Loom Workflow Engine: Collaboration through portable, shareable data analysis Nathan A. Hammond1, Isaac Liao1, Sowmi Utiramerur2, Somalee Datta1

1Stanford Center for Genomics and Personalized Medicine 2Stanford Heath Care

NathanHammond-nhammond@stanford.eduIsaacLiao–iliao@stanford.eduinfo@loomengine.org

Contact

•  Aworkflowframeworkcanensurereproducibilityand

implementothercommonfuncAonsinaconsistentwayacrossallsteps.

•  Thisiseasier,cleaner,andsaferthandependingonthe

pipelinedevelopertoimplementthesefuncAonsforeverystepinineveryworkflow.

Whyuseaworkflowframework?

Portabilityarchitecture

Reproducibility&Traceability

•  LoomabstractsplaEorm-levelservicessuchasfilestorage,compute,and

databaseoperaAons.Withsimpleadaptors,itcanrunonmanydifferentplaEorms.

•  Loom’sclient-serverarchitectureallowsittoscalefromasingleuser

runningitononedesktoptomanyuserssharingaremoteLoomserver.

DockermakesrunAmeenvironmentsbothportableandreproducible.

•  PaloAltoVAHospital•  PhilTsao•  CuipingPan

•  StanfordClinicalGenomicsService•  StanfordHealthCare•  LucilePackardChildren’sHospital

SpecialthankstoourpartnersResourcesStanfordCenterforGenomicsandPersonalizedMedicinehRp://scgpm.stanford.edu/hRps://github.com/StanfordBioinformaAcs/loomhRps://pypi.python.org/pypi/loomengine

Toreproduceananalysis,youneedtoreassembleandverify:•  Inputdata•  RunAmeenvironment•  Commandsexecuted

LoomautomaAcallykeepstrackoftheseforyou.FilesarealwaysidenAfiedbyhash,andverifiedbydefault.RunAmeenvironmentissavedusingDockerandtrackedbyanimmutableimageID.

WithLoom,thesameworkflowyourunonyourlaptopcanberuninthecloudwithoutmodificaAon.

Ge@ngstartedLoomissAllinpre-releasebutweinviteyoutocheckitoutandletusknowwhatyouthink!Youcanfindusongithub:hRps://github.com/StanfordBioinformaAcs/loom

ThinkbacktoacomputaBonalresult

from3yearsago•  Howdidyougeneratethisresult?

•  Whatwastheinputdata?Canyouverifyit?

•  WhatwerethesoFwareversions?Areyousure?

•  Canyoureruntheanalysisandverifytheresult?

•  Cansomeoneelseruntheanalysiswithoutyourhelp?

ACADEMICRESEARCHmustbe

REPRODUCIBLE

Stand-aloneserver

Cloudprovider