the bioinformatics training landscape · the bioinformatics training landscape toronto area...

TheBioinformaticsTrainingLandscapeTorontoAreaBioinformaticsUserGroup(TorBug)

November29,2017

JasonWilliamsColdSpringHarborLaboratory,DNALearningCenter

@JasonWilliamsNY

What is the Bioinformatics Training Landscape?

What is bioinformatics? How do you define bioinformatics vs. comp bio?

Is bioinformatics biology?

Knowledge

FAIRprinciples

Dataintegration

Algorithmsandmethods

Metadataandstandards

Datastorage/acquisition/management/sharing

Bioinformatics Buzzword PyramidThere’s a road ahead, but where are we going?

Bioinformatics Buzzword PyramidThere’s a road ahead, but where are we going?

Talk outline

• What do we know about the needs of researchers and educators?

• Roadblocks and opportunities

• What do you think?

What is the Bioinformatics Training Landscape?

• Startedin2008asiPlantCollaborative

• $100Million,10YearNSFinvestment

• 40K+users,~3PBuserdata;national

andinternationalfederation

• Make“BigDataBiology”accessible to

theaveragebiologist

330+workshops,conferences,andseminarssince2009

Beginner(ordon'tuse

bioinformatics)53%

Intermediate35%

Advanced12%

“Howdoyourateyourlevelofbioinformaticsskills?”

93%ofsurveyrespondentsindicatetheyareorwill

beworkingwithlargedatasets

SurveyofNSFPIs– UnmetneedsforBioBigData

• 2016,Collected704/3987respondentsacrossthe4NSFBio

• Askedaboutcurrentandfutureneedsintrainingandinfrastructure

• Stratifiedbyresearchgroupsize/directorate

“Withwhattype(s)ofdatadoyoucurrentlyworkinyourresearch?”

“Isthiscurrentlyimportantinyour

research?

Doyouthinkthiswillbeimportanttoyour

researchin3years?”

“Doesyourinstitutionmeetthisneed?”(‘no’responses)

Training is the biggest need!

• NSFResearchCoordinationNetwork;UndergraduateBiologyEducation

• ~30Undergraduateeducators,expertsinassessment,industry,andotherfields

• https://qubeshub.org/groups/niblse

• Interestedin:

o FacultyandStudentPreparation

o Methodsandresourcesforintegration

o Assessment

Largest-eversurveyonbioinformaticsinundergraduateeducation(U.S.)

• ~1260responses

• Somegoals:

• Understandfacultyperceptionsandbehaviorsinaddressing

bioinformatics(Isitimportant?Areyouincluding?Ifnotwhy?)

• Gatherinformationonbioinformaticsrelatedsyllabi

(Whatdoyouteach,when,how?)

Compositesurveyrespondentisawhitemale/femalePhD,self-taughtinbioinformatics,withaPhDdegreeearnedin2000–2009.S/heworksatanon–minority-serving,doctoral-grantinginstitutionwithanundergraduateenrollmentoflessthan5,000.

Question NumberofKeyword-codedResponses

1.Inyouropinion,whatdoyouthinkarethemostimportant challengescurrentlyfacingthoseeducatingundergraduatelifescientistsinbioinformatics? 734(59.6%)

2A. Whatisthelevelofthecoursesyouteachinwhichyouwouldliketoincludebioinformaticscontent?(multiplechoice)

2B.Pleasedescribebriefly;includeanybarrierstodevelopmentand/orimplementation

364(29.6%)

3*.Whatispreventingyoufromincludingbioinformaticscontentinthesecourses? 313(25.4%)

4.Atyourcurrentinstitution,doyoufaceanytechnicalbarriersinteachingbioinformatics,e.g.,availabilityofacomputerlab,differentoperatingsystems,accesstohighperformancecomputingforteaching,ITsupport?Pleasedescribe

511(41.5%)

*- onlyaskedtothosewhoindicatedtheyarenotintegratingbioinformatics

95%ofsurveyrespondentsindicatethatbioinformaticsshouldbeintegratedintothelifesciencecurriculum.

40% offacultyreportachievingthis.

Trainingisthebiggestneed!

41%ofsurveyrespondentswhoare

underrepresentedminoritiesinSTEMreporttrainingbarriersvs.28% ofnon-URMfaculty.

Trainingisthebiggestneed!

“Lackoftraininginthearea,asmanyofusearnedourPhDsbeforebioinformaticswaswidelyusedandavailable.”

“Lackoffacultyexpertiseintherapidlychangingdisciplinesofgenomics/bioinformaticsandrelatedtechnologies.”

“Alackoftrainingandexperienceinbioinformatics.”

Barriersdifferbyinstitutiontype

MCA: Institution type

23%ofsurveyrespondentsatminority-serving

institutionsreportintegratingbioinformaticsvs.43% annon-minority-servinginstitutions.

MCA:Integrationstatus

Studentstakingdedicatedcourseslessprepared?

