Summary
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.
Reference
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 http://bioinformatics.oxfordjournals.org/content/31/7/1044.
Installation
Prerequisite Install docker
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)Examine the image in docker
# docker images
Start the container - mapping and using port 8282
# docker run -i -t -p 8282:8282 openssbd/public:latest /bin/bash
Setting up within the container
- Start up postgresql
root@[container]:~/# /etc/init.d/postgresql start
- Start up OpenSSBD
root@[container]:~/# cd /usr/src/OpenSSBD
root@[container]:/usr/src/OpenSSBD/# python manage.py runserver 0:8282
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
- Start up postgresql
For more details: https://github.com/openssbd/OpenSSBD