Systems Science of Biological Dynamics database (SSBD:database)
is an added-value database for biological dynamics.
It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological
objects,
such as single-molecule, cell, tissue, individual, etc., and software tools for analysis.
Quantitative biological data and microscopy images are collected from a variety of species, sources, and
methods.
These include data obtained from both experiments and computational simulations.
Find the dataset from the search box above, or see the dataset list on the
Resources.
SSBD:database started operation in 2013,
under the life science database integration promotion project of the Japan Science and Technology (JST),
National Bioscience Database Center (NBDC).
Currently, it is funded by RIKEN, JST, and
Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and
Technology of Japan (MEXT).
For the overview of the SSBD:database/repository, please refer to the paper,
Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami S. (2016)
"SSBD: a dataset of quantitative data of spatiotemporal dynamics of biological phenomena."
Bioinformatics, 32(22): 3471-3479. https://doi.org/10.1093/bioinformatics/btw417
Systems Science of Biological Dynamics database (SSBD:database)は、生命動態に関する付加価値付きデータベース(added-value
database)です。
本データベースは最先端の技術で取得した高品質の顕微鏡画像データとそれらの画像から画像解析技術を用いて取得した生命動態の定量データ、
計算機シミュレーションを用いて導出した生命科学の定量データ、
およびこれらのデータを解析するためのツールを収集し、共有します。
本データベースは、さまざまな生物種における一分子から細胞、組織、個体などの幅広い生命現象を対象としてます。
SSBD:databaseおよびSSBD:repositoryの概要については、
Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami S. (2016)
"SSBD: a dataset of quantitative data of spationtempral dynamics of biological phenomena."
Bioinformatics, 32(22): 3471-3479.
https://doi.org/10.1093/bioinformatics/btw417 をご参照ください。
SSBD:databaseは専門家によるキュレーションを行い、高品質な顕微鏡画像や定量データを豊富なメタデータ付き提供する
付加価値付きデータベース(added-value database; Ellenberg, J. et
al. (2018) Nat Methods)です。
SSBD:database へのデータ登録は、キュレーターからの提案を主としていますが、
もし登録されたい顕微鏡画像や生命動態のデータがございましたら、SSBD:repositoryの利用をご検討いただくか、
メールにてお問い合わせ下さい。
Calcium response and shape changes in oocyte of C. elegans
DIC image of nuclear division dynamics in C. elegans embryo
TEM image of retinal tissue from human embryonic stem cells
Quantitative Data
Nuclear division dynamics in D. rerio wild-type embryo
Nuclear division dynamics in C. elegans wild-type embryo
Single molecule dynamics in E. coli wild-type
Share your data in SSBD:database
SSBD:database is an added-value database (Ellenberg, J.
et
al. (2018) Nat Methods)
for quantitative data and microscopy images of biological dynamics with expert curation;
therefore, our curators will offer to register your data in SSBD database.
If you have any data of biological dynamics that you would like to deposit,
please consider using SSBD:repository, or contact us
via e-mail.
2022-04-08, SSBD:database the second half of 2021 update
We are pleased to announce the second half of the SSBD 2021 update in the cherry blossom season in Japan. The update includes 755 image datasets (569 GB) and one quantitative dataset (13MB).
The added datasets are 131-Wen-NeuronalNucDyn, 138-Ito-SPBDyn, 164-Ono-NeuPMCA, 170-Tsutsui-HookBM, 172-Yoshida-ERKTracheaDev, 177-Kinjo-cAMPsignalingDyn, 178-konagaya-CellMigration, 179-Kobachi-BLVRAactivity, 180-Watabe-Biosensoractivity, 183-Iwasaki-SpineDyn, 184-Tanaka-SpineDyn, 185-Hoshino-MyotubeCa2Signal, 188-Ipponjima-NHEKsCornification, 189-Kobayashi-NSCsDyn, 190-Iguchi-SpineDyn, 192-Hiroshima-SingleMolDyn, 194-Obashi-SpineDyn, 196-Sueda-GeneExpReg, 202-Miyagawa-ChemotaxisDyn, 203-Tanabe-SingleDyn, 205-Shen-CellPatterning, 206-Miyamoto-CiliaryMorphology, 207-Kuroda-FinMorphology, 211-Hiroshima-EGFRTracking, 212-Kajikawa-GeckoEmbryos, 213-Yoshida-SpindleDyn, 217-Sakai-iRFPactivity.
2021-11-30, SSBD:database the first half of 2021 update
We are pleased to announce the first half of the SSBD 2021 update, which includes 1799 image datasets (8TB) and four quantitative datasets (6MB). We have a plan for the second half of the 2021 update until next spring. Added datasets are 70-Yoshida-KTMTDyn, 72-Kyogoku-CytoplasmNucDyn, 120-Ding-CentromericDyn, 126-Imanishi-CellMorNuCyM, 127-Konishi-ERKDyn, 128-Muta-IECsERKDync, 129-Komatsu-ERKBiosensorActivity, 130-Sano-CellMigrationDyn, 161-Tanaka-MEFMitochondrial, 165-Kinjo-ERKactivity, 166-Takubo-ECsTrajectory, 171-Ochi-Hes1DynNPCs.
2021-05-26, [Press Release] Launch of “NeuroGT Database”, a brain atlas of neurogenic tagging CreER mouse drivers
Drs. Yukako Tohsato and Hiroya Itoga in our SSBD team, together with Prof. Tatsumi Hirata (NIG) and colleagues, developed the “NeuroGT database,” which contains whole-brain image data of tagged neurons based on time of neurogenesis. Through NeuroGT, researchers can find suitable neurogenic tagging driver lines for their research.
https://so.riken.jp/2021/05/26/press-release-launch-of-neurogt-database-a-brain-atlas-of-neurogenic-tagging-creer-mouse-drivers/
2021-05-24, REMBI: Recommended Metadata for Biological Images
Our TL Dr Onami joined discussions on metadata standards in biological image data sharing with an international bioimaging community lead by EMBL-EBI. They propose global metadata guidelines, REMBI: Recommended Metadata for Biological Images. https://so.riken.jp/2021/05/24/rembi-recommended-metadata-for-biological-images/
2021-05-11, [Press Release] Recommendations for global standards of open image data formats and repositories.
TL Dr Shuichi Onami and Prof. Jason Swedlow (University of Dundee, UK) along with Global Bioimaging, an international consortium of the leading experts in bioimaging communities, released recommendations for bioimage data format standards and open access image data repositories. These recommendations contribute to accelerating the development of the bioimaging field through data sharing.
https://so.riken.jp/2021/05/11/sharing-global-standards-of-open-image-date/
2020-12-24, SSBD 2020 Update
SSBD 2020 update, the metadata database fully renewed, and 77 image datasets (7GB) and 4 quantitative datasets are added. We are plaining next database update in a half year for COVID-19 situation.
2020-08-12, A new paper on BD5 is published in PLOS ONE
A new paper "BD5: an open HDF5-based data format to represent quantitative biological dynamics data" is now published in PLOS ONE. https://doi.org/10.1371/journal.pone.0237468