Highlights from the Era of Open Source Web-Based Tools

被引：14

作者：

Anderson, Kristin R. ^{[1
,2
,3
,4
,5
,6
]}

Harris, Julie A. ^{[7
]}

Ng, Lydia ^{[7
]}

Prins, Pjotr ^{[8
]}

Memar, Sara ^{[9
]}

Ljungquist, Bengt ^{[10
,11
]}

Furth, Daniel ^{[12
]}

Williams, Robert W. ^{[8
]}

Ascoli, Giorgio A. ^{[10
,11
]}

Dumitriu, Dani ^{[1
,2
,3
,4
,5
,6
]}

机构：

[1] Columbia Univ, Dept Pediat, New York, NY 10032 USA

[2] Columbia Univ, Dept Psychiat, New York, NY 10032 USA

[3] New York State Psychiat Inst & Hosp, Div Dev Psychobiol, New York, NY 10032 USA

[4] Columbia Univ, Sackler Inst Dev Psychobiol, New York, NY 10032 USA

[5] Columbia Univ, Columbia Populat Res Ctr, New York, NY 10027 USA

[6] Columbia Univ, Zuckerman Inst, New York, NY 10027 USA

[7] Allen Inst Brain Sci, Seattle, WA 98109 USA

[8] Univ Tennessee, Hlth Sci Ctr, Ctr Integrat & Translat Genom, Dept Genet Genom & Informat, Memphis, TN 38163 USA

[9] Western Univ, Schulich Sch Med & Dent, Robarts Res Inst, BrainsCAN, London, ON N6A 3K7, Canada

[10] George Mason Univ, Ctr Neural Informat Struct & Plastic, Krasnow Inst Adv Study & Dept Bioengn, Fairfax, VA 22030 USA

[11] George Mason Univ, Volgenau Sch Engn, Dept Bioengn, Fairfax, VA 22030 USA

[12] Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA

来源：

JOURNAL OF NEUROSCIENCE | 2021年 / 41卷 / 05期

基金：

美国国家卫生研究院;

关键词：

online repositories; open access; open science; open source; neuroscience; web-based tools; RESEARCH DOMAIN CRITERIA; DIGITAL RECONSTRUCTIONS; GENE-EXPRESSION; BRAIN; FRAMEWORK; CONNECTIVITY; RDOC; NEUROSCIENCE; CONNECTOME; SYSTEM;

D O I：

10.1523/JNEUROSCI.1657-20.2020

中图分类号：

Q189 [神经科学];

学科分类号：

071006 ;

摘要：

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.

引用

页码：927 / 936

页数：10

共 104 条

[11] The critical importance of basic animal research for neuropsychiatric disorders [J].

Bale, Tracy L. ;

Abel, Ted ;

Akil, Huda ;

Carlezon, William A., Jr. ;

Moghaddam, Bita ;

Nestler, Eric J. ;

Ressler, Kerry J. ;

Thompson, Scott M. .

NEUROPSYCHOPHARMACOLOGY, 2019, 44 (08) :1349-1353

[12] MouseBytes, an open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment [J].

Beraldo, Flavio H. ;

Palmer, Daniel ;

Memar, Sara ;

Wasserman, David I. ;

Lee, Wai-Jane V. ;

Liang, Shuai ;

Creighton, Samantha D. ;

Kolisnyk, Benjamin ;

Cowan, Matthew F. ;

Mels, Justin ;

Masood, Talal S. ;

Fodor, Chris ;

Al-Onaizi, Mohammed A. ;

Bartha, Robert ;

Gee, Tom ;

Saksida, Lisa M. ;

Bussey, Timothy J. ;

Strother, Stephen S. ;

Prado, Vania F. ;

Winters, Boyer D. ;

Prado, Marco A. M. .

ELIFE, 2019, 8

[13] Containers and Cloud: From LXC to Docker to Kubernetes [J].

Bernstein, David .

IEEE CLOUD COMPUTING, 2014, 1 (03) :81-84

[14] An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology [J].

Bijari K. ;

Akram M.A. ;

Ascoli G.A. .

Brain Informatics, 2020, 7 (01)

[15] Toward discovery science of human brain function [J].

