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

doi:10.1186/1471-2164-14-S5-S13

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

^*Corresponding author for this work

Research output: Contribution to journal › Conference paper › peer-review

2 Citations (Scopus)

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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.

Original language	English
Article number	S13
Pages (from-to)	1-4
Number of pages	4
Journal	BMC Genomics
Volume	14
Issue number	Suppl 5
DOIs	https://doi.org/10.1186/1471-2164-14-S5-S13
Publication status	Published - 2013
Event	Twelfth International Conference on Bioinformatics - Taicang, China, Taicang Duration: 20 Sep 2013 → 22 Sep 2013

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.

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title = "Simple re-instantiation of small databases using cloud computing",

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.",

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

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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 journal › Conference paper › peer-review

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T1 - Simple re-instantiation of small databases using cloud computing

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.

AB - 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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U2 - 10.1186/1471-2164-14-S5-S13

DO - 10.1186/1471-2164-14-S5-S13

M3 - Conference paper

C2 - 24564380

AN - SCOPUS:84908217218

VL - 14

SP - 1

EP - 4

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - Suppl 5

M1 - S13

T2 - Twelfth International Conference on Bioinformatics

Y2 - 20 September 2013 through 22 September 2013

ER -

Simple re-instantiation of small databases using cloud computing

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