SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

Bioinformatics. 2016 Nov 15;32(22):3471-3479. doi: 10.1093/bioinformatics/btw417. Epub 2016 Jul 13.


Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis.

Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis.

Availability and implementation: SSBD is accessible at CONTACT:

MeSH terms

  • Animals
  • Biological Phenomena*
  • Databases, Factual*
  • Humans
  • Microscopy
  • Software