Public Repository

Last pushed: 3 years ago
Short Description
OpenSSBD - Open source version of SSBD (Systems Science of Biological Dynamics) database engine
Full Description


OpenSSBD is an open-source version of SSBD. It is mainly created for biologists and others for storing and retrieving quantitative data of biological dynamics.

Systems Science of Biological Dynamics (SSBD) database provides a rich set of resources for analyzing spatiotemporal dynamics of biologcial objects, such as single molecules, nuclei, and gene expressed cells. OpenSSBD provides the backend database engine for storing and retrieving quantitative biological data which can be collected from a variety of species, sources and methods. Quantitative numerical data are represented in a new Biological Dynamics Markup Language (BDML). The new data format allows users to exchange, store, compare and analyze data through the OpenSSBD database engine.


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 31(7): 1044-1052


  1. Prerequisite Install docker

  2. Get a copy of the image from from Docker Hub
    # docker pull openssbd/public
    This image includes OpenSSBD database engine together with 1 dataset "Quantitative information about nuclear division dynamics in wild-type embryo of C. elegans" (see Reference)

  3. Examine the image in docker
    # docker images

  4. Start the container - mapping and using port 8282
    # docker run -i -t -p 8282:8282 openssbd/public:latest /bin/bash

  5. Setting up within the container

    1. Start up postgresql
      root@[container]:~/# /etc/init.d/postgresql start
    2. Start up OpenSSBD
      root@[container]:~/# cd /usr/src/OpenSSBD
      root@[container]:/usr/src/OpenSSBD/# python runserver 0:8282
    3. OpenSSBD can now be accessed by a web browser http://localhost:8282

      note: For Windows and MacOS users, you need to find out the IP address of the Docker-Machine using the command below. You can then access it on the web browser by using http://[ip address]:8282

    # docker-machine ip default

For more details:

Docker Pull Command