SSBD: Systems Science of Biological Dynamics

What is SSBD?

Systems Science of Biological Dynamics (SSBD) is an open database; consists of the SSBD:database - added-value database and SSBD:repository - archive service for sharing and reusing bioimaging data and quantitative data of biological dynamics data with spatiotemporal information.

SSBD:database started operation in 2013 under the Life Science Database Integration Project National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST).
Currently, this database is supported by JST NBDC Grant Number JPMJND2201, Life Science Database Integration Project (Database Integration Coordination Program), Department of NBDC Program, JST. The database is also funded by RIKEN, Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT), and Strategic Basic Research Programs (CREST), JST.

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. doi:10.1093/bioinformatics/btw417

Images are stored in original or raw file format and are downloadable. SSBD:database utilises OMERO internally to manage and preview microscopy images.

Quantitative data are represented in unified data format, the BDML (Biological Dynamics Markup Language) and BD5 (data format based on HDF5 format). We provide tools for BDML/BD5 and data visualization on the web.

SSBD also provides a REST API allowing 3rd party applications, such as R, Python, Java, and C/C++, to access the data directly from the database. In addition, SSBD provides Resource Description Framework (RDF) formatted meta-information of the quantitative data and microscopy images at RIKEN Meta Database and NBDC RDF Portal.

Database Search

You can search quantitative biological dynamical data and microscopy images in SSBD using Data Search and Image Search, respectively. To search by organism, select Organism from the fields, and then enter an organism's name. To search for other fields, please use the pull-down menus to select a field label on the advanced search. 'All fields' are searched by default. You can search the following fields:

  • title: Short title for the project
  • description: Short summary of the content of the project, dataset, and how they can be interpreted.
  • organism: Name of the scientific name of organism.
  • datatype: Type of data, e.g. single molecule dynamics.
  • paper: Author name, title, and journal for related paper.
  • contact: Contact information, name, organization, etc.
  • contributors: Contributors for the dataset.

The search term makes no distinction between capital and lowercase letters in Data Search. A search for "C. elegans" will find "c. elegans" as well and also "C. ELEGANS".

Summary View of BDML

When you select the URLs within searching results, you will see a summary of the selected BDML-file. The URL are constructed by combining '' and a unique ID of the selected BDML file: e.g. .

A JavaScript viewer is being implemented for synchronous viewing of quantitative information through a web browser. BDML and PDPML files are available for download via http. These URLs can be used as scripted for batch downloads using utilities such as wget. When the source images were stored in SSBD:database, image files were compressed into a single zip archive and they are available for download via http. You can access it through the 'Summary of Images' section. You can find a direct link to datasets using a URL in OMERO.web in the 'Summary' view. For example, to link to Dataset 15 on OMERO.web hosted at the full URL will be: .

BDML page summary
BDML page summary


OMERO.server is a global standard for managing and storing biological microscope images. OMERO.web is a basic Web application which allows for the viewing images, datasets, and projects from the OMERO.server. If you cannot view images on the OMERO.web, please click on the drop-down arrow to the right of the 'Public user' on the bar above the data tree (see the enclosed image for details). Please select 'Public' group and 'public data' owner in the group to view the imaegs. Please refer to OME website and user guide for OMERO.web in OMERO 5.4.4 documentation for more details.

OMERO group selection
OMERO group selection


Database Team 2019
Database Team 2019