CyVerse Education, Outreach, and Training€¦ · Transforming Science Through Data -driven Discovery Parker Antin Nirav Merchant Eric Lyons Matt Vaughn Doreen Ware Dave Micklos CyVerse

TransformingScienceThroughData-drivenDiscovery

CyVerseEducation,Outreach,andTrainingiDigBio Webinar

JasonWilliams– Lead,CyVerse– Education,Outreach,TrainingColdSpringHarborLaboratory

[email protected] [@JasonWilliamsNY]

WebinarOutline

• CyVerseprojecthistoryanddescription• Education,Outreach,andTraining• DNASubway:CyberinfrastructureforEducation

CyVerseEvolution

iPlant2008EmpoweringaNewPlant

Biology

iPlant2013CyberinfrastructureforLife

Science

CyVerse2016TransformingScienceThroughData-Driven

Discovery

CyVerseEvolution

CyVerse2016TransformingScienceThroughData-Driven

Discovery

Vision:Transformingsciencethroughdata-drivendiscovery

Mission:Design,develop,deploy,andexpandanationalcyberinfrastructure forlifescienceresearch,andtrainscientistsinitsuse

Morethan30Kusers,PBofdata,andhundredsofpublications,courses,anddiscoveries

WhatisCyberinfrastructure?

Platforms,tools,datasets Storageandcompute Trainingandsupport

WhatisCyberinfrastructure?

•Datastorage•Software•High-performancecomputing•People

organizedintosystemsthatsolveproblemsofsizeandscopethatwouldnototherwisebesolvable.

WearefundedbytheNationalScienceFoundation

• Weareyourcolleaguesandcollaborators!• $100Millionininvestment• Freelyavailabletothecommunity• Spurnational/internationalcollaboration• CiteCyVerse:

CyVerse.org/acknowledge-cite-cyverse

DBI-0735191andDBI-1265383

CyVerseEvolution

CyVersesupportsalldomainsoflifescience

Plant/MicrobialAnimal BiomedicalEcological/Climate

CyVerseisbuiltforData

CyVerseproductstackReadytousePlatforms

FoundationalCapabilities

EstablishedCIComponents

ExtensibleServices

EaseofU

se

HowwasCyVersebuilt?

CyVerseInstitutions

• WestrivetobetheCILegoblocks• Danish'leggodt'- 'playwell’• Alsotranslatesas'Iputtogether'inLatin

• IfasolutionisnotavailableyoucancraftyourownusingCyVerseCIcomponents

CyVerseProducts

• Abilitytoaccessandmanagedata• Softwaretoanalyzedata• Computingresources• Skillsandhelptousesoftwareandinterpretresults

• Metadatamanagement• Abilitytosharedataandworkflows• Opensourcesustainabletools

• High-performanceandscalablecomputing• Abilityautomateandcollaborate• Fundingspentonscience,notsoftwareorhardware

IncreaseProductivity

EnsureReproducibility

GetScienceDone

CyVerseFeatures

WebinarOutline


93% ofresearchersareworkingwithlargedatasetsnow(ornext6months).34% feeltheirinstitutionprovidesadequatecomputationalresources.Mostalsofeeltheydon’thaveenoughskillstodothebioinformaticstheirsciencerequires. – iPlantSurveys(2010-14)

Never use(d) bioinformatics toolsBeginner

Intermediate

Advanced

Howwouldyourateyourbioinformaticsskilllevel?

Whereare“BenchBiologists”at?Gapsinneedsandskills

Hands-ontrainingWorkshopsthatreachuserswheretheyare

Tools&Services GenomicsinEducation

• Twodays;targetedtoresearchers• Hands-onlearningmodulestailortointerests• Individualconsultations• 1026participantssince2011

• Twodays;targetedtoeducators• Pairbioinformaticswithclassroomlabs• Helpforgeneratinglessonplans• 748participantssince2010

SeminarsWhatgraduatestudentsshouldknowaboutcyberinfrastructure

LifeScienceUser

• Labprotocolsareaprimaryexpressionoftheirresearchinterest

• AccustomedtoGUIs• Writes“quickanddirty,”non-optimized

scripts(Perl,Python,R)• Datadriven• HighThroughput

TraditionalHPCUser

• Writingcodeisaprimaryexpressionoftheirresearchinterest!

• Accustomedtothecommandline• Writesperformanceconscious,parallelcode(C,Fortran)!

• Simulationbased!• MassivelyParallel!

