Publications

SSBD (Systems Science of Biological Dynamics)

  • Yukako Tohsato, Kenneth H. L. Ho, Koji Kyoda, Shuichi Onami (2016)
    SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena,
    Bioinformatics, Volume 32, Issue 22, 15 November 2016, Pages 3471–3479, https://doi.org/10.1093/bioinformatics/btw417

BDML (Biological Dynamics Markup Language) and BD5

  • Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami (2020)
    BD5: An open HDF5-based data format to represent quantitative biological dynamics data,
    PLOS ONE, Volume 15, Issue 8, August 2020, Pages e0237468, https://doi.org/10.1371/journal.pone.0237468.
  • Koji Kyoda, Yukako Tohsato, Kenneth H. L. Ho, Shuichi Onami (2015)
    Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data ,
    Bioinformatics, Volume 31, Issue 7, 1 April 2015, Pages 1044–1052, https://doi.org/10.1093/bioinformatics/btu767

Global Standards

  • Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C Darrow, Jan Ellenberg, David Grunwald, Jean-Karim Hériché, Andrii Iudin, Gabriel G Martins, Terry Meehan, Kedar Narayan, Ardan Patwardhan, Matthew Robert Geoffrey Russell, Helen R Saibil, Caterina Strambio-De-Castillia, Jason R Swedlow, Christian Tischer, Virginie Uhlmann, Paul Verkade, Mary Barlow, Omer Bayraktar, Ewan Birney, Cesare Catavitello, Christopher Cawthorne, Stephan Wagner-Conrad, Elizabeth Duke, Perrine Paul-Gilloteaux, Emmanuel Gustin, Maria Harkiolaki, Pasi Kankaanpää, Thomas Lemberger, Jo McEntyre, Josh Moore, Andrew W Nicholls, Shuichi Onami, Helen Parkinson, Maddy Parsons, Marina Romanchikova, Nicholas Sofroniew, Jim Swoger, Nadine Utz, Lenard M Voortman, Frances Wong, Peijun Zhang, Gerard J Kleywegt, Alvis Brazma (2021)
    REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
    Nature methods, 10.1038/s41592-021-01166-8. Advance online publication. https://doi.org/10.1038/s41592-021-01166-8
  • Jason R. Swedlow, Pasi Kankaanpää, Ugis Sarkans, Wojtek Goscinski, Graham Galloway, Leonel Malacrida, Ryan P. Sullivan, Steffen Härtel, Claire M. Brown, Christopher Wood, Antje Keppler, Federica Paina, Ben Loos, Sara Zullino, Dario Livio Longo, Silvio Aime, Shuichi Onami (2021)
    A global view of standards for open image data formats and repositories.
    Nature methods, 10.1038/s41592-021-01113-7. Advance online publication. https://doi.org/10.1038/s41592-021-01113-7

Sister databases (Powered by SSBD)

NeuroGT database

  • Tatsumi Hirata, Yukako Tohsato, Hiroya Itoga, Go Shioi, Hiroshi Kiyonari, Sanae Oka, Toshihiko Fujimori, Shuichi Onami (2021)
    NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons,
    Cell Reports Methods, 100012, ISSN 2667-2375, https://doi.org/10.1016/j.crmeth.2021.100012

Movies

口頭発表セッション「バイオイメージングデータのグローバルなデータ共有システムの構築」 @ トーゴーの日シンポジウム2022 (in Japanese)

トーゴーの日シンポジウム2022 ライトニングトーク ポスター番号43 (in Japanese)

トーゴーの日シンポジウム2022 ライトニングトーク ポスター番号42 (in Japanese)

イメージングデータベースに画像を登録し、画像を活用する @ AJACSオンライン12 (in Japanese)

BD5: an open format for representing quantitative biological dynamics data - Koji Kyoda, RIKEN BDR

糸賀裕弥, SSBD, トーゴーの日シンポジウム2021 ライトニングトーク (in Japanese)

Hiroya Itoga, SSBD:database and SSBD:repository, OME Community Meeting 2021 Flash Talk

BDZ: Zarr-based format of quantitative biological dynamics data (OME Community Meeting 2021)

糸賀裕弥, SSBD, トーゴーの日シンポジウム2020 ライトニングトーク (in Japanese)

SSBD:database and SSBD:repository for sharing quantitative biosystems dynamics data and bioimaging data, Shuichi Onami, RIKEN

SSBD: 細胞・発生画像情報と生命動態情報の統合データベース@第41回日本分子生物学会年会 (in Japanese)

【トーゴーの日シンポジウム2017】生命動態情報と細胞・発生画像情報の統合データベースの現状と今後の展開 (in Japanese)

Introducing SSBD Database