BioVLAB-MMIA

A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Micro RNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As vast amounts of micro RNA expression profile data are now publicly available, the integration of those data sets with gene expression profiles represents an extremely active area of life science research. However, the ability to conduct genome-wide micro RNA-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 extending BioVLAB cloud workbench to develop an environment for the integrated analysis of micro RNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by 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.

Original languageEnglish
Title of host publicationProceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
Pages494-499
Number of pages6
DOIs
StatePublished - 2011
Event2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Other

Other2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Fingerprint

Cloud computing
RNA
MicroRNAs
Workflow
Messenger RNA
Genes
Developmental Biology
Informatics
Biological Science Disciplines
Bioinformatics
Computational Biology
Transcriptome
Gene expression
Computer science
Genome
Cloud Computing
Research
Neoplasms
Datasets

Keywords

  • Cloud computing
  • microRNAs
  • mRNAs
  • Scientific workflows

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Lee, H., Yang, Y., Chae, H., Nam, S., Choi, D., Tangchaisin, P., ... Kim, S. (2011). BioVLAB-MMIA: A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 (pp. 494-499). [6120491] https://doi.org/10.1109/BIBM.2011.93

BioVLAB-MMIA : A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis. / Lee, Hyungro; Yang, Youngik; Chae, Heejoon; Nam, Seungyoon; Choi, Donghoon; Tangchaisin, Patanachai; Herath, Chathura; Marru, Suresh; Nephew, Kenneth; Kim, Sun.

Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 494-499 6120491.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Lee, H, Yang, Y, Chae, H, Nam, S, Choi, D, Tangchaisin, P, Herath, C, Marru, S, Nephew, K & Kim, S 2011, BioVLAB-MMIA: A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis. in Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011., 6120491, pp. 494-499, 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBM.2011.93
Lee H, Yang Y, Chae H, Nam S, Choi D, Tangchaisin P et al. BioVLAB-MMIA: A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 494-499. 6120491 https://doi.org/10.1109/BIBM.2011.93
Lee, Hyungro ; Yang, Youngik ; Chae, Heejoon ; Nam, Seungyoon ; Choi, Donghoon ; Tangchaisin, Patanachai ; Herath, Chathura ; Marru, Suresh ; Nephew, Kenneth ; Kim, Sun. / BioVLAB-MMIA : A reconfigurable cloud computing environment for microRNA and mRNA integrated analysis. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. pp. 494-499
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