Hands-ontraining,workshops,seminarsGlobalCoverage

Majorworkshopsandseminarsatmorethan58academicinstitutionsworldwide

VirtualTrainingReachingthewidestaudience

Webinars Livestream

• ‘Orientation’for~700newuserspermonth• Quickdemos,Q&A• PublishedtoYouTube

• Double-diponworkshops• Virtualattendeesparticipatethroughchat• Recordingavailableinstantly

OnlinelearningmaterialsDocumentation,tutorials,andhelp

LearningCenter

• wiki.cyverse.org• Documentation

Wiki Forum

• cyverse.org/learning-center• Tutorialsandquick-starts

• ask.iplantcollaborative.org• Communityhelp/Q&A

Partnering“Findthebest,thenshareit”

• PartnersarecrucialtoEOTsuccess• Leverageexistingtools• Formalandinformalrelationships• Dowhatisrightfortheuser

WebinarOutline


GenomicsinEducation

Challenge– bringingstudentsintothefold

Research Education

Studentscanworkwiththesamedataatthesametimeandwiththesametoolsasresearchscientists.

DNA SubwayEducationalworkflowsforGenomes,DNABarcoding,RNA-Seq

ü Commonlyusedbioinformaticstoolsinstreamlinedworkflows

ü Teachimportantconceptsinbiologyandbioinformatics

ü Inquiry-basedexperimentsfornoveldiscoveryandpublicationofdata

DNASubwayBigdatainbiology

ImageCredits :Genomesequencingcosts :http:/ /www.genome.gov/ images/content/costpergenome2015_4.jpgOxfordnanopore sequencer:https :/ /www.nanoporetech.com/Agricultural drone: http:/ /purdue.imodules .com/s/1461/ images/gid1001/editor/alumnus/2014_mar/drones_main.jpgFitbit: http:/ /www.fitbit.com/force

• 100Kfoldcostsdecreaseinsequencing• Hand-heldsequencers• Drones• Biologicalsensors

Biologyisswimmingindata

Canyounavigatethetools?

Whatareyourchallengesinteachingbioinformaticsintheclassroom?

DNASubwayClassroomfriendlybioinformatics

FacultyidentifiedguidingrequirementsthatshapedthedevelopmentofCyVerseeducationalplatforms:

• Mixlectureandlab– haveawetbench“hook”• Student-scientistpartnerships– someonehastocareaboutthedata

• Co-investigation– projectsshouldpotentiallyleadtopublications• Scale – platformsshouldsupportprojectsmultipleclassroomscanjoin.

DNASubwayClassroomfriendlybioinformatics

Morethan13,000usersMorethan28,000studentprojectsin2015

DNASubwayRed Line: Genome annotation

Red Line

• Analyze up to 150 KB of DNA sequence

• De novo gene prediction

• Construct evidence-based gene models

• Visualize genome sequence in browser

DNASubwayYellow Line: Genome prospecting

Yellow Line

• Analyze DNA or protein sequence

• Search plant genomes using TARGeT

• Explore gene duplications, transposons, and non-coding sequences not detectable in conventional BLAST searches

DNASubwayBlueLine:DNAbarcoding,andphylogenetics

• Analyze DNA or protein sequence

• Search plant genomes using TARGeT

• Explore gene duplications, transposons, and non-coding sequences not detectable in conventional BLAST searches

Blue Line

DNASubwayGreen Line: Transcriptome analysis

Green Line

• Examine RNA-Seq data for differentialexpression

• Use High-performance computing to analyze complete datasets

• Generate lists of genes and fold-changes; add results to Red Line projects

• Iconic,simplelaboratory• Distributedprojects• Subsumesmanyimportantbiologicalconcepts• Integratesgeneticswithecologyandconservationbiology• Combineslabexperimentationwithbioinformatics• Opportunitiesforstudentdiscoveryandpublicationofnovelsequences

DNASubwayDNA Barcoding: The “Do Everything” Lab

DNASubwayDNA Barcoding: Inspiration

DNASubwayDNA Barcoding: Workflow

Collect samples

Exportsequences

Wet-lab Bioinformatics


DNA is extracted using a safe, cost-effective kits and equipment

DNA extraction ~ 1 hourPCR and Electrophoresis ~1.5 - 2 hours


GENEWIZ provides low-cost sequencingSequence data available within 24-48 hours

DNASubwayDNA Barcoding: Student Projects

www.urbanbarcodeproject.org

DNASubwayDNA Barcoding: 2012 Winners – Content of Ginko products

TransformingScienceThrough Data-drivenDiscovery

ParkerAntinNiravMerchant

EricLyons

MattVaughn DoreenWareDaveMicklos

CyVerseissupported bytheNationalScienceFoundation underGrantNo.DBI-0735191andDBI-1265383.

CyVerseExecutiveTeam

Documents

CyVerse Education, Outreach, and Training€¦ · Transforming Science Through Data -driven Discovery Parker Antin Nirav Merchant Eric Lyons Matt Vaughn Doreen Ware Dave Micklos CyVerse