BioVLAB-MMIA: A cloud environment for microrna and mRNA integrated analysis (MMIA) on amazon EC2

Hyungro Lee, Youngik Yang, Heejoon Chae, Seungyoon Nam, Donghoon Choi, Patanachai Tangchaisin, Chathura Herath, Suresh Marru, Kenneth P. Nephew, Sun Kim

Research output: Contribution to journalArticle

18 Scopus citations

Abstract

MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research. However, the ability to conduct genome-wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extended the BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by the XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an as needed basis; 4) distributed orchestration supports complex and long running workflows asynchronously. We believe that BioVLAB-MMIA will be an easy-to-use computing environment for researchers who plan to perform genome-wide microRNA-mRNA (gene) integrated analysis tasks.

Original languageEnglish (US)
Article number6298043
Pages (from-to)266-272
Number of pages7
JournalIEEE Transactions on Nanobioscience
Volume11
Issue number3
DOIs
StatePublished - Sep 26 2012

Keywords

  • Cloud computing
  • microRNAs
  • mRNAs
  • scientific workflows

ASJC Scopus subject areas

  • Pharmaceutical Science
  • Medicine (miscellaneous)
  • Bioengineering
  • Computer Science Applications
  • Biotechnology
  • Biomedical Engineering
  • Electrical and Electronic Engineering

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    Lee, H., Yang, Y., Chae, H., Nam, S., Choi, D., Tangchaisin, P., Herath, C., Marru, S., Nephew, K. P., & Kim, S. (2012). BioVLAB-MMIA: A cloud environment for microrna and mRNA integrated analysis (MMIA) on amazon EC2. IEEE Transactions on Nanobioscience, 11(3), 266-272. [6298043]. https://doi.org/10.1109/TNB.2012.2212030