:  Sci Rep       Date:  2011-09-13       Impact factor: 4.379

7.  Topic choice contributes to the lower rate of NIH awards to African-American/black scientists.

Authors:  Travis A Hoppe; Aviva Litovitz; Kristine A Willis; Rebecca A Meseroll; Matthew J Perkins; B Ian Hutchins; Alison F Davis; Michael S Lauer; Hannah A Valantine; James M Anderson; George M Santangelo
Journal:  Sci Adv       Date:  2019-10-09       Impact factor: 14.136

8.  A null model of the mouse whole-neocortex micro-connectome.

Authors:  Michael W Reimann; Michael Gevaert; Ying Shi; Huanxiang Lu; Henry Markram; Eilif Muller
Journal:  Nat Commun       Date:  2019-08-29       Impact factor: 14.919

9.  A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.

Authors:  Jason W Bohland; Caizhi Wu; Helen Barbas; Hemant Bokil; Mihail Bota; Hans C Breiter; Hollis T Cline; John C Doyle; Peter J Freed; Ralph J Greenspan; Suzanne N Haber; Michael Hawrylycz; Daniel G Herrera; Claus C Hilgetag; Z Josh Huang; Allan Jones; Edward G Jones; Harvey J Karten; David Kleinfeld; Rolf Kötter; Henry A Lester; John M Lin; Brett D Mensh; Shawn Mikula; Jaak Panksepp; Joseph L Price; Joseph Safdieh; Clifford B Saper; Nicholas D Schiff; Jeremy D Schmahmann; Bruce W Stillman; Karel Svoboda; Larry W Swanson; Arthur W Toga; David C Van Essen; James D Watson; Partha P Mitra
Journal:  PLoS Comput Biol       Date:  2009-03-27       Impact factor: 4.475

10.  Module for SWC neuron morphology file validation and correction enabled for high throughput batch processing.

Authors:  Damien M O'Halloran
Journal:  PLoS One       Date:  2020-01-23       Impact factor: 3.240

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  1 in total

1.  A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy.

Authors:  Juan C Sanchez-Arias; Micaël Carrier; Simona D Frederiksen; Olga Shevtsova; Chloe McKee; Emma van der Slagt; Elisa Gonçalves de Andrade; Hai Lam Nguyen; Penelope A Young; Marie-Ève Tremblay; Leigh Anne Swayne
Journal:  Front Neuroanat       Date:  2021-12-06       Impact factor: 3.856

  1 in total

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