The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide Article Swipe

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Michael Hawrylycz , Maryann E. Martone , Patrick R. Hof , Ed S. Lein , Aviv Regev , Giorgio A. Ascoli , Jan G. Bjaalie , Hong‐Wei Dong , Satrajit Ghosh , Jesse Gillis , Ronna Hertzano , David R. Haynor , Yongsoo Kim , Yufeng Liu , Jeremy A. Miller , Partha P. Mitra , Eran A. Mukamel , David Osumi-Sutherland , Hanchuan Peng , Patrick L. Ray , Raymond Sanchez , Alex Ropelewski , Richard H. Scheuermann , Shawn Zheng Kai Tan , Timothy L. Tickle , Hagen Tilgner , Merina Varghese , Brock A. Wester , Owen White , Brian D. Aevermann , David Allemang , Seth A. Ament , Thomas L. Athey , Pamela Baker , C L Baker , Katherine Baker , Anita Bandrowski , Prajal Bishwakarma , Ambrose Carr , Min Chen , Roni Choudhury , Jonah Cool , Heather H. Creasy , Florence D. D’Orazi , Kylee Degatano , Ben Dichter , Song‐Lin Ding , Tim Dolbeare , Joseph R. Ecker , Rongxin Fang , Jean‐Christophe Fillion‐Robin , Timothy P. Fliss , James C. Gee , Tom Gillespie , Nathan W. Gouwens , Yaroslav O. Halchenko , Nomi L. Harris , Brian R. Herb , Houri Hintiryan , Gregory Hood , S. Horvath , Dorota Jarecka , Shengdian Jiang , Farzaneh Khajouei , Elizabeth Kiernan , Hüseyin Kır , Lauren Kruse , Changkyu Lee , Boudewijn P. F. Lelieveldt , Yang Eric Li , Hanqing Liu , Anup Markuhar , James C. Mathews , Kaylee L. Mathews , Michael I. Miller , Tyler Mollenkopf , Shoaib Mufti , Chris Mungall , Lydia Ng , Joshua Orvis , Maja Puchades , Lei Qu , Joseph P. Receveur , Bing Ren , Nathan Sjoquist , Brian Staats , Carol L. Thompson , Daniel J. Tward , Cindy T. J. van Velthoven , Quanxin Wang , Fangming Xie , Hua Xu , Zizhen Yao , Zhixi Yun , Hongkui Zeng , Guo‐Qiang Zhang , Yun Zhang , W. Jim Zheng , Brian Zingg ·

YOU? · · 2022 · Open Access · · DOI: https://doi.org/10.1101/2022.10.26.513573

Characterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate cell types in controlled ways, and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data generating centers, data archives and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain and demonstration of prototypes for human and non-human primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed, and to accessing and using the BICCN data and its extensive resources, including the BRAIN Cell Data Center (BCDC) which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted by the BICCN toward FAIR (Wilkinson et al. 2016a) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

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Type: preprint
Language: en
Landing Page: https://doi.org/10.1101/2022.10.26.513573
PDF: https://www.biorxiv.org/content/biorxiv/early/2022/10/30/2022.10.26.513573.full.pdf
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Cited By: 7
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Title: The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide

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Language: en

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Publication year: 2022

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Publication date: 2022-10-30

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Authors: Michael Hawrylycz, Maryann E. Martone, Patrick R. Hof, Ed S. Lein, Aviv Regev, Giorgio A. Ascoli, Jan G. Bjaalie, Hong‐Wei Dong, Satrajit Ghosh, Jesse Gillis, Ronna Hertzano, David R. Haynor, Yongsoo Kim, Yufeng Liu, Jeremy A. Miller, Partha P. Mitra, Eran A. Mukamel, David Osumi-Sutherland, Hanchuan Peng, Patrick L. Ray, Raymond Sanchez, Alex Ropelewski, Richard H. Scheuermann, Shawn Zheng Kai Tan, Timothy L. Tickle, Hagen Tilgner, Merina Varghese, Brock A. Wester, Owen White, Brian D. Aevermann, David Allemang, Seth A. Ament, Thomas L. Athey, Pamela Baker, C L Baker, Katherine Baker, Anita Bandrowski, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heather H. Creasy, Florence D. D’Orazi, Kylee Degatano, Ben Dichter, Song‐Lin Ding, Tim Dolbeare, Joseph R. Ecker, Rongxin Fang, Jean‐Christophe Fillion‐Robin, Timothy P. Fliss, James C. Gee, Tom Gillespie, Nathan W. Gouwens, Yaroslav O. Halchenko, Nomi L. Harris, Brian R. Herb, Houri Hintiryan, Gregory Hood, S. Horvath, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth Kiernan, Hüseyin Kır, Lauren Kruse, Changkyu Lee, Boudewijn P. F. Lelieveldt, Yang Eric Li, Hanqing Liu, Anup Markuhar, James C. Mathews, Kaylee L. Mathews, Michael I. Miller, Tyler Mollenkopf, Shoaib Mufti, Chris Mungall, Lydia Ng, Joshua Orvis, Maja Puchades, Lei Qu, Joseph P. Receveur, Bing Ren, Nathan Sjoquist, Brian Staats, Carol L. Thompson, Daniel J. Tward, Cindy T. J. van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhen Yao, Zhixi Yun, Hongkui Zeng, Guo‐Qiang Zhang, Yun Zhang, W. Jim Zheng, Brian Zingg

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Concepts: Computer science, Neuroinformatics, Data science, Profiling (computer programming), Modalities, Visualization, Vulnerability (computing), Data type, Neuroscience, Data mining, Biology, Social science, Computer security, Programming language, Operating system, Sociology

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