SSBD:database
Introduction
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.
See Citation Policies（PDF) for citation instructions.
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
Samples
Microscopy Images
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.
See image_submission_guidelines_en
(PDF) for image
submission,
and also see quantitative_data_submission_guidelines_en
(PDF) for quantitative data submission.
News
-
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 - Older news...
