About bookshelf

It is a tool to install a simple database system for curating and keeping track of molecular simulation data useful for a simulation-based laboratory to keep track of its data in a relatively simple and easy way.The application is developed in python in conjunction with a mysql database for the deposition of the trajectories from molecular dynamic simulation to catalogue the large volume of data generated in a research laboratory.The users can search the database using keywords and retrieve the files to analyse the trajectories and rerun the simulation or run an extension of current simulation with modified parameters. The development of such a database will ease the comparison of the results of MD simulation . A web-interface is also developed to have easy access to the metadata.

The source code is made available as a gzipped tar file. To build the application you will need Python (MySQLdb module in Python for connection to database)and MySQL. Full instructions for installation and how to run Bookshelf are available in "Bookshelf_db/docs" folder.

Contact Information

Bookshelf is maintained by Structural Bioinformatics and Computational Biochemistry Unit at the Department of Biochemistry in the University of Oxford.The project was funded by BBSRC.

In case of concerns, questions or problems please contact Dr. Shabana Vohra or Dr. Philip Biggin.


Shabana Vohra, Benjamin A. Hall, Daniel A. Holdbrook, Syma Khalid, and Philip C. Biggin Bookshelf: a simple curation system for the storage of biomolecular simulation data (2010). Database(Oxford) Vol. 2010, Article ID baq033, doi:10.1093/database/baq033

Bug reports

We welcome comments, feature requests and improvements. If you have problem downloading, installing or running Bookshelf, contact by Email.