DecadeofHighest Degree

Earned

FormalBioinformaticsTraining(%)

FacultyIntegratingBioinformatics(%)

1980-1989 8.4 35.4

1990-1999 11.3 41.9

2000-2009 35.1 41.7

2010-2016 48.3 25.2

New,bettertrainedfacultyaren’tintegratingbioinformatics!

MCA:DecadeofDegree

Accesstoresourcesdiffersbysex?

Talk outline

• Whatdoweknowabouttheneedsofresearchersandeducators?

• Researchersandeducatorsstillexperienceatraininggap

• Trainingmorepressinganeedthantechnology/infrastructure

• Researchtrainingneedsaresophisticated(evolving?)

• Facultytrainingdoes!=touseintheclassroom

• Disparitiesintrainingexistandneedtobebetterunderstood

Talk outline

• What do we know about the needs of researchers and educators?

• Roadblocks and opportunities

• What do you think?

• Longitudinalstudyof294PhDstudentsfrom53USinstitutions

• Nostatisticallysignificantoutcomesover115variables(e.g.Publication/abstracts,

writingsamples,scholarlyengagement,etc.)

• Consistentwithpublishedpedagogicalresearchthatbootcamps cannotleadto

sustainablelearning*

• Meta-analysis of published assessments in genomics and bioinformatics

education

• Most studies assessed summative learning gains

• Less than 10% of studies provided reliability/validity evidence for assessments

(only one study provided both)

But doesn’t training work?

But doesn’t training work?

Towards evidence-based training and assessment

Somekeyinsightsforinformaltraining

SeeDr.Tractenberg’s slides:https://www.academia.edu/34607065/Learning_goals_teaching_goals_and_assessment_in_bioinformatics_training

• Rememberthedifferencebetweenformal/informaltraining– muchof

theliteratureassumesaeducation trajectory(longterm)vs.training

whereskillacquisitionisprimary

• Goodtrainingmusthaveclearlyarticulatedlearningoutcomes

• Soundsobvious,butlearnerscanonlyreachthelevelofskilluseyouare

actuallyabletoconveyinyourcourse(Bloom’sTaxonomy)

• Learnersneedtobeguidedonhow/why/when skillsshouldbeused

• DataCarpentry– Basicdataorganization/management(R/Linux)anduseofcommand-linebioinformaticstools(Unix)

• SoftwareCarpentry – Basiccomputingskillsincludingautomation(Linux/Make),scripting(PythonorR),versioncontrol(Git/GitHub)

LessonDevelopment2015

Teachingpilotsandrefinements2016

GlobalCommunity2017

GenomicsDataCarpentry

InteractingwithComputers• CouldComputing• Connectingtoremotecomputing(SSH/PuTTY)• FileTransfer(FileZilla,othercommand-linetools:

scp,rsynch,wget,etc.)

DataManagementandOrganization• Opensource• Metadataandreproducibility• Importantgenomicsfileformats(CSV/TSV,FastQ,

SAM/BAM,VCF,etc.)• Organizingafilesystemforcomputationalprojects(Linux)• UnixShell(command-line:ls,cd,mkdir,cp,rm,wc,grep,

cut,columns,head,tail,lessetc,)• R:Creatingprojects,scripts,andexaminingdata

DataCleaningandvisualizationR:variouspackagesandfunctionsR:dplyrR:ggplotFastQC - qualitycontrolofhigh-throughputsequencedataTrimmomatic - filteringandtrimmingofhigh-throughputsequencedataIntegratedGenomeViewer

AutomationandscriptingRscripting'For'loopsBuildingautomatedpipelinesUsingmultithreadedapplications

LearningGoalsGenomicsDataCarpentry

Carpentry Assessment

Thelong-termsurveyassessedconfidence,motivation,andotheroutcomesmorethansixmonths afterrespondentsattendedaCarpentryworkshop.

• 77%ofrespondentsreportedbeingmoreconfidentinthetools thatwerecovered

duringtheirworkshopcomparedtobeforetheworkshop.

• 54%ofrespondentshavemadetheiranalysesmorereproducible asaresultof

completingaworkshop.

• 65%ofrespondentshavegainedconfidenceinworkingwithdata asaresultof

completingaworkshop.

• 74%ofrespondentshaverecommendedourworkshops toafriendorcolleague.

Talk outline

• Roadblocksandopportunities

• Thereisalotofroomforimprovementinhowweassesstheimpactoftraining/(includingcoordinationandstandardizationofdisparateefforts)

• Sincethemajorityofbioinformaticseducationis(willremain?)informal,trainingneedstointegrateinsightsfromcognitivesciences

• Carpentriesapproachissucceedinginmanywaysweneedtopayattentionto,improve,andcriticize

Thanks!

Sorry!

Talk outline

• Whatdoyouthink?

• Howareyouinvolvedintraining?• Whatresponsibilitiesdobioinformaticianshavetocontribute?

• Howcanthenon-bioinformatician keepupwiththepaceofchange?