Biswal, Bharat B. ;

Mennes, Maarten ;

Zuo, Xi-Nian ;

Gohel, Suril ;

Kelly, Clare ;

Smith, Steve M. ;

Beckmann, Christian F. ;

Adelstein, Jonathan S. ;

Buckner, Randy L. ;

Colcombe, Stan ;

Dogonowski, Anne-Marie ;

Ernst, Monique ;

Fair, Damien ;

Hampson, Michelle ;

Hoptman, Matthew J. ;

Hyde, James S. ;

Kiviniemi, Vesa J. ;

Kotter, Rolf ;

Li, Shi-Jiang ;

Lin, Ching-Po ;

Lowe, Mark J. ;

Mackay, Clare ;

Madden, David J. ;

Madsen, Kristoffer H. ;

Margulies, Daniel S. ;

Mayberg, Helen S. ;

McMahon, Katie ;

Monk, Christopher S. ;

Mostofsky, Stewart H. ;

Nagel, Bonnie J. ;

Pekar, James J. ;

Peltier, Scott J. ;

Petersen, Steven E. ;

Riedl, Valentin ;

Rombouts, Serge A. R. B. ;

Rypma, Bart ;

Schlaggar, Bradley L. ;

Schmidt, Sein ;

Seidler, Rachael D. ;

Siegle, Greg J. ;

Sorg, Christian ;

Teng, Gao-Jun ;

Veijola, Juha ;

Villringer, Arno ;

Walter, Martin ;

Wang, Lihong ;

Weng, Xu-Chu ;

Whitfield-Gabrieli, Susan ;

Williamson, Peter ;

Windischberger, Christian .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (10) :4734-4739

[16] A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale [J].

Bohland, Jason W. ;

Wu, Caizhi ;

Barbas, Helen ;

Bokil, Hemant ;

Bota, Mihail ;

Breiter, Hans C. ;

Cline, Hollis T. ;

Doyle, John C. ;

Freed, Peter J. ;

Greenspan, Ralph J. ;

Haber, Suzanne N. ;

Hawrylycz, Michael ;

Herrera, Daniel G. ;

Hilgetag, Claus C. ;

Huang, Z. Josh ;

Jones, Allan ;

Jones, Edward G. ;

Karten, Harvey J. ;

Kleinfeld, David ;

Kotter, Rolf ;

Lester, Henry A. ;

Lin, John M. ;

Mensh, Brett D. ;

Mikula, Shawn ;

Panksepp, Jaak ;

Price, Joseph L. ;

Safdieh, Joseph ;

Saper, Clifford B. ;

Schiff, Nicholas D. ;

Schmahmann, Jeremy D. ;

Stillman, Bruce W. ;

Svoboda, Karel ;

Swanson, Larry W. ;

Toga, Arthur W. ;

Van Essen, David C. ;

Watson, James D. ;

Mitra, Partha P. .

PLOS COMPUTATIONAL BIOLOGY, 2009, 5 (03)

[17]

Bonapersona V, 2019, BIORXIV, DOI [10.1101/, DOI 10.1101/]

[18] Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function [J].

Chesler, EJ ;

Lu, L ;

Shou, SM ;

Qu, YH ;

Gu, J ;

Wang, JT ;

Hsu, HC ;

Mountz, JD ;

Baldwin, NE ;

Langston, MA ;

Threadgill, DW ;

Manly, KF ;

Williams, RW .

NATURE GENETICS, 2005, 37 (03) :233-242

[19] Genetic correlates of gene expression in recombinant inbred strains - A relational model system to explore neurobehavioral phenotypes [J].

Chesler, EJ ;

Wang, JT ;

Lu, L ;

Qu, YH ;

Manly, KF ;

Williams, RW .

NEUROINFORMATICS, 2003, 1 (04) :343-357

[20] Synchronization dependent on spatial structures of a mesoscopic whole-brain network [J].

Choi, Hannah ;

Mihalas, Stefan .

PLOS COMPUTATIONAL BIOLOGY, 2019, 15 (04)

← 1 2 3 4 5 6 7 8 9 10 →