Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

This article is part of the supplement: Twelfth International Conference on Bioinformatics (InCoB2013): Computational Biology

Open Access Research

Simple re-instantiation of small databases using cloud computing

Tin Wee Tan1*, Chao Xie2, Mark De Silva2, Kuan Siong Lim2, C Pawan K Patro1, Shen Jean Lim1, Kunde Ramamoorthy Govindarajan1, Joo Chuan Tong13, Khar Heng Choo1, Shoba Ranganathan4 and Asif M Khan56*

Author Affiliations

1 Department of Biochemistry, National University of Singapore (NUS), Singapore

2 Bioinformatics Centre, Life Science Institute, NUS, Singapore

3 Computing Science Department, Institute of High Performance Computing, Singapore

4 Department of Chemistry and Biomolecular Sciences, Macquarie University, Australia

5 Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, USA

6 Perdana University Graduate School of Medicine, Selangor, Malaysia

For all author emails, please log on.

BMC Genomics 2013, 14(Suppl 5):S13  doi:10.1186/1471-2164-14-S5-S13

Published: 16 October 2013

Abstract

Background

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress.

Results

We describe a Web-accessible system, available online at http://biodb100.apbionet.org webcite, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com webcite), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases.

Conclusions

Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Keywords:
Database archival; Re-instantiation; Cloud computing; BioSLAX; biodb100; MIABi