IRIDA:Canada’sfederatedplatformforgenomic

epidemiologyWilliamHsiao,Ph.D.

William.hsiao@bccdc.ca@wlhsiao

BCCentreforDiseaseControlPublicHealthLaboratoryandUniversityofBritishColumbia

IRIDAPlatformOverview

• IRIDA=Integrated Rapid Infectious DiseaseAnalysis

• Afree,opensource,standardscompliant,highqualitygenomicepidemiologyanalysisplatformtosupportreal-timediseaseoutbreakinvestigations

CoreFunctions:• Managementofstrainandgenomicsequencedata• Rapidprocessingandanalysisofgenomicdata• Informativedisplayofgenomicresults• Sample,Case,andaggregatedata(“metadata”)Management

Targetaudience:• Publichealthagencieswhoneedaplatformtomanageand

processgenomicdata• Publichealthagencieswhoneedaplatformtousegenomicsfor

outbreakinvestigations

IRIDA

SequencingInstruments

WebApplication

Datamanagement

Built-inAnalyticalTools

ExternalGalaxy

Command-lineTools

10simplerules(wishlist)tobuildabetterpublichealthmicrobiologygenomicepidemiologyanalysissystemDownloadLatestversionathttps://github.com/phac-nml/irida

1: Engage the Users Through the Entire Software Development Cycle

NationalPublic Health Agency

Provincial Public Health Agency Academic/Public

- ProjectTeamhasdirectaccesstostateoftheartresearchinacademia

- ProjectTeamisdirectlyembeddedinuserorganization

2: Have A Simple User Interface

LineListView(undertesting)

TimelineView(Conceptualization)

Selectablefields

Travel

SymptomsandOnset

ExposureTypes

Hospitalization

Launchapipeline

BeLike

3: Build a Robust, Extensible Platform

• IRIDAusesGalaxytomanageworkflows

• Addingadditionalpipelinesisrelativelyeasy

• UsingastandardAPItoallow3rd partytoolstoobtaindatafromIRIDA(e.g.IslandViewer andGenGIS)

IRIDA

ServletContainer

RESTAPI CentralFileStorage

WebInterface

ApplicationLogic

ComputeClusterGalaxy

$~>_ Galaxy

http://www.pathogenomics.sfu.ca/islandviewer/http://kiwi.cs.dal.ca/GenGIS/Main_Page

4: Have Extensive Documentation

• Documentationshouldbeavailablefor• Users – stepbysteptutorialwithscreenshots/FAQ• SystemAdministrators– installationinstructions/issuetrackers• Developers– opensource,collaborativedevelopment/IRCChannel

• EasilyAccessibleathttps://irida.corefacility.ca/documentation/

5: Implement QC Throughout the Whole Application

• Genomicsissensitiveandsequencedataareinherentlynoisy

• Genomicsisarapidlyadvancingtechnology• Standardizingpipelinesdifficultandcanstifleinnovation• Bettertostandardizetheperformanceandreportingmetricsandensureanyvalidatedpipelinesmeetthetestingcriteria

• DevelopingageneralQCtestingmodule(RCQC)thatuseontologytostandardizeQCmetrics(https://github.com/Public-Health-Bioinformatics/rcqc)

• DataProvenanceandVersionControl(data+Pipelines)aremust’sforDiagnosticLabs

6: Build to Enable Collaboration

• Beabletocomparepipelines• PipelineimplementedusingGalaxy– transparentandshareable

• DefineQCcriteriausingontologytocomparethedifferentpipelinesofthesamepurpose

• Beabletosharedatainstandardformatstominimizedatare-entryfromoneplatformtoanother

• FederationofplatformsusingstandardAPItosharedataandanalysisresults

7: Use Compatible Data Standards

• Sequencedataaremorecompatible/shareablebutmetadataarecurrentlyinsiloandincompatible

• CollaborationandSharingaredifficultwhendataareincompatible

• Compatibility!=Sameness

• UseOntologytoallowcustomizationoftermlistbutalltermswithsamemeaning(semantics)shouldhavethesameuniversalID(e.g.anURL)tofacilitatemappingofterms

8: Implement Fine Grained Access Control

DetailedView RestrictedView

E.g.Userrolepermissions controlvisibilityandeditingofcontent

Authorization

• Industry-standardauthenticationandauthorizationmechanisms

• Localauthorizationperinstance.

• Method-levelauthorization.• Object-levelauthorization.

9: Use Technology to Safeguard Patient Privacy

It’seasytolosecontroloftheExcelLineList-someonecanmakeacopyofthecontentandpassitaroundwithoutyourknowledge;typosarecommonandcumulative!

Technologycancontrolwhoseeswhatandwhen

Separateoutsensitivepatientdatafrompathogensequencedatabutbeabletobringthemtogetherwhennecessarywithoutresortingtoemailingoflinelists!

10: Have Multiple, Flexible Access Options

• Noonesizefitsallsolution;Havingmanyplatformstochoosefromisagoodthing(butdatashouldbeportableacrossplatforms!)

• IRIDAisavailableinseveraldifferentflavours:LocalInstall VirtualMachine CloudInstance PublicVersion

Advantages Fullcontrolofthesystem; yourdataneverleaveyourcentre

Fullcontrolofthesystem;Easytosetup

Fullcontrolofthesystem;doesnotrequirelocalcomputinginfrastructure

Nosetuprequired,uploadyourdataandhaveitprocessedusingComputeCanadaResource

Disadvantages Computinginfrastructure andITsupportneeded tomaintheresource

Not reallyscalableifrunonyourowndesktop;someperformance loss

Datago intoacloudenvironment;uploading tocloudenvironmentcanbeslow

Datagointoapublicinstance(dataremainprivatetoyouraccount);uploadcanbeslow

AcknowledgementsProjectLeadersFionaBrinkman– SFUWillHsiao– PHMRLGaryVanDomselaar – NML

UniversityofLisbonJoᾶoCarriҫo

NationalMicrobiology Laboratory (NML)FranklinBristowAaronPetkauThomasMatthewsJoshAdamAdamOlsonTarah LynchShaunTylerPhilipMabonPhilipAuCelineNadonMatthewStuart-EdwardsMoragGrahamChrystalBerryLorelee TschetterAleisha Reimer

Laboratory forFoodborne Zoonoses (LFZ)EduardoTaboadaPeterKruczkiewiczChadLaingVicGannonMatthewWhitesideRossDuncanStevenMutschall

SimonFraserUniversity(SFU)MelanieCourtotEmmaGriffithsGeoffWinsorJulieShayMatthewLairdBhavDhillonRaymondLo

BCPublicHealthMicrobiology &ReferenceLaboratory (PHMRL)andBCCentre forDiseaseControl (BCCDC)Judy Isaac-RentonPatrickTangNataliePrystajeckyJenniferGardyDamion DooleyLindaHoangKimMacDonaldYinChangEleni GalanisMarshaTaylorCletusD’SouzaAnaPaccagnella

UniversityofMarylandLynnSchriml

CanadianFood Inspection Agency(CFIA)BurtonBlaisCatherineCarrilloDominicLambert

DalhousieUniversityRobBeikoAlexKeddy

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McMasterUniversityAndrewMcArthurDaim Sardar

European NucleotideArchiveGuyCochranePetratenHoopenClaraAmid

European FoodSafetyAgencyLeibana Criado ErnestoVernazza FrancescoRizzi Valentina

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IRIDAAnnualGeneralMeetingWinnipeg,April8-9,2015