BioVLAB-MMIA: A Cloud Environment for microRNA and mRNA Integrated Analysis (MMIA) on Amazon EC2

Abstract

MicroRNAs,byregulatingtheexpressionofhundredsoftargetgenes,playcriticalrolesindevelopmentalbiologyandtheetiologyofnumerousdiseases,includingcancer.AsavastamountofmicroRNAexpressionprofiledataarenowpubliclyavailable,theintegrationofmicroRNAexpressiondatasetswithgeneexpressionprofilesisakeyresearchprobleminlifescienceresearch.However,theabilitytoconductgenome-widemicroRNA-mRNA(gene)integrationcurrentlyrequiressophisticated,high-endinformaticstools,significantexpertiseinbioinformaticsandcomputersciencetocarryoutthecomplexintegrationanalysis.Inaddition,increasedcomputinginfrastructurecapabilitiesareessentialinordertoaccommodatelargedatasets.Inthisstudy,wehaveextendedtheBioVLABcloudworkbenchtodevelopanenvironmentfortheintegratedanalysisofmicroRNAandmRNAexpressiondata,namedBioVLAB-MMIA.TheworkbenchfacilitatescomputationsontheAmazonEC2andS3resourcesorchestratedbytheXBayaWorkflowSuite.TheadvantagesofBioVLAB-MMIAovertheweb-basedMMIAsysteminclude:1)readilyexpandedasnewcomputationaltoolsbecomeavailable2)easilymodifiablebyre-configuringgraphiciconsintheworkflow3)on-demandcloudcomputingresourcescanbeusedonanasneededbasis4)distributedorchestrationsupportscomplexandlongrunningworkflowsasynchronously.WebelievethatBioVLAB-MMIAwillbeaneasy-to-usecomputingenvironmentforresearcherswhoplantoperformgenome-widemicroRNA-mRNA(gene)integratedanalysistasks.