Simple re-instantiation of small databases using cloud computing

Tin Wee Tan, Chao Xie, Mark De Silva, Kuan Siong Lim, C. Pawan K Patro, Shen Jean Lim, Kunde Ramamoorthy Govindarajan, Joo Chuan Tong, Khar Heng Choo, Shoba Ranganathan, Asif M. Khan

Research output: Contribution to journalConference paperResearchpeer-review

Abstract

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. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, 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), 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. 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.

LanguageEnglish
Article numberS13
Pages1-4
Number of pages4
JournalBMC Genomics
Volume14
Issue numberSuppl 5
DOIs
Publication statusPublished - 2013
Event Twelfth International Conference on Bioinformatics - Taicang, China, Taicang
Duration: 20 Sep 201322 Sep 2013

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Databases
Computational Biology
Cloud Computing
Online Systems
Publications

Bibliographical note

This version is archived for private and non-commercial use under the terms of this BioMed Central open access license ("license") (see http://www.biomedcentral.com/about/license). The work is protected by copyright and/or other applicable law. Any use of the work other than as authorized under this license is prohibited. For further rights please check the terms of the license, or contact the publisher.

Cite this

Tan, T. W., Xie, C., De Silva, M., Lim, K. S., Patro, C. P. K., Lim, S. J., ... Khan, A. M. (2013). Simple re-instantiation of small databases using cloud computing. BMC Genomics, 14(Suppl 5), 1-4. [S13]. https://doi.org/10.1186/1471-2164-14-S5-S13
Tan, Tin Wee ; Xie, Chao ; De Silva, Mark ; Lim, Kuan Siong ; Patro, C. Pawan K ; Lim, Shen Jean ; Govindarajan, Kunde Ramamoorthy ; Tong, Joo Chuan ; Choo, Khar Heng ; Ranganathan, Shoba ; Khan, Asif M. / Simple re-instantiation of small databases using cloud computing. In: BMC Genomics. 2013 ; Vol. 14, No. Suppl 5. pp. 1-4.
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Tan, TW, Xie, C, De Silva, M, Lim, KS, Patro, CPK, Lim, SJ, Govindarajan, KR, Tong, JC, Choo, KH, Ranganathan, S & Khan, AM 2013, 'Simple re-instantiation of small databases using cloud computing', BMC Genomics, vol. 14, no. Suppl 5, S13, pp. 1-4. https://doi.org/10.1186/1471-2164-14-S5-S13

Simple re-instantiation of small databases using cloud computing. / Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C. Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M.

In: BMC Genomics, Vol. 14, No. Suppl 5, S13, 2013, p. 1-4.

Research output: Contribution to journalConference paperResearchpeer-review

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AU - Tan, Tin Wee

AU - Xie, Chao

AU - De Silva, Mark

AU - Lim, Kuan Siong

AU - Patro, C. Pawan K

AU - Lim, Shen Jean

AU - Govindarajan, Kunde Ramamoorthy

AU - Tong, Joo Chuan

AU - Choo, Khar Heng

AU - Ranganathan, Shoba

AU - Khan, Asif M.

N1 - This version is archived for private and non-commercial use under the terms of this BioMed Central open access license ("license") (see http://www.biomedcentral.com/about/license). The work is protected by copyright and/or other applicable law. Any use of the work other than as authorized under this license is prohibited. For further rights please check the terms of the license, or contact the publisher.

PY - 2013

Y1 - 2013

N2 - 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. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, 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), 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. 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.

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Tan TW, Xie C, De Silva M, Lim KS, Patro CPK, Lim SJ et al. Simple re-instantiation of small databases using cloud computing. BMC Genomics. 2013;14(Suppl 5):1-4. S13. https://doi.org/10.1186/1471-2164-14-S5-S13