title: BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.
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.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47404, USA. lee212@indiana.edu
authors.forename: Hyungro
authors.initials: H
authors.lastname: Lee
authors.forename: Youngik
authors.initials: Y
authors.lastname: Yang
authors.forename: Heejoon
authors.initials: H
authors.lastname: Chae
authors.forename: Seungyoon
authors.initials: S
authors.lastname: Nam
authors.forename: Donghoon
authors.initials: D
authors.lastname: Choi
authors.forename: Patanachai
authors.initials: P
authors.lastname: Tangchaisin
authors.forename: Chathura
authors.initials: C
authors.lastname: Herath
authors.forename: Suresh
authors.initials: S
authors.lastname: Marru
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
mesh_terms: D045744:Cell Line, Tumor; D003628:Database Management Systems; D030541:Databases, Genetic; D019008:Drug Resistance, Neoplasm; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger