DBDS Handbook 2024/25 by stanforddbds

BiomedicalDataScienceGraduateProgram

StudentHandbook

Updated 9/4/24

1. Introduction and overview of Stanford resources

1.1. DBDS

1.2. Academics

1.3. Stanford Catalog

1.4. Computing

1.5. NLM / NIH

2. For students

2.1. How to get a computer

2.2. How to get ergonomic equipment

2.3. How to stay updated on DBDS events

2.4. How to reserve a conference room

2.5. How to send DBDS email

2.6. How to submit a help request

2.7. Personal wellness

2.8. What to do in a personal emergency

2.9. What to do in a Stanford emergency

2.10. What to do in a non-emergency

2.11. How to receive and send US Mail

2.12. How to use Cardinal Print

3. Academics and Research

3.1. Monday Talks: Research in progress/journal club

3.2. Advisors

3.3. Course registration

3.3.1. Study list

3.3.2. Grading basis and minimum GPA

3.3.3. Units

3.3.4. Cross-listed courses

3.4. Waivers and Transfer Units

3.5. Course flowsheet

3.6. Annual Flowsheet Review with yourAdvisor (Annually)

3.7. Teaching Assistant (TA) requirements and guidelines

3.7.1. TAGuidelines

3.8. Publishing a paper and NIH PublicAccess Policy

3.8.1. Review of Publications by Stanford faculty

3.8.2. NIH PublicAccess Policy and PMCIDs

3.8.3. Issues about authorship

3.9. MS degree

3.9.1. Curriculum

3.9.2. Milestones

3.9.3. HCP MS Details

3.9.4. Academic MS research rotation and research paper (Practicum)

3.9.5. Funding Support for MS students

3.9.6. Terminal Graduate Registration and Part-Time Enrollment

3.10. PhD degree

3.10.1. Curriculum

3.10.2. Academic milestones overview

3.10.3. Research rotations

3.10.4. Graduate Student Tracking System

3.10.5. Annual Progress Report

3.10.6. Individual Development Plan (IDP)

3.10.7. Funding support and finances

3.10.8. Qualifying Examination (Quals)

3.10.9. Research in Progress Talk

3.10.10. Setting your doctoral dissertation reading committee

3.10.11. University Oral Examination (Dissertation Defense)

3.10.12. Old Thesis Proposal Defense (entered PhD program before July 1, 2018)

3.10.13. Submitting your dissertation

3.10.14. Getting an MS while in the PhD program

3.10.15. Applying to the PhD program while enrolled in the MS program

4. Travel

4.1. NLM Travel Funding and conference

4.2. How to request support for travel

4.3. How to make travel arrangements

4.4. Receipts

4.5. Reimbursement after you travel

4.6. Local Travel

4.7. Foreign travel

5. Time away

5.1. Leave of absence

5.2. Family leave

5.3. Internships

5.3.1. Special Notes for International Students

6. External employment

7. Finances

7.1. Fellowship Stipends

7.2. Assistantships (Salary)

7.3. Direct Deposit

7.4. Holds

7.5. Taxes

8. Graduation

8.1. Graduation Photo

8.2. Degree Conferral

8.3. Notice of Intention to Graduate

8.4. Graduation Quarter

8.5. Commencement

9. Change log

1.IntroductionandoverviewofStanfordresources

Thishandbookcontainspolicies,procedures,andadvicefortheDepartmentofBiomedical DataScience(DBDS)graduateprogram,andaugmentsotherinformationfromtheSchoolof Medicine'sBiosciencesProgram,andStanfordUniversity.Relevantinformationcanbefound onthefollowingwebpages,whicharelistedhereforreference.

1.1. DBDS

• StanfordBulletinsectionsonDBDS(withcurriculumrequirements):PhD,MS,PhD Minor

• DepartmentofBiomedicalDataScienceWebsite

• DBDSFormsandDownloads

• DBDSCurrentStudentsHomepage

1.2. Academics

• Informationfornewgraduatestudents

• CurrentStudents|StanfordBiosciencesPhDPrograms

• GraduateStudentTrackingsystem

• GraduateEducation|StanfordUniversity

• GraduateAcademicPoliciesandProcedures

• Students|Registrar'sOffice

• InformationforCurrentStudents|OfficeoftheViceProvostforGraduateEducation

• OfficeofCommunityStandards|StudentAffairs (HonorCodeandFundamental Standard)

1.3. Stanford Catalog

• StanfordUniversityExploreDegrees(a.k.a.Bulletin)

• StanfordUniversityExploreCourses

1.4. Computing For research For course projects

On Prem

Sherlock X Low/Moderate

Point of Contact / Notes

Run by SRCC

Carina X High X Run by SRCC

SCG X Low/Moderate Run by Genetics dept.

Farmshare X X Low/Moderate Run by SRCC

Cloud NERO

GCP X High X

GCP X Low, Moderate and High * X See Cloud Acct Mgt Svc Page.

Azure X Low, Moderate and High * X See Cloud Acct Mgt Svc Page.

AWS X Low, Moderate and High * X See Cloud Acct Mgt Svc Page.

Cloud Acct Mgt service page: https://uit.stanford.edu/service/cloudacctmgmt (For access to GCP, AWS and MS Azure services and support.)

Google Cloud Credit request form: https://forms.gle/9o7FpRp8mYZiJnn76

More Information on Stanford Research Computing website on Stanford HPC Systems: https://srcc.stanford.edu/support/gettingstarted-hpc

1.5. NLM/NIH

• NLM-fundedtrainingprograms:https://www.nlm.nih.gov/ep/GrantTrainInstitute.html

• NIHpublicaccesspolicy: https://publicaccess.nih.gov/

• Trackyourpublications(andchecktheircompliancestatus)in https://www.ncbi.nlm.nih.gov/sites/myncbi/

• NIH-fundedpeer-reviewedarticles,publiclyavailableon PubMedCentral

• NIHManuscriptSubmissionSystem(NIHMS)

2.Forstudents

IfyouarenewtoStanford(ornewlyadmittedtotheprogram),checkoutthe GatewayforNew GraduateStudentsbytheOfficeoftheViceProvostforGraduateEducation.Ithasawealthof information.

Inaddition,theDBDSDepartmentholdsanannualretreatjustbeforethestartofthefall quarter. AttendanceisrequiredforallPhDstudentsandAcademicMSstudents. Honors CooperativeProgramMSstudentsandCotermMSStudentsarewelcometoattend ifsoable. Duringtheretreat,youmeetstudents,faculty,staff,andsomealumniinaninformalsetting. Youwilllearnaboutthefaculty’sresearchandlabs.Youwillalsohearthelatestregarding studentresearchduringpostersessions. Onthelastdayoftheretreat,thereisanorientation sessionfornewstudents,andreturningstudentsmeetin“huddles”totalkaboutkey milestonesfortheirupcomingyear. Therearelotsofopportunitiesduringtheretreattolearn aboutoneanother,theprogram,andStanford.

2.1 How to get a computer

DBDSloanslaptopcomputerstofirst-yearPhDstudents,and,whentherearesufficient computers,AcademicMSstudents.Ifyouborrowalaptop,youshouldreturnitattheendof yourfirstyear.Yourresearchsupervisorisresponsibleforyourcomputingresourcesfrom thenon.

2.2 How to get ergonomic equipment

Firstyearstudent:contactDBDSStudentServices.Others:thisistheresponsibilityofyour researchsupervisor.Generalinformationcanbefoundon Stanford’sEnvironmentalHealth& Safetywebpage

2.3 How to stay updated on DBDS events

TostayinformedofDBDS,studentswillreceivetheweeklyDBDSDigestandbeinvitedtojoin theDBDSStudentSlackChannel.TheDBDSWeeklyDigestcontainsinformationonthelatest happeningswithintheprogram,includingresearchopportunities,news,andupcoming

events.Youcanalsosubscribetothedigest here.Oncematriculatedintheprogram,students willalsoreceiveaninvitationtojointheDBDSStudentSlackChannelfromoneofourstudent representatives.TheSlackChannelisavaluablecommunitybuildingtool,whereresources andinformationaresharedinformallybetweenpeerswithintheDBDSprogram.

2.4 How to reserve a conference room

QRcodesarepostedattheentranceofeachconferenceroominMSOBSuite300.Youcan scanthecodetoviewavailability.Tomakeareservation,emailtheDBDSStudentServices Officerwhichroom,date,andtimeyouwouldliketoreserve.Largerrooms(suchasMSOB x303)andotherspacescanberequestedthroughMedscheduler.

2.5 How to send DBDS email

• Toreachstudentservicespleaseusethefollowingemail: Dbds-studentservices@stanford.edu

• ThefollowingarethekeyDBDS-relatedemaillists.Sendto listname@lists.stanford.edu.Ifyousendfromanon-Stanfordemailaddress,your messagewillbeheldformoderation.

• Ifyouneedtofindallthelistsyouareon,subscribe,orneedhelp,check https://uit.stanford.edu/service/mailinglists/tools

• MostoftheseusetheMailmantool(mailman.stanford.eduisashortcuttotheabove)

Listname Description

dbds-program-exec

dbds-students

dbds-coterms

dbds-honors-coop

dbds-phdms-students

dbds-phd-students

dbds-ms-students

dbds-all-people

dbds-job-openings

dbds-colloquia-tu

dbds-other-seminars

2.6 How to submit a help request

DBDSGraduateProgramExecutive Committee

AllDBDSStudents

CoterminalMSStudents

HCP:HonorsCooperativeMSStudents

PhD&AcademicMSstudents

PhDstudentsonly

AcademicMSstudentsonly

EveryoneaffiliatedwiththeDepartmentof BiomedicalDataScience

JobOpeningsinBiomedicalDataScience

AnnouncementsforDBDScolloquia

Otherseminarsofinterest

YoucansubmitahelprequestonawidevarietyoftopicsthroughStanfordServices(formerly HelpSU).Thisincludescomputer/informationtechnologyissues,andthoseinvolvingthe registrar,finance,andotheradministrativeoffices. YoucancontacttheUITServiceDeskat 5HELPor(650)725-4357,orsubmitaHelprequest.

• SUServices-ServicesPortalHome

TheDBDSstudentservicesteamcanalsohelpwithmanyissues,includingworkingwiththe Registrar’sOffice.

2.7 Personal wellness

Stanfordhasmanyresourcestopromotestudenthealthandwellness.Ifyouneedhelp,feelfree toreachouttotheDBDSstudentservicesteamatanytime.Hereareafewpointers:

• Counseling&PsychologicalServices(CAPS)https://vaden.stanford.edu/caps -including theabilitytogeturgenthelpnow

• Generalwell-beingresourcesatStanford:https://vaden.stanford.edu/well-being

• Bioscienceshealthandwellnessresources: https://biosciences.stanford.edu/currenthttps://biosciences.stanford.edu/currentstudents/resources/health-and-wellness-resources/students/resources/health-andwellness-resources/

• Stanford’sOfficeofAccessibleEducation,whichprovidessupportforthosewith disabilities,includingprovidinglettersofaccommodationtoinstructorsandprograms: https://oae.stanford.edu/

2.8 What to do in a personal emergency

• GraduateLifeOffice|StudentAffairs

2.9 What to do in a Stanford emergency

• EmergencyInformation|StanfordUniversity (Intheeventofadisasteroremergency affectingtheStanfordcommunity,thissitewillprovideup-to-dateinformationand importantinstructionspertainingtothesituation)

• StanfordEmergencyResources|EmergencyInformation (general“whattodoif”)

• EmergencyInformation|StanfordUniversityEH&S (contactinfo,preparedness,hotlines, etc.Alsoresourcesforyourout-of-townrelativesincaseStanfordisunreachable)

• AlertSUFAQs-SUDPSAlertSUisStanfordUniversity’semergencynotificationsystem usedtocommunicatetime-sensitiveinformationduringanemergencyeventaffecting campus.Besuretokeepyourinformationuptodatein Axesstoreceivealerts.

2.10 What to do in a non-emergency

• GatewayforNewGraduateStudents|OfficeoftheViceProvostforGraduateEducation Informationabouthealthandwellness,housing,finances,studentlife,support,etc.

2.11 How to receive and send US Mail

DBDSstudentshavemailboxspaceintheMSOB3rdfloorDepartmentofBiomedicalData Sciencesuite(3West).DBDS-relatedU.S.outgoingmailrequireseitheradequatepostageaffixed oradepartmentalpostagecode,availablethroughStudentServices.TheDBDScampusmail codeforinterdepartmentalmailisMC5464.

TheUSPSmailingaddressis:

BiomedicalDataScienceGraduateTrainingProgram

StanfordUniversitySchoolofMedicine 1265WelchRd,MSOB,X-343,MC5464 Stanford,CA94305-5464

2.12 How to use Cardinal Print

CardinalPrintmultifunctiondevices(MFD)havebeeninstalledattheAdministrationcubes (betweenx3C57andx3C59)andx397intheDBDSsuite. Printingcostsare$0.05/pageforcolor and$0.008/pageforblackandwhite.

LearntouseCardinalPrint

ThereareseveralwaysthatyoucanlearnhowtouseaCardinalPrintMFD:

1. CheckouttheQuickReferenceGuides.ThesewillbepostedbyallCardinalPrint deviceswithinstructionsonhowtoprint,copy,andscan.

2. VisittheCardinalPrintwebsite.Reviewtheshortvideos,User’sGuide,andFAQs availableonline.

3. Watchanon-demandtraining.ArecordedtrainingsessionisavailableontheCardinal Printwebsite.MoredetailsaboutupcomingZoomtrainingsessionswillbecomingsoon.

Ensureyouhavetherequiredprintdriver

TheCardinalPrintservicenamed CardinalPrint-SUshouldnowbeinstalledonyourdevice.Ifit isnot,simplydownloadityourselfatthe CardinalPrintwebsite.Ifyouneedhelp,contactyour localITsupportstaff.

Gethelporreportanissue

ForhelpwithaCardinalPrintdevice,contacttheUITServiceDeskat5-HELPor(650)725-4357, orsubmitaHelprequest Ifyoureportaserviceissue,removetheDeviceIdentificationLabel cardfromthepouchandturnitoversoothersknowtheissueisbeingaddressed.

3.AcademicsandResearch

3.1.

Monday Talks: Research in progress/journal club

DBDShasaregularseminarseriesthatmeetseachMonday,12:15pm–1:15pm.AllPhDand Academic MS students are required to attend. All Coterminal and HCP students are encouragedtoattend.

YoucangetoneunitofcoursecreditbysigningupforBIOMEDIN201.Youmayenrollupto3 times.

Eachsessionhastwo30-minutestudenttalks.Second-yearandlaterstudentspresenttheir research-in-progress.First-yearstudentscandothat,orpresentajournalclub.Duringthe SummerQuarterthereisaspecialformatinwhichDBDSfacultyleadadiscussionofapaperof theirchoosing.

• JournalClub.Thepurposeofajournalclubpresentationistogainpracticeinoral presentationskills,andtolearntopresentandfairlycritiqueapublishedpaperinsome areaofbiomedicaldatascience.

1. Pickapaper.

2. ClearitwithyourAcademicAdvisor.

3. Prepareyourtalk/slidepresentation.

4. PracticethatwitheitheryourAcademicAdvisororyourResearchAdvisor,usually theweekbeforethescheduledpresentation.

5. Givethepresentation.

Thepapershouldreflectyourowninterests,andengageotherstudents.Apaperabout biomedicaldatasciencemethodspublishedinthelastcoupleofyearswithatleastamoderate numberofcitationsisideal.Pleaseavoidpapersthatareverylongorthatrequireexcessive backgroundinsomenicheareaofbiologyormedicine.Draftsorpapersinpressarenot acceptable.ThereismoreJournalClubadviceonourwebsite: https://dbds.stanford.edu/forhttps://dbds.stanford.edu/for-current-students/currentstudents/#presentations

• Research-in-Progress.Thepurposeofaresearch-in-progresstalkistogainmorepractice inpresentationskills,topresentyourworktotheDBDScommunity,andtogetuseful feedbackonbothyourpresentationandyourwork.Youshould:

1. Prepareyourtalk/slidepresentationinconsultationwithyourPI.

2. PracticeitwithyourAcademicAdvisororyourResearchAdvisor,usuallytheweek beforethescheduledpresentation.

3. Givethepresentation.

Becausethisvenueisopenthepublic,itisimportantthatyoudiscussissuesaboutdisclosureof intellectualpropertywithyourresearchsupervisorpriortogivingthetalk.Thetalktitleand abstractareviewablebytheoutsideworld,andanyonemayattendthetalk.Thisisdifferent frompresentationsatlabmeetings,whichareconsideredtobeclosedmeetings.Youmay includeaslideatthebeginningofyourtalk,saying:"Thisisresearchinprogressandnotfor publicdisclosure.Pleasedonottakephotosoftheslidesordiscussoutsideofthisvenue."

Foreitherformat,ifyouuseoradaptfiguresortablesfromtheworkofothers,pleasemakesure thereisanappropriatecitationtothatsourceontherelevantslide.

3.2. Advisors

• AcademicAdvisor:Eachincomingstudentisassignedanacademicadvisor.Ifyoulater jointhelabofyouracademicadvisor,anewacademicadvisorwillbeassigned.Youmake anappointmentandmeetwithyouracademicadvisoratleastonceayeartoreviewyour courseflowsheetandmakesurethatyouareontrackforgraduation.Youracademic advisorcanalsogiveyoucurriculumadviceasneeded,ofcourse.Notethatyouare ultimatelyresponsibleforensuringyourprogressthroughtheprogram;theadvisorisjust givingadvice.

Ifyouareconsideringsubmittingacoursewaiverrequest(forcurriculumrequirements thatcorrespondtocoursesyouhavealreadytaken),youshoulddiscussthiswithyour academicadvisorbeforesubmittingwaiverrequests.Pleasegettheirapprovalbefore submittingyourwaiverrequestformtoDBDSstudentservices.

Feedbackontheeffectivenessandengagementlevelofthestudent-advisorrelationship isappreciated.Usually,theacademicadvisorservesforthedurationofthestudent’s study,buttheremaybeaneedordesiretochangeadvisors. Theprocessistonotify StudentServices,explainingthereasonforthechangeand(optionally)requestingan alternativeadvisor.Youmayrequestthatthisbekeptconfidential.StudentServiceswill assignanewadvisor,inconsiderationofthestudent’srequestaswellas otherprogram andfacultyconstraints.

• ResearchAdvisor:EachstudentintheAcademicMSandPhDdegreeprogramswillhave atleastoneresearchadvisor,chosenbymutualagreementbyendofthestudent’sfirst yearintheprogram.ThisresearchadvisorshouldbeeitheraPrimaryorSecondary DBDSFacultymember,orontheAdvisingFaculty listontheDBDSwebsite Ifyour researchadvisorisontheCollaboratingFacultylist,thenyouwillneedtochoosea coadvisorfromthePrimary,SecondaryorAdvisingfacultylists. Youmayalsochooseto haveaco-advisorforotherreasonsaswell.

• Co-Advisors:Ifyouhavemorethanoneadvisor,there’sauniversityrequirementto identifyoneortheotherofyouradvisorsastheprimarymentor,andtheotherasthe comentor. Theprimarymentor/advisorshouldbeontheDBDSPrimary/Secondary FacultyorAdvisingFacultylist. Bydefault,theprimaryadvisorwillbeincharge,but otherplansarepossibleaslongaseveryoneagrees.Thisneedstobediscussedaheadof time,thatis,whentheadvisorsareagreeingtobeadvisors,notlater. DBDSisnot responsibleforsettingthisup youandyouradvisorsare. Youshouldmakesurethat theydiscusswhoisultimatelyresponsibleformonitoringyourresearchprogress,andthe detailsofyourfinancialsupport. PleasesendallupdatestoDBDSStudent Servicesand cctheExecutiveDirector.

ToaddnewmemberstotheDBDSGraduateStudentAdvisingFaculty,pleasesendyour request to DBDS Student Services for consideration by the DBDS Graduate Program ExecutiveCommittee.

3.3. Course registration

3.3.1.

Studylist

By5pmonthefirstdayofclasseachquarteryoumustsubmitastudylistin Axesstoregisterfor classes.Notethatthereisalatefee.

3.3.2.

GradingbasisandminimumGPA

RefertotheDBDSsectionofExploreDegreesfordetailsofwhichcoursesmustbetakenfora grade,andwhichcanbetakenCredit/NoCredit.IfyousignupfortheCredit/NoCreditoptionin acoursethatshouldhavebeentakenforalettergrade,youshouldemailtheinstructortoask whatthelettergradewouldhavebeen,thenforwardtheresponsetotheStudentServices Officertobeincludedinyourfile.

StudentsmustmaintainanoverallGPAof3.0.IfyourGPAdoesnotmeettheminimum requirement,theDBDSGraduateProgramExecutiveCommitteemayrequirethatyousubmita planthatexplainshowyouwillremediateanydeficiencies,resolveanyincomplete grades,and bringyourGPAbackabovethethreshold.

3.3.3.

Units

AllfundedDBDSstudentsarerequiredtoenrollin10unitseveryquarter.Ifyouenrollinmore than10units,youwillberesponsibleforpayingtheadditionalunitratechargedbythe Registrar'sOffice.

WithResearchAssistantships(RAships),the10-unitrateisconsideredhalftime(20hoursper week),meaningthatfor20hoursperweekyouareworkingontheresearchproject,andfor20 hoursperweekyouaretakingclassestowardsyourdegreerequirements.Thisiscalleda50% RAship.Notethatthiscanbeadjustedproportionally:a25%RAshipwouldpayfor10hoursper weekofresearch.

3.3.4.Cross-listedcourses

WhentakingacoursethatislistedinbothDBDSandanotherdepartment(suchasComputer Science),pleasesignupforitundertheBIOMEDINorBIODSnumber.Thisisespeciallyimportant forBIOMEDIN299DirectedReadingandResearch.

3.4. Waivers and Transfer Units

Studentswhohavebeenadequatelytrainedinaparticularareathroughgraduate-level courseworkatanotherinstitutionmaybepermittedtowaivecoursesandsubstitutemore advancedwork.First-yearstudents(MSandPhD)maypetitiontheDBDSGraduateProgram ExecutiveCommitteeforwaiversforspecificcoursesordomainunitrequirements. Thesecourse waiverrequestsaredueinearlyNovemberofyourfirstyear.Waiverrequestsafteryourfirst yearintheprogramwillnotbereviewed.StudentServiceswillsenddetailedinstructionstoyou byemailearlyintheAutumnQuarterofyourfirstyear.Pleasecompletethatpaperwork,and discusswithyourAcademicAdvisorbeforesubmittingitforfinalapprovalbytheDBDSExec.

ForMSstudents:NotethatpriorcourseworkfromoutsideStanfordcannotreducethe45unit residencyrequirementfortheMSdegree.

ForPhDstudents:Notethatthereisa residencyrequirementof135units(ofwhichamaximum of24maybetransferredfromoutsideorfromaStanfordM.A.orM.S.degree),andarequirement for52unitsofformalcoursework(meaningaclassroom-basedcourse,notresearchunits).

Newpolicy(April2023)regardingTransferUnitsforPhDs: Theintentistoenablestudents enteringtheDBDSPhDprogramwithpriorgraduatedegreecourseloadinrelevantcoursestogo throughtheDBDSgraduateprogramcurriculuminlesstimeandgettoresearchsooner. A maximumof24unitsforgraduateworkcompletedatanotherinstitutionmaybeappliedtothe requirementsforthedegreesofPh.D. TransferofunitswillbeevaluatedbytheDirectorof GraduateStudiesandotherdepartmentfacultymembersonacoursebycoursebasis.Graduate workacceptedfortransferofresidencydoesnotautomaticallyexemptastudentfromhavingto completeacourserequirementforthedegree.Universitypoliciesrelatedtotransferofcreditfor graduateworkdone elsewhereislocatedinGAP3.2.1ResidencyPolicyforGraduateStudents. Details:

• PhDscanapplyfortransferunits aftertheirfirstquarterintheprogram,usingthe waiverform.

• Wewillgrandfatherinthisnewpolicy

• NowaiversofDBDSProgramcorecourses(BIOMEDIN202,212,214and215)

• Onlyallowedforgraduatelevelcoursestakenwithinthelast4years

3.5. Course flowsheet

TheDBDSMSandPhDcourseflowsheetsareavailableonthe DBDSFormsandDownloads webpage.

Whensubmittingacourseflowsheet:

1. Makesureyouputyournameandthedateonit.

2. Listthecoursenumberinthecolumnontheleft.Listallcourses,past,present,and future.Putonecourseperline.

3. Putthenumberofunitsforthecourseinmainpartofthegrid.

4. Waivedcoursesandunitsshouldbenotedinthe“Course”column,butzerounitsshould beattributedtothem.

5. BIOMEDIN299researchunitsneedtobeincludedinthe“unrestrictedsection”.

6. Enterthegrade(A+,CR)inthegradecolumnneartheright.FortheJanuaryreport,make sureitincludesgradesfromAutumnQuarter.

7. Ifyoudon'tseemeaningfulrowandcolumnsums,andtheflowsheetdoesnotcompute yourGPA,thenyouhavedonesomethingwrong.

3.6. Annual Flowsheet Review with your Advisor (Annually)

MeetwithyourAcademicAdvisoraccordingtothefrequencyinthefollowingtable.ForPhDand AcademicMSstudents:oncearesearchadvisorhasbeenestablishedmeetwiththeminstead. Youshouldreviewanup-to-dateflowsheetwithyouradvisor:include gradesforcompleted courses,andallprojectedcoursework.Notethatyouareresponsibleformakingsureyouareon tracktomeetthedegreemilestones.

TheDBDSExecutiveDirectorwillautomaticallyreviewgradeseveryquarter. ReachouttotheED withanygradingconcerns.

AllPhDstudentsarerequiredtocompletetheIndividualDevelopmentPlan(IDP)annually; thisisaseparaterequirementfromtheDBDSFlowsheetReview.

Degreeprogram,status Todo

MS -MS/HCP/co-term

PhD,year=1

PhD,year>=2,stillinclasses

PhD,year=3,donewithclasses

MeetwithAcademicAdvisoratleast1x/year:review flowsheet,reviewwaiverrequesttogetadvisor approval,gooverclassesandinterests.Submit flowsheettoSSOafterfirstquarterofattendance.If changestoflowsheetoccur,resubmitupdated flowsheettoSSO.

MeetwithAcademicAdvisoratleast1x/year:review flowsheetandgooverclassesandinterests.Submit flowsheettoSSO.Ifchangestoflowsheetoccur resubmitupdatedonetoSSO.ChooseaResearch advisorbysummer.Do3labrotations,pickalab.

MeetwithResearchAdvisoratleast1x/year:Establish IDPmeeting,reviewflowsheettomakesureyouare ontracktograduate,practicestudentseminartalk withadvisor,prepforQualsexams.Complete1 unpaidTAassignment.

MeetwithResearchAdvisoratleast1x/year: Review flowsheettomakesurestudentisontracktograduate, practicestudentseminartalk,finalize doctoral dissertation readingcommitteeandpreparefor Research-in-Progresstalk(occurs6-9moafterQuals). Complete1unpaidTAassignment.

PhD,year=4

PhD,year=5

MeetwithResearchAdvisoratleast1x/year:review flowsheetandmakesureyouareontracktoTGRby completing135unitsbytheendofwinterquarter, practicestudentseminartalk.MeetwithDoctoral Dissertation ReadingCommittee.

Meet with Research Advisor at least 2x/year: Meet with advisor to discuss options for an out-of departmentoralscommitteechair.Scheduleorals. Submitdissertation.Graduate.

SummaryofMilestonesforeachPhDcohortafterchoosingaResearch Advisor:

2 Quals(written&oral)

3 ResearchinProgress Talk

4 FinalizeDissertation ReadingCommittee Members

5 OralDefense

* 2ndyearProgressReport-1quarteronly

** ResearchinProgressTalkcountsasyourdissertationreadingcommitteeinyour3rdyear

***MeetwithReadingCommitteetwiceinthe5th year.OralDefensecountsasonemeeting.

3.7. Teaching Assistant (TA) requirements and guidelines

TherearefourkindsofstudentteachingpositionsinDBDS:

1. Assigned.TheDBDSGraduateProgramExecutiveCommitteedeterminestheTA assignmentsonceayear,typicallyinJuly.Typically,theassignmentsthatsatisfythe DBDSrequirementaretoDBDScorecourses.PhDstudentsarerequiredtoTAtwo (3+unit)courses.AcademicMSstudentsreceivingfellowshipsupportthroughDBDSare requiredtoTAone(3+unit)course.Others,includingHCPandco-termMSstudents,are exemptedfromthisrequirementunlesstheyreceivefellowshipsupportfromtheDBDS programatanypointwhileintheprogram.TheTArequirementisusuallycompleted afteryourfirstyearintheprogram.TA'sareexpectedtoreviewandunderstandtheTA Guidelines(below).

2. Voluntary.Theinstructorandstudentagreethatthestudentwillhelpwithcourse developmentorserveascourseassistant.WerefertothesepositionsinformallyasTAs, buttheyarenotformal(e.g.25%or50%)TAships.Thismaybeforpay(“moonlighting''). ForDBDScourses,suchpaywillbeintheformofstipendthatdependsontheexpected workload(e.g.thenumberofunitsofthecourse).Ifnotforpay,thestudentcanpetition DBDSGraduateProgramExecutiveCommitteetohavethiscounttowardstheDBDSTA requirement.Typically,thesemoonlightingTApositionsgotoseniorgraduatestudents whohavepassedtheirQuals,andcompletedtheircourseworkandTArequirements.

3. FormalTAship.Somedepartments(suchasCS,but notDBDS)offerstudentsformal TAshippositions,whichmaycovermostorallofyourstipendandtuition.Sometimes theseareofferedtoDBDSstudents.

4. Assistancewithseminarseries.Forsomeseminarseries,suchasBIOMEDIN205and208, atraineeorfellowmayassistthecoursedirectorwithlogistics,scheduling,and administration.Arrangementsforthesecoursesarebetweentheinstructors,theDBDS program,andindividualtraineesorfellows,anddonotsatisfytheDBDSTArequirement.

3.7.1.TAGuidelines

Thepurposeoftheteachingassistant(TA)requirementistohelpstudentsunderstandthe processoforganizinganddeliveringacourseasanintellectualacademicexercise,andlearn aboutcourseadministration.Studentsshouldconsidertheirunfundedteachingpartlyasa contributionbacktotheprogramandtheirfellowstudents,aswellasanopportunitytolearn pedagogicalmethods.

Eachcoursemayhavedifferentspecificrequirements,butthesearegeneralguidelinesfor facultyandTAtouseasastartingpointfordiscussion.Theseshouldbereviewedbeforeeach coursebeginstosetcommonexpectations.

1. Thetimecommitmentisintendedtoberoughly10hoursperweekduringtheTAship. Wewillmakesuretheinstructorsareclearabouttheballparkhoursperweek. Also,we recommendthatyouinformyourresearchadvisorsthatyouwillbeTA’ingforonequarter sotheycanscalebackexpectationsduringthatperiod. Ifyoufindthatyouaredoingway morethan10hoursperweek,ie20hoursaweekandnotimeforresearch,pleasedon’t hesitatetodiscusswiththeinstructorofthecourseasthatisnottheintent.

2. Itisexpectedthatacoursewillhaveadministrativepersonnel(oftentheadministrative assistantoftheinstructor)whowillhandleroutineadministrativeissuessuchasroom reservations,copying,logisticalcoordinationofguestlecturesandprocurementof suppliesforthecourse.

3. TAsmaybeassignedin-classlogisticalsupporttasks,suchasin-classhomeworklogistics (distribution/acceptingassignments),videotaping,informationdissemination,and communicationwiththeadministrativesupportpersonnel.

4. TAsshouldhaveregularofficehoursforinteractionwithstudents.

5. Unlessspecificallyexempted,TAsshouldattendallclasses.Vacationsshouldnotbe scheduledduringthequarter,unlessitispre-arrangedwiththeInstructor.

6. TAsmaycreateandgradeassignmentsandexams.Instructorsshouldexamineand approvethese,andmusttakeoverallresponsibilityforthem.

7. TAsareencouragedtogiveatleastonelectureduringthecourse,inordertohavethe experienceofpreparingacourselectureandtoappreciatethedifferencesfromresearch talks.

8. TAsmaybeaskedtomaintainacoursewebsite,withrelevantmaterials.Routine administrationofthesesitesshouldbesharedwiththeadministrativesupport personnel.

9. TAsmaybeaskedtocreateclassnewsgroupsoremaillists,andtomonitoractivityon these,andrespondappropriately.

10. Decisionsaboutfinalgradesrestwiththefaculty,buttheyareencouragedtoconsult withtheTAstolearnofextenuatingcircumstances,particularlyiftheTAshavehadthe majorresponsibilityforgradinghomeworkassignmentsand/orexaminations.

SpecialchallengesmayariseinsupportingthedistanceeducationstudentswhotakeDBDS coursesviaSCPD,theStanfordCenterforProfessionalDevelopment.Thesestudentshavethe taskoffollowingtheclasswithoutthebenefitofliveinteractionwithfaculty,TAorother students.Oftenthesestudentsdonotknowwheretolookforinformationthatmightbe consideredcommonknowledge.

1. TAsshouldfamiliarizethemselvesbeforethecoursewithSCPDpoliciesandprocedures. SCPDoffersorientationstofacultyandTAs.YoucancontactSCPDat http://scpd.stanford.edu

2. TAsshouldarrangeaprocedurefortalkingwithSCPDstudentsonthephoneorbyemail duringofficehours.ThehardestpartaboutTA-inganSCPDcourseisfiguringoutwhen SCPDwillsupportthestudentandwhenyouhavetostepin.Mainly,yourjobisto cover thematerialintheclass,notprovidetechnicalassistancetothestudent.

3. SCPDhandlesstudentregistrationandtuition.

4. Thestudentsshouldknowthedifferencebetweenanincompleteandawithdrawal.They shouldknowifacrisisoccurstheycanrequestanincomplete.

5. ManySCPDstudentsareunawareofthedifference(ifany)betweentheSCPDcourse descriptionandthecoursedescriptionintheStanfordBulletin.Mostofthetime,the coursedescriptionsontheSCPDwebpagesareadequate.

3.8. Publishing a paper and NIH Public Access Policy

3.8.1.ReviewofPublicationsbyStanfordfaculty

Allpapersandabstractssubmittedtojournals,conferences,booksorotherpublicationsmustbe reviewed by a Stanford faculty member. This policy applies to any publication, regardless of authorship,thatdescribesworkdoneatStanford,hasresearchsupportthroughStanford,orthat mentions a Stanford affiliation. It is the responsibility of the first author to ensure that sufficient timeisallocatedforthisreviewprocess.Nopublicationmaybemailedtoajournalorconference withoutfinalapprovalfromthefacultymember.

3.8.2.NIHPublicAccessPolicyandPMCIDs

IfyouoryourworkhasbeensupportedbyNIH (even if you are 17th author on a manuscript),then youarerequiredtocomplywiththe NIHPublicAccessPolicy Inparticular,eachpublication mustbesubmittedtoPubMedCentral(PMC),andgetaPMCIDassignedwithin3monthsof submission.Thisisextremelyimportant.Followtheinstructionsontheirwebpage. NIH Policy:Toadvancescienceandimprovehumanhealth,NIHmakesthepeer-reviewedarticlesit fundspubliclyavailableonPubMedCentral.ThisappliestoallstudentsfundedthroughourT15 (NLM)traininggrantatanytimewhileworkingonanypartofsuchpapersortheresearch reportedoninthem(aswellastoanyoneelsereceivingNIHfunding).TheNIHpublicaccess policyrequiresscientiststosubmitfinalpeer-reviewedjournalmanuscriptsthatarisefromNIH fundstoPubMedCentralimmediatelyuponacceptanceforpublication throughtheNIH ManuscriptSubmissionSystem(NIHMS).Thisalsoaffectsanypublicationagreement/copyright transferagreementyou(orthefirstauthor)mighthavetosignwhensubmittingpapers,somake sureyoureadthepolicyandactaccordingly.

Wearerequiredtoreportallpublicationsbytrainees,andthepublicationtrackingsystem automaticallyflagsasnon-compliantpublicationsnotsubmittedforopenaccessinPMC.Itis yourresponsibilityasanNIH-supportedresearcher,notours,to“catch”andsubmitthem.

ACTION:

1. Youcantrackyourpublications(andchecktheircompliancestatus)in https://www.ncbi.nlm.nih.gov/sites/myncbi/

2. Ifyouareaco-author(notjustfirstauthororseniorauthor)onanypublishedpaper, andyouwerefundedbytheNLMT15traininggrantatanytimewhenyoudidworkon thepaper–thenyouMUSTensurethatthepaperissubmitted –see https://publicaccess.nih.gov/

3. ADVISORS –alsopleasewatchthisasyourtraineesletyouknowabouttheir submissionsandpublications.

Pleasedonotbesloppy,late,orlackadaisicalaboutthis,asitcanpotentiallyputour fundingforyouandforallothertraineesatrisk.

3.8.3.Issuesaboutauthorship

Itisbesttodiscussthescopeandownershipofaprojectatthebeginning;thisincludeswhowill beanauthorandinwhatordertheywillbelisted.Itisimportanttoincludeallwhohave contributedinsomenon-trivialwaytotheresearch.Thefirstauthor(orco-firstauthors)usually takeprimaryresponsiblyfordraftingthepaper,andthemechanicsofsubmittingit.Allofthe coauthorsmaycontributetothewritingasappropriate,andallshouldreviewthepaperpriorto submission.Theseniorauthor(listedlast)isusuallytheproject'sprincipalinvestigator.If problemsariseoverauthorship,firstraisethemwiththePI;ifissuesremainthenconsidering askingyourAcademicAdvisor,orStanford's OfficeofTheOmbuds.

1. Whomtoacknowledge:

The NIH requires that each publication, press release, or other document about research supportedbyanNIHawardmustincludeanacknowledgmentofNIHawardsupportanda disclaimersuchas:

Research reported in this publication was supported by the National Library of Medicine of the National Institutes of Health under Award Number T15LM007033. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Anyoneinvolvedintheworkdescribedinapaperandnotlistedasanauthorshouldbeincluded intheacknowledgmentssection,asshouldthosewhoprovidedotherfinancialsupportorgifts ofequipment.Theprimaryauthorofthepapershouldconferwithallco-authorstomakesure thatallappropriategrantsupportislisted.

2. Mailingcosts:

TheDBDSprogramwillpayforregularmailcharges,butnotExpressMailorFederalExpress costs,unlessspecificallyapprovedbyamemberoftheseniorstaff.Pleasetakethisconstraint intoconsiderationwhenworkingagainstadeadlineformailinganabstractorotherpublication.

3.9. MS degree

3.9.1.Curriculum

TheMScurriculumisdescribedinfulldetailinthe StanfordBulletin.Thecurriculumconsistsof fourmaincomponents:

1. CoreDBDSclasses

2. ElectivesfromComputerScience,Statistics,Mathematics,andEngineering.The completelistofallowablecoursesislistedat DBDSElectives.

3. SocialandEthicalIssues.AcompletelistofallowablecoursesislistedatExploreCourses byentering"dbds::ethics".NotethatMD'sandcurrentmedicalstudentsareexempted fromthisrequirement;replacethisrequirementwiththeequivalentnumberof UnrestrictedGraduateElectives.

4. UnrestrictedGraduateElectives.Anycourseatthelevel100orgreatermaycount.

Notethatthereareadditionalrulesinthe StanfordBulletinaboutthenumberofP/Fcourses, andthenumberof100-199coursesthatmaybecounted. ThereismoreontheDBDSwebsitefor CoterminalMS andHCPMSstudents.

3.9.2.Milestones

Duringtheirfirstquarterintheprogram,allMSdegreestudentsmustsubmittheir Course FlowsheetbydegreetoStudentServices.

3.9.3.

HCPMSDetails

TheHCPMSdegreeisdesignedprimarilyfortheworkingprofessional.Therearesomespecial considerationsforHCPstudents:

• Althoughmanyclassesnecessaryforthedegreeareavailableonline,somerequirements maybefulfilledthroughimplementationofanalternativeplantobeapprovedbythe program.Example:

o Stats200wasnotofferedremotelybeforeSpring2020 –suggestedalternatives: MS&E226orEPI259andEPI261 o BIOMEDIN212requires specialarrangementswiththeinstructor Studentsshouldconsidertheavailabilityofcourses onlinebeforerequestingto switchfromfull-timetopart-time,especiallyifthismayinterferewiththeirabilityto satisfytherequirementsofthedegree.

• HCPstudentswholivelocallymayattendtheircoursesoncampus.

• AllHCPstudentsarestronglyencouragedtoattendMondayTalks(inpersonor remotely),astheyprovideacriticalopportunitytogettoknowothersintheprogram.

• Studentshaveuptofiveyearstocompletetheprogram(ratherthanthreeyearsforthe AcademicMSdegree).

• Typically,studentsenrollinonecourseperquarter.Notenrollingforanycoursesduring aquarter(withouttakingaformalleaveofabsence)willresultinthestudent’sprogram beingdiscontinued.ReinstatementrequiresapetitiontoGraduateAdmissionshttps://gap.stanford.edu/handbooks/gap-handbook/chapter-5/subchapter-4/page-54https://gap.stanford.edu/handbooks/gap-handbook/chapter-5/subchapter-4/page-5-411#anchor-466

• Researchprojectsareoptional;ifinterested,thestudentmustmakearrangementswith programfaculty.

Requeststotransferfrompart-time(HCP)tofull-time(AcademicMS)arereviewedbythe DBDSExeconacase-by-casebasis.FinaldecisionsareattheDBDSExec'sdiscretion.Please notethefollowinglimitations(forstudentsenrollingintheHCPprogramstartingFall2020):

• Studentsmustcompleteaminimumoftwo(2)quartersinthepart-timeprogram excludingsummerquarterorenrollmentasanon-degreeoptionstudent,before requestingtotransfertofull-time.Therefore,thesoonestthetransfercanbediscussed

andapprovedisduringthefirstDBDSExecmeetingofthethirdquarterofthestudentin theHCPprogram.

• Studentsmustcompleteaminimumof10unitsofletter-gradedcoursesthatmeet requirementsfortheDBDSMSdegreebeforecommencingtheirfirstfull-time(Academic MS)quarter

• GPAwillbeconsideredaspartoftherequest

• Studentscanmakeamaximumoftwo(2)transfersduringtheprogram(e.g.transfer frompart-timetofull-timeandbacktopart-time)

3.9.4.AcademicMSresearchrotationandresearchpaper(Practicum)

AllstudentsintheAcademicMSprogramshouldbeengagedinbiomedicaldatascience-related researchunderthesupervisionofaDBDSPrimary,Secondary,orAdvisingFacultymember. Officially,youarenotrequiredtodoone-quarterresearchrotations,butyouarewelcometodo so.Youshouldpickalabbymutualagreementbetweenyouandtheresearchsupervisor.Please notifytheDBDSStudentServicesOfficerwhenyouhavedoneso.

BeforegraduatingfromtheAcademicMSprogram,youarerequiredtowritearesearchpaper, sometimescalledaresearchpracticum.Thispapershouldbepublishable,althoughitisnot requiredthatitbesubmittedorpublished.Itisrequiredthatthismanuscriptbereviewedand approvedbytwofacultymembers;typically,thesewouldbetheseniorauthorofthemanuscript whoisyourresearchsupervisor,andoneotherPrimary/Secondary/AdvisingDBDSFaculty. PleasesendthisinformationtotheStudentServicesOfficerwellinadvanceofyourgraduation sothatitisnotdelayed.

Ifyoutransferfrom theAcademicMSprogramtotheHCPMSprogram,thisrequirementno longerapplies.However,ifyoudidsignificantresearchwhileintheAcademicMSprogram,we stronglyencourageyoutocompleteandpublishit.

3.9.5.FundingSupportforMSstudents

WehavefundingthroughtheNLMtraininggrantforthosewhohavepostdoctoralstatus(MD,or PhD).Youcanapplyforthepost-doctoralMSbeforeyourdoctoraldegreehasbeenawarded,but youcannotbeplacedonpostdoctoralNLMfundinguntilyourdoctoraldegreehasbeen conferred,sotheremaybeproblemsifyourgraduationisdelayed.NotethatNLMtraininggrant fundscanonlysupportUScitizensorpermanentresidents.Otherswillneedtoconsider alternativesourcesoffunding.

ForstudentsenrolledfortheMSdegreewhodonotalreadyhaveaPhD,MD,orsimilardoctoral degree,someinformationaboutaidandloansisavailablethrough https://financialaid.stanford.edu/

SomeMSstudentsfindResearchAssistantshipsupportatStanfordbydirectlycontacting professors.CoterminalMSstudentsareeligibleforRAshipsaswell,aftertheyhaveswitchedto theGraduateTuitionGroup(typicallyaftercompleting180units).

ManyofthecoreandadvisingfacultyintheDBDSprogramhaveresearchfundssupporting RAships.PleasecontacttheStudentServicesteamforaccesstothegoogledocwithupdated

informationregardingDBDSaffiliatedfacultylabprojects. Somefacultyareopentohavingan MSstudentonRAship.

3.9.6.TerminalGraduateRegistrationandPart-TimeEnrollment

1. TerminalGraduateRegistration

Studentsenrolledinmaster'sprogramswitharequiredproject(suchasDBDSpost-docsfunded bytheNLMtraininggrant)shouldapplyforTerminalGraduateRegistrationStatus upon completionofallrequiredcoursesandcompletionof45residencyunitsatStanford.Youthen enrollinBIOMEDIN801.

2. GraduatePetitionforPart-TimeEnrollment

Ifyouneedonly3-7unitsinthelastquarterbeforequalifyingtogoTGR,orinthelastquarter beforegraduation,discussthe"GraduatePetitionforPart-TimeEnrollment"withtheStudent ServicesOfficerpriortothefirstdayofthequarter.

Ifthepetitionisgranted,youmayenrollin3-7units.Co-terminalstudentswithanactive undergraduatedegreeprogramandinternationalstudentsarenoteligibleforthispetition. Beforeregisteringatlessthantheregularfull-tuitionrate,consider theeffectsofthatregistration onyourdegreeprogressandoneligibilityforfinancialaidandawards,visas,defermentof studentloans,andresidencyrequirements.SubmittheformpriortothePreliminaryStudyList deadline(5pmfirstdayofclasses)oftheeffectivequarter.

3.10 PhD Degree

3.10.1.Curriculum

ThePhDcurriculumisdescribedinfulldetailin ExploreDegrees Thecurriculumconsistsoffive maincomponents:

1. CoreDBDSclasses

2. ElectivesfromComputerScience,Statistics,Mathematics,andEngineering.The completelistofallowablecoursesforthiscomponentappearsat DBDSElectives.Note: youcanhavenomorethan9unitsincoursesbelowthe200level.

3. SocialandEthicalIssues.Acompletelistofallowablecoursesis listedatExploreCourses byentering"dbds::ethics".NotethatMD'sandcurrentmedicalstudentsareexempted fromthisrequirement;replacethisrequirementwiththeequivalentnumberofDBDS relatedGraduateElectives.

4. Unrestrictedgraduateelectives.Anycoursesatthelevel100orgreatermaycount.

5. Biology/MedicineElectives

3.10.2.Academicmilestonesoverview

Aninformaloverviewofthemajormilestonesbyyear:

• Year1:Takeclasses,dolabrotations,pickalab,submitapplicationsforoutsidefunding.

• Year2:Takeclasses,TA,doresearch,takethe oralandwrittenqualifyingexams,submit applicationsforoutsidefunding.

• Year3:Finishupclasses,TA,doresearch,starttoestablishyourDoctoralDissertation ReadingCommitteeattheendofthethirdyear,give Research-in-Progresstalk,submit applicationsforoutsidefunding.

• Year4:Doresearch, finalizeDoctoralDissertationReadingCommitteebymid-4th year andmeetwiththemonce.

• Year5:Finishresearch,defendandsubmitDissertation,graduate.

SummaryofMilestonesforeachPhDcohort,afterchoosingalab:

2 Quals(written&oral)

3 ResearchinProgress Talk

4 FinalizeDissertation ReadingCommittee Members

* 2ndyearProgressReport-1quarteronly

** ResearchinProgressTalkcountsasyourdissertationreadingcommitteeinyour3rdyear

***MeetwithReadingCommitteetwiceinthe5th year.OralDefensecountsasonemeeting.

SeethesubsequentsectionsformoreinformationontheMilestones,Progressreport,IDPetc.

3.10.3.

Researchrotations

Researchrotationsarecriticalforstudentsinchoosingtheirresearchlaborproject.Inaddition, rotationsbroadenastudent'sresearchexperienceandfamiliarizestudentswithongoing researchprojects.Rotationsaresetupbymutualagreementbetween thestudentandthe facultymember.

PleasecontacttheStudentServicesteamforaccesstothegoogledocwithupdatedinformation regardingfacultywhoareinterestedinhavingDBDSPhDstudentsintheirlabforresearch rotations. Studentsshouldcontactfacultydirectlytodetermineifthereisarotationspot available.

PhDstudentsshoulddothreeresearchrotations,exceptforinextenuatingcircumstances. Rotationsaretypicallyonequarterinlength,butthestudentcanarrangeshorterrotations,or

endearlyifthelabisnotagoodfit.Rotationslongerthanonequarterarediscouraged,asthe primarypurposeoftherotationistofindasuitablethesislab,nottoobtainpublicationquality results.Studentsarestronglyencouragedtomaketheirlabchoicebytheendofspringquarter. Studentsmustchoosetheirlabandresearchadvisorbytheendoftheirfourthquarterinthe program.Typically,thisistheendofthesummerquarteroffirstyear.Thereissomeadvicehere: ChoosingRotationsandaThesisLab|IncomingStudents|StanfordBiosciencesPhDPrograms

WhenyouandaPIhavereachedamutualagreementaboutyoujoiningtheirlab,letDBDS StudentServicesknow.

Pleasealsoreviewtheinformationinthesectionbelowonsettingupadoctoral dissertation readingcommitteewithrespecttothecommitteemembership,andwhocanbeaprimary advisor.

3.10.4.GraduateStudentTrackingSystem

Biosciencesisnowusingaweb-basedsystemfortrackingsomeimportantmilestones.Youenter informationdirectlyintothatsystem.Youcanreadmoreaboutiton theGSTpage Itwas designedtoprovideinformationabouteachstudent’sacademicprogress,andtoaidwiththe accomplishmentofcertainacademicmilestonesinaPh.D.career labrotations,qualifying examinations,andboththesiscommitteeandIndividualDevelopmentPlan(IDP)meetings.

3.10.5.AnnualProgressReport

ThisannualprogressreportformisseparatefromtheBiosciencesIDPandisintendedtogivethe DBDSdepartmentleadershipandStudentServicesanupdateofstudentprogramprogress,any concerns,andmentor/studentcommunication.TheProgressReportformwillbesenttoPhD studentsandtheirresearchadvisor/sinordertosetexpectationsbetweenstudentsandtheir researchadvisor(s)fortheyear.Alinktotheformcanbefound here.Itdoesnothavetobevery lengthy,aparagraphforeachpartoftheformwillsuffice.

Anannualmeetingbetweenresearchadvisor/sand theiradviseesisrequiredinordertodiscuss professionalgoals&reviewcoursework,academicprogressandresearchprogress.Thismeeting willsufficetocompleteboththeIDPformandtheProgressReport,whicharedueatdifferent timesduringtheyear.TheProgressReportalsohelpstosupportresearchadvisorswhen mentoringadviseesontheirresearchprogress,andtokeeptheirstudentsontrackfor graduation.

PleaseseechartbelowtoconfirmwhentheProgressreportisdue,versusotherannual milestones.

SummaryofMilestonesforeachPhDcohort,afterchoosingalab:

3 ResearchinProgress Talk

4 EstablishDissertation ReadingCommittee

5 OralDefense

5+ OralDefense,ifnot earlier

* 2ndyearProgressReport-1quarteronly

1x/yr**

1x/yr

2x/yr***

2x/yr

**ResearchinProgressTalkcountsasyourdissertationreadingcommitteeinyour3rdyear. You shouldinvitepotentialdissertationcommitteememberstothistalk.

***MeetwithReadingCommitteetwiceinthe5th year.OralDefensecountsasonemeeting. SeethesubsequentsectionsformoreinformationontheMilestones,Progressreport,IDPetc.

Pleasemakesuretoenteryourmeetingdatesinthe GraduateStudentTrackingSystem.

3.10.6.IndividualDevelopmentPlan(IDP)

TheIDPisanannualprocesstoreviewyourprofessionaldevelopmentwithyourresearch advisor. Itiskeptconfidentialbetweenyouandyourresearchadvisor. Itisimportantand requiredforallPhDstudents.FailuretocomplywithIDPrequirementswillnegativelyimpact Stanford'sabilitytoreceiveNIHfunding,andcreateaholdonyourregistration.TheIDPis separatefromanyDBDSprogressreport.

Thedetails,includingdeadlinesandformsareatthe BiosciencesIndividualDevelopmentPlan page

WhenyouhavecompletedyourIDPforagivenyear,pleaserecordthatyouhavedonesousing theGraduateStudentTrackingSystem.Theformsandthecontentofyourdiscussionsremain private.

3.10.7.Fundingsupportandfinances

ThankstostrategicsupportfromtheSchoolofMedicineandStanfordBiosciences,aswellas generoussupportthroughtraininggrantsfromtheNationalLibraryofMedicine,andvarious fellowships,assistantships,endowmentandphilanthropy,andfacultyfunds,weaimtofully fundourPhDstudentsfor4years.WedonotbasethefundingplanforincomingPhDstudents onResearchAssistantships,assuchassistantshipsrestrictastudenttoaparticularfaculty memberandlab.OurtraininggrantsfromtheNationalInstitutesofHealthcoveronlyUS Citizensorpermanentresidents,sothefundingplanforinternationalstudentstypically dependsonexternalfellowshipsupport(includingfellowshipsfromtheirgovernmentwhich guaranteestheirabilitytosupport theirentirestudies).

3.10.7.1. Applying for outside funding:

AllDBDSPhDstudentsareadmittedwithafundingplaninplace.However,youarerequiredto applytointernalandexternalfundingforwhichyouareeligible.Receivingsuchfunding

providesvalidationofyourresearchideas,andalsoallowsustosupportmorestudents.Please contactstudentservicesforthelinktotheFundingOpportunitiesgooglesheet.

NSFGraduateResearchFellowship:ThissectiondescribestheprocessforapplyingforNSF GraduateResearchfellowshipprogram,athree-yeargraduatefellowshipaimedatpromoting diversityandsupportingexcellenceinscienceandengineering.

DBDSstronglyencouragesyoutoapplytotheNSFGRFP. Thefellowshipprovidesa$37,000 annualstipendperyearplus$16,000cost-of-educationallowance,whichStanfordwill supplementuptostandardstipendlevels.TheNSFislookingtofundoutstandinggraduate studentswhoarepursuingresearch-baseddoctoraldegreesinSTEM.Fellowsareexpectedto contributesignificantlytoresearch,teaching,andinnovationsinSTEM(beawell-rounded scientificambassador).Critically, thereisnoobligationtocarryouttheproposedresearchif yougetthefellowship.Achievingfundingisalsoamajorwaytocontributetoensuringthere arespotsinourprogramforfuturedeservingstudents!

Thefellowshipisprestigiousandcompetitive –thoseplanningtoapplyshoulddevotesincere efforttotheirapplicationandgetstarted asearlyaspossible.TheGrantWritingAcademyand StanfordBiosciencesareheretohelpstudentsthroughtheprocess (https://grantwriting.stanford.edu/nsf-grfp/).Weencourageyoutotakeadvantageofthese resourcesandsolicitlotsofhelpandfeedbackwithyourapplication.FacultyintheDepartment ofBiomedicalDataScienceareheretohelp. Currently,ProfessorAaronNewmanisour departmentrepresentativefortheNSFGRFPandcanprovideyouwithsupport,resources,and feedbacktoassistyouinapplying.

Additionalinformationandnextsteps:

TheNSFapplicationdeadlines forallofthevariousSTEMdisciplines(suchasLifeSciences, ComputerandInformationScienceandEngineering)areinmid-October.Specificdeadlinesfor eachSTEMdisciplinecanbereviewedindetail here.

LifeSciences–October16,2024

ComputerandInformationScienceandEngineering –October18,2024

Youareencouragedtojointhe StanfordBiosciencesStudentAssociation’sPeerMentoring Program,astudentrunprogramthatmatchesfirstandsecondyearscholarswithformerNSF GRFPAwardeesorHonorableMentionsforgrantwritingmentorship.

Only1stand2ndyeargraduatestudentscanapply.Youcanonlyapply once.

DetailsaboutNSFreviewcriteriacanbefoundbelow.

PleaseletDr.AaronNewman(amnewman@staford.edu)knowatyourearliestopportunityifyou plantoapply.

PleasealsosendDr.NewmanthenameandemailaddressofyourFallRotationAdvisor.

AdditionalinformationaboutGWAresourcescanbefoundhere: https://grantwriting.stanford.edu/nsf-grfp/

Thekeypointsofeligibilityarethefollowing:

(1) MustbeaUScitizen,national,orpermanentresident

(2) Nodegreepreviouslyearnedhigherthanbachelor’sorBS/MSjointunlessa2yeargap

(3) Ineitheryourfirstorsecondyearofgraduateschool

(4) Havenotappliedbeforeasagraduatestudent

NRSAFellowships:ThissectiondescribestheprocessforapplyingforNRSAfellowships.Youdo notneedtoapplyforNRSAF31fundingif:

• youareaninternationalstudent,or

• ifyouhavebothSGFandNSFfunding,or

• ifyouhaveSIGF,HHMIorotherfundingthatwillcarryyouthroughthe5thyear.

DetailsandTiming:

• PleaseletDBDSAdminknowaboutyourplansearly.Theprocessisabitcomplicated andyouwillneedhelp.

• TheF31programisdescribedhere: https://researchtraining.nih.gov/programs/fellowships/F31.

• Youshouldapplysometimebetweenthesummerofyoursecondyearandthe summerofyourthirdyear.Youshouldstartthinkingaboutthisevenearlier:theskills youlearninBIOMEDIN212aboutproposalwritingandyourwrittenQualsareboth valuableinconstructingastrongNRSAapplication.

• Youmusttakea3-hourclassatStanford,"NRSAFSeriesComputerLabSession," beforeyouapply.Thefellowshipapplicationrequiresalotofforms,soyoushould taketheclassseveralmonthsinadvanceofapplying,perhapsevenforanearlier cycle.Youregisterfortheclassusingthiswebsite: https://doresearch.stanford.edu/training/national-institutes-health-nih

• GrantapplicationsaresubmittedthroughStanford'sResearchManagementGroup (RMG),whichrequiressubmissionatleast5fullworkingdaysbeforetheNIH deadline.

• Youmustaskforastartdateinyourgrantapplication;thesedependonthecycleand arelistedinthetable.Generally,werecommendthatyouapplyforCycleIII.

Whatyoushoulddo CycleII

CycleIII

Takerequiredclass June/earlyJulyorearlier! Oct/earlyNovorearlier!

Applicationdueat StanfordRMG August1st December1st

Startdateifawarded AskforJuly1st

3.10.7.2. Terminal graduate registration (TGR):

AskforSept1st

WhenPhDstudentshavecompletedtheUniversity'sresidencyrequirement,been admittedtocandidacy,completed135unitsofcoursework,andsubmittedtheDoctoral DissertationReadingCommitteeform,theyshouldapplyfor TerminalGraduate RegistrationStatus.TGRgreatlyreducesthetuitionrate.Typically,youareeligibleforTGR statusintheSpringofyourfourthyear.WhenenrollingunderTGRstatus,astudentmay onlyenrollinonly1-3unitsofnon-requiredcoursework(withPI'sknowledge),inaddition tothezero-unitTGRcourse(BIOMEDIN802).Itisthestudent'sresponsibilitytobeaware ofwhenhe/sheiseligibleforTGR.TobeconsideredonTGRstatus,thestudentmust submittheTGRformtotheRegistrarpriortothebeginningofthequarterforwhichthe requestisbeingmade.Ifyourfellowshiprequiresthatyoubeenrolledinoneormore unitsevenduringthecourseofaninternship,youshouldsignupforCurricularPractical Training(BIOMEDIN390A,BIOMEDIN390B,BIOMEDIN390C).

3.10.7.3. Graduate Petition for Part-Time Enrolment:

Ifyouneedonly3-7unitsinthelastquarterbeforequalifyingtogoTGR,orinthelast quarterbeforegraduation,discussthe"GraduatePetitionforPart-TimeEnrollment"with theStudentServicesOfficerpriortothefirstdayofthequarter.

Ifthepetitionisgranted,youmayenrollin3-7units.Beforeregisteringatlessthanthe regularfull-tuitionrate,considertheeffectsofthatregistrationonyourdegreeprogress andoneligibilityforfinancialaidandawards,visas,defermentofstudentloans,and residencyrequirements.SubmittheformpriortothePreliminaryStudyListdeadline(5 pmfirstdayofclasses)oftheeffectivequarter.

3.10.8.QualifyingExamination(Quals)

ThegoaloftheQualifyingExaminationistoevaluatethesuitabilityofastudenttoadvance toPhDcandidacy.Theexaminationconsistsoftwocomponents:(1)theOralcontent exam,and(2)thewrittenresearchproposal.

Theoralcontentexamteststhestudent’sbroadfoundationinthefieldandtheabilityto synthesizeandcommunicatethatfoundationalknowledge.Itisthestudent’s responsibilitytobuildthisfoundationthroughcorecoursework,requiredtechnical electives,attendingseminars,engagementwithfacultyandpeers,researchactivities,and independentstudy.TheDBDScorecurriculumcoursesaredesignedtocontributetosuch asolidandbroadfoundation.Preparingforthequalifyingexamwilltakesignificanttime, typicallyduringthe2nd yearofthePhDprogram.Youshouldconsidersettingupstudy groupstoprepare.

Theinstructions,process,andcontentoutlinesfortheoralqualifyingexamwillbesentto allparticipatingstudentsinthefallquarteroftheir2nd year.

Thewrittenqualifyingexamisaresearchproposalbasedontheworkyouhaveconducted underyourresearchsupervisor.TheproposalshouldbeanNIH-stylegrantproposalinR01 format,includingtitle,abstract,specificaims,detailson“Significance,Innovation, Approach”,environment(advisor,othersinvolved) andreferences. Theinstructionsand processtimelineforthewrittenqualifyingexamwillbesenttoallparticipatingstudentsin thewinterquarteroftheir2ndyear.

Thepossibleoutcomesofaqualifyingexamare:

• QualifyingExaminationOverallPASS(bothelements):Studentisinvitedto advancetocandidacy.

• OralQualifyingExamFAIL:Studentmaybeofferedapartialexam(infocused areasofweakness)orcompleteretakeofexamwithin2-4months.

• WrittenResearchProposalFAIL:StudentmayresubmitResearchProposal within1-2months.

Studentswhoeitherfailordonotcompleteeithercomponentasecondtimewillhave theirperformancereviewedbytheDBDSGraduateProgramExecutiveCommitteeforthe suitabilityofcontinuinginthegraduateprogram.

AfterpassingtheQualifyingExam,studentsmustsubmittherequired Applicationfor CandidacyforDoctoralDegreeformtoDBDSStudentServices.

• 4.6.1DoctoralDegrees,Candidacy:Policy|GraduateAcademicPoliciesand Procedures

3.10.9.ResearchinProgressTalk

TheResearchinProgressTalkisawork-in-progresstalkthatyougiveduringyourthird year.Youshouldplanonitroughly6to9monthsaftertheQualsexam.Thepurposeisto

showpreliminaryresults,modificationstothespecificaims,andtogetfeedbackonyour methodologicalapproachandinnovations.Itwillalsogiveyousomeinsightintowhatwill beexpectedinyourthesisdefense,asthefacultywillasktoughquestions.TheResearchin ProgressTalkcountsasoneoftherequiredcommitteemeetings. Thetalklasts90minutesintotal.Thefirst45minutesisinpublic,followedbyaprivate sessionfor45minuteswithyourcommittee.Itisimportantthatthestudentinvitethose facultymemberswhomheorsheisplanningtohaveontheDissertationReading Committee. HereisfurtheradviceonpreparingyourResearchinProgresstalk: Research inProgressTalkGuidelines

Pleasesendcopiesoftheslidesaheadoftimetoyourcommittee,andsupplythemwith papercopesatthetalk.Makesureyourslideshaveslidenumbersforeasyreference.

3.10.10.SettingyourDoctoralDissertationReadingCommittee

EachPhDcandidateisrequiredtoestablishadoctoraldissertationreadingcommitteefor thedoctoraldissertationbylate3rdyear-early4thyear.Studentsshouldconsult frequentlywithallmembersofthecommitteeaboutthedirectionandprogressofthe dissertationresearchandarerequiredtomeetannuallywiththeirwholecommittee. Studentsmusthaveatleastthreefacultymembers:

• theprincipaldissertationadvisor,

• twootherreadersserveontheirDoctoralDissertationReadingCommittee,toread andcertifytheirdissertation.

AtleasttwomembersmustbeontheStanfordAcademicCouncil.Ifthefacultymember withwhomyouworkmostcloselyisnotontheAcademicCouncil,thenyouwillneedto addanotheradvisorwhois.Youareresponsibleforcheckingthis,andformakingsurethat everyoneonthecommitteeunderstandstheirrole.

Pleasenote:theDissertationReadingCommitteedoesnothavetoincludetheexactsame facultyastheOralDefensecommittee;however,oftenthesetwocommitteeshavethe samemembers. Eachoperatesseparatelyanditisuptoyoutomanagetheexpectations foreachcommittee.

TheDoctoralDissertationReadingCommitteeFormshouldbecompletedandfiledwith DBDSStudentServicesbeforeschedulingaUniversityoralexaminationthatisadefenseof thedissertation.Onoccasion,thedepartmentchairmayapprovetheappointmentofa readerwhoisnotontheAcademicCouncil,ifthatpersonisparticularlywell-qualifiedto consultonthedissertationtopicandholdsaPh.D.orequivalentforeigndegree.Approval isrequestedonaPetitionforDoctoralCommitteeForm.

Onedoctoraldissertationreadingcommitteemember,whomustbeacurrentmemberof theAcademicCouncil(typicallytheprincipaldissertationadvisor),readsthedissertation initsfinalformandcertifiesonthe CertificateofFinalReading thatdepartment(DBDS Program)anduniversityspecificationshavebeenmet.Thisisthe“finalsignature”.

Pleaseseethemilestoneschartinsection3.10.2onthetimingandexpectationsfor meetingwithyourDissertationReadingcommittee.Notethatstudentsmustmeetwiththe readingcommittee2xperyearintheirfifthyearandbeyond.

3.10.11.UniversityOralExamination(DissertationDefense)

Youarerequiredtodefendyourthesisresearchinapublicoralexaminationwitha committee.TheUniversityoralexaminationcommitteehasatleastfivemembers:atleast fourexaminers(includingyourprimaryadvisor)andaUniversitychair. Tobeclear:the oralexaminationcommitteedoesnotnecessarilyneedtohavethesamemembersasthe dissertationreadingcommittee,althoughthesamefacultycanserveonbothcommittees. YouareresponsibleforfollowingStanfordpolicies,listedat:

• GraduateDegrees|StanfordUniversity

• 4.7.1DoctoralDegrees,UniversityOralExaminations&Committees:Policy| GraduateAcademicPoliciesandProcedures

• 4.7.2DoctoralDegrees,UniversityOralExaminations&Committees: Implementation|GraduateAcademicPoliciesandProcedures

1. Preparethedissertationdraft:

Theprimaryadvisorshouldreadandapproveyourdraftdissertationbeforeitissenttothe restoftheoralexaminationcommittee.Alloftheoralexamcommitteemembersshould haveanopportunitytoreadandprovidecommentsonthedraft. Whenyousendyourdraft finalthesistotheoraldefensecommitteefortheirinput(atleast3weeksinadvance),also sendthefinaldraftversiontoyourdissertationreadingcommitteefortheirinputaswell. ThisshouldhappenatleastTHREEWEEKS(notdaysorhours)beforetheoralexamination. Alloftheoralexamcommitteeandreadingcommitteemembersmustbesatisfiedwith yourdraftbeforeyouproceedtothedefense.

Itisacourtesytoprovideyouroralscommitteechairwithacopyofyourdissertationand theOralsGuidelines,andtooffertomeetwiththembeforetheevent.

2. Structureandcontentofthedissertation:

Itsacceptabilityisjudgedbyyouradvisorandyourcommittee.Ingeneral,youshould writeacompletedocument(text,figures,tables,references)thatmakesascholarlycase fortheproblembeingaddressed,includesrelevantpreviouswork,andpresents your methodsandresultsinalogicalway.

3. Scheduletheexam:

Startatleasttwomonthsbeforeyourdesireddate.Planononehourforapublic presentation,includingtimeforquestionsfromtheaudience,followedbyupto90 minutesofclosedsessionwithyourcommittee,leadingtoavote.Thismeansthat committeemembersshouldsetaside2-1/2to3hours.

4. Findachair:

Whenadateandtimefortheoralexamisidentified,thenworkwiththeDBDSStudent ServicesOfficertoidentifytheexamcommitteechair.Thechairoftheexamining committeemaynotshareadepartmentorjointappointmentwithyourprimaryadvisor, normaythechairoftheexaminingcommitteebeontheDBDSGraduateProgram ExecutiveCommittee.

Oncethefullcommitteeischosen,fillouttheUniversity-mandatedpaperworkand providetheformalongwithyourtitleandabstracttoStudentServicesOfficer atleast threeweekspriortotheDefense.

5. Meetwiththeoraldefensecommittee:

Makesurethatyoumeetwithallmembersoftheoraldefensecommittee(andoptionally, thechair)asneededinthemonthsleadinguptotheexam.Besurethattheyunderstand whatyouaredoing,andagreethatwhatyouaredefendingisworthyofaStanfordPhD.

6. Planyourpresentation:

Dissertationdefensesshouldbeseriousscientificpresentationsofyourdissertation research.

Pleasesendcopiesoftheslidesaheadoftimetoyourcommittee,andprovidethemwith papercopiesatthetalk.Makesureyourslideshaveslidenumbersforeasyreference.

7. Aftertheexam:

Youshouldworkwithyourprimaryadvisoronaplantosubmitthefinaldissertation, whichmayrequiresomerevisionasaresultoftheexam.

Underthenewsystem,thereisnoFinalTalk.TheDepartmentofBiomedicalDataScience holdsaspecialeventtocelebrateallgraduatesduringgraduationweekend.YourPIand labmayalsoscheduleacelebration.

3.10.12.

OldThesisProposalDefense(enteredPhDprogrambeforeJuly 1,2018)

Ifyouenteredundertheoldsystem,youmayfollowtheserulesorchoosethenewrules withjusttheThesisDefense,describedabove.Undertheoldsystem,youpresentaThesis ProposalDefense,andthenabout6-9monthslater,yougiveyourFinalTalk.Therestof thissectioncontainstheoldrules.

3.10.12.1.

Thesis Proposal Defense (University Oral Examination)

TheDBDSThesisProposalDefenseistheUniversityOralExaminationandrepresentsthe lastmajormilestoneforcompletionofthePhDdegree.Inmostotherdepartments,the finaldefenseisthefinaltalk.ForDBDS,thisissplitintotheThesisProposalDefense (occurringearlierthanfinaldefenses),andtheFinalTalk.

Stanford'srequirementsarelistedat GraduateDegrees|StanfordUniversity and4.7.1

DoctoralDegrees,UniversityOralExaminations&Committees:Policy|GraduateAcademic PoliciesandProcedures

TheUniversityoralexaminationcommitteehasatleastfivemembers:atleastfour examinersandaUniversitychair.

1. Scheduletheexam:

2. BookaclassroominEdwards/Alway:

Viewthelistofroomsandtheiravailability:

Onceyoufindanavailableslotthatsuitsyourneeds,filloutthisformandwaitforan emailconfirmationfromMedSchedulerregardingyourbooking.

Pleasenote:Anyonecanusetheformstobookaclassroom thereisnoneedforstaffto makethebookingonyourbehalf.

3.Findachair:

Whenadateandtimefortheoralexamisidentified,thensearchfortheexamcommittee chair.TheChairneedstobesomeonewho'snotfromyourPI'sdepartment.Youcould chooseanyonewhoisfromanotherdepartmentthatisrepresentedonthecommitteeby oneoftheexaminersotherthanyourthesisadvisor.Thechairmustbeamemberofthe StanfordAcademicCouncil.Oncethefullcommitteeischosen,fillouttheUniversity mandatedpaperworkandprovidetheformalongwithyourtitleandabstracttoStudent ServicesOfficeratleasttwo-threeweekspriortotheDefense.

4.Meetwiththecommittee:

Makesurethatyoumeetwithallmembersofthecommittee(andoptionally,thechair)as neededinthemonthsleadinguptotheexam.Besurethattheyunderstandwhatyouare doing,agreewithyourthesisstatementandevaluationplan,andbelievethatwhatyou areproposingisworthyofaStanfordPhD.

5.Planyourpresentation:

Developyouroraldefenseinconsultationwithyourthesisadvisor.Decideinadvancewhat pointsyouneedtomake,whatbackgroundneedstobeprovidedtotheaudience,and whatyoucanleaveoutorsaveforquestions.

Practicethetalk.Goovertheslideswithyouradvisor.Avoidglibness,orexcessive informality;thisisonetimewhenapresentationneedstoberatherformal.Youaretrying todemonstratethatyouarealreadymasterofafieldandarestrikingoutto breaknewand importantgroundofsomekind.Eventhoughyouwillhavesharedyourproposalwithyour

committeeandoftenwithothermembersoftheaudience,donotassumethateveryone willhavedigesteditindetail.

Dissertationdefensesshouldbeseriousscientificpresentationsofastudent'sdissertation research,similartoapostdocinterviewtalk,ratherthanatalkaimedatalayaudience. Stateyourgoalsclearly;makesurepeopleunderstandthemotivationfor whatyouare doing,aswellasthetechnicaldetails.Thedefenseshouldclosewithasummaryofwhat remainstobedonebeforeyourdissertationwillbecomplete,includingadetailedtime lineoftasks,milestones,andtheiranticipatedcompletiondates.Studentsshouldlimit acknowledgementstooneslideandacoupleofminutes,savingmoreextended acknowledgementsoffriendsandfamilyfortheFinalTalk.

Pleasesendcopiesoftheslidesaheadoftimetoyourcommittee,andsupplythemwith papercopiesatthetalk.Makesureyourslideshaveslidenumbersforeasyreference.

6.Preparethewrittenproposal:

Theproposaldocumentissupposedtobeacompleteandcompellingdocumentthat presentstheproblem,reviewstheliterature,andthendescribesyourplanforcompletion. Itshouldbepolishedandhaveafullsetofreferences,figuresetc.ItisNOTadraft dissertationbutshouldbeacompellingandcompleteproposalforworktobedone. Althoughthisdocumentmayyieldsignificantfragmentsthatendupinthefinal dissertation,itshouldpresentadefendableproposal.Itsacceptabilityisjudgedbythe oral defensecommittee,usingtheirjudgment.Ingeneral,youshouldwriteacomplete document(text,figures,tables,completereferences)thatmakesascholarlycaseforthe problembeingaddressed,relevantpreviouswork,andpresentsascientificallylogical planforhowitwillbeapproached.Onepossibleoutlinewouldbe:

• Ch.1:Introducetheproblemyouareaddressing,whyitisimportant,whyit maybesolvable,andwhatyouconsidertobethekeythingsyouwill investigateandtrytomakecontributionsto.

• Ch.2:Deep,criticalandscholarlyliteraturereviewoftherelevantareas.

• Ch.3:Preliminaryworkthathasbeencompleted.Youcanusepapersthat youhavewritten(asfirstauthor),eachinitsownchapter.Thekeything thereisthatthewritingshouldbeyourown,andsoyourfulldraftisbetter thansomethingthatwasheavilyeditedbyco-authors.

• Ch.4:Proposedworktobedoneindetailwithvalidation,possible problems,andbackupplans,alongwithaschedule/timeline.

• Ch.5:Summaryofanticipatedcontributionstobiomedicineandbiomedical datascience.

Thedocumentshouldbefullyreferenced,withfigures,tables,completesentences,andno sections that are empty. There is no length requirement (or limit) but most proposals are between30-501.5-spacedtypedpages.

Theprimaryadvisorshouldreadandapprovetheproposaldocumentbeforeitissentto thecommittee.Thisistoensurethatthestudentandtheadvisorhaveaclearandshared understandingoftheproposedworkplan,andthatithasbeencapturedbythestudentin thewrittenproposaldocument.

Inthecasewhereoneormorecommitteemembersisnotsatisfiedbythewritten proposal,thereareseveraloptions:

• Theoraldefensecanbepostponed,butthiswouldbeanextraordinary eventbasedonconversationswiththeadvisorandprogramdirector,and wouldhavetobeconsideredwellin-advanceofthescheduleddateofthe oraldefense.

• Theoraldefensecangoon,andiftheoraldefenseandQ&Aisanotherwise passingperformance,thecommitteecaneither:(1)provideinformal feedbackabouthowtoimprovethedocument,or(2)granta"conditional pass"conditionedonsubmissionwithina designatedtimeofanacceptable proposaldocument.

Workoutanarrangementwithyourthesisadvisortoassurethatheorshehasreadall chaptersofyourproposalandhasagreedthattheyareadequatenolaterthanTHREE WEEKSPRIORTOYOUREXAM.Ifyouradvisorhasnotseendraftsofallchaptersbythis time,andagreedthateverythingisontrack,itishisorherresponsibilitytonotifyStudent ServicesOfficerthatthescheduledexamshouldbecancelled;youwillneedtoreschedule itatatimewhenthe3-weekwindowislikelytobeachievable.

Incorporatecommentsfromyouradvisorandgenerateafinalthesisproposalfordelivery toyourcommitteenolaterthanTWOWEEKSPRIORTOYOUREXAM.Thisprovidesyour committeewithenoughtimetohaveareasonablechanceofreadingthedocumentprior toyouroraldefense.Failuretomeetthisdeadlinewillalsotriggeracancellationoftheoral exambyyourthesisadvisorsothattheexamcanberescheduledforatimewhenthe committeewillhavehadadequatetimetoreadtheproposal.

Itisacourtesytoprovideyouroralscommitteechairwithacopyoftheproposalandthe OralsGuidelines,andtooffertomeetwithhim/herbeforetheevent.Theywillgenerally notrequirethatyoudothis,butmaketheoffer.Also,besuretheyunderstandthatyouwill bedefendingaproposalandnotacompleteddissertation.

TheUniversityOralExaminationformshouldbesubmittedtotheStudentServicesOfficer atleastthreeweekspriortotheexaminationdate.

7.ThesisProposalDefenseOralPresentationGuidelines

1. Whatisthescientificprobleminthebiological/medicaldomainthat motivatedyourresearch?

2. Whyisthatproblemimportanttosolve?

3. Whatotherresearchhasbeenpreviouslyattemptedtosolvetheproblem describedinQuestion2above?

4. WhatarethelimitationsoftheexistingapproachesdescribedinQuestion4 above?

5. WhatareyourhypothesesabouthowtoovercomethelimitationsinStep5, andhowwelldoyoupredictitwillresolvetheproblemsdescribedinStep 2?

6. Inafewminutesdescribetheunderlyingcomputationalapproachthatyou havetakentoaddressabiological/medicaldataanalysisproblem.

7. Describeindepththedetailsofyourresearchaimedatthelevelofexpertise ofyourcommittee.

8. HowwillyoushowthattheresearchdescribedinQuestion7resolvesthe problemsdescribedinQuestion2?

9. Howdoyouproposetocompleteyourresearchandevaluationduringthe timeremainingbeforeyougraduate?

10. WhatarethecontributionstoBiomedicalDataScienceandwhatarethe contributionstothebiological/medicaldomain?

3.10.12.2. Final talk:

TheFinalTalkisasummaryoftheworkaccomplishedonthePhDresearch,andshould occurwhenthestudentisstillmatriculated.Thefinaltalkshouldprimarilyemphasizethe researchthathasbeencompletedsinceyourthesisproposaldefensepresentation.Itlasts aboutanhour,includingtimeforquestions.Extendedacknowledgementsoffamilyand friendsareappropriateinthiscelebratoryvenue.

Thestudent'sFinalTalkmustbescheduledduringtheregularacademicquarter,andmay notbescheduledduringfinalsweekorduringthebreakbetweenquarters.Thereisno mandatoryattendancebythecommittee(althoughthisisencouraged)andtherefore thereshouldbenoparticularlyonerousschedulingconstraints.

3.10.13.Submittingyourdissertation

Universityregulationsspecifythecompositionoftheoralexaminationcommitteeandthe formatofthedissertationdefense.SeetheRegistrar'sDissertationandThesisSubmission page.

A thesis draft should be submitted to your oral examination committee four weeks before theRegistrar’sdepositdeadline.Theoralexaminationcommitteeshouldhavenolessthan two additional weeks to read the final dissertation before the deadline for signing off and depositwiththeRegistrar'soffice.

OnceyourthesishasbeensubmittedtotheRegistrar,theStanfordUniversitylibrarieswill provideelectronicaccessthroughtheSearchWorksWebcatalogintheProQuestDigital Database.BoundcopiesofdissertationscanbepurchasedthroughtheHFGroup Thesison DemandincontractwiththeUniversitytoprovidethestandardredbinding.Pleasecheck theRegistrar'swebsiteforcurrentinformationandinstructions.

3.10.14.

GettinganMSwhileinthePhDprogram

3.10.14.1. Getting an MS from DBDS:

ThereisnotraditionintheBiosciencesofroutinelyofferingMSdegreesonthewaytoa PhD,althoughourprogramhasawardedtheminthepastunderspecialcircumstancesat therequestofthestudent.TheDBDSGraduateProgramExecutiveCommitteewill considerrequeststobeawardedanMSdegree.UponcompletionofMScoursework requirements,studentsmustsubmitaMaster'sProgramProposal,submita Graduate AuthorizationPetition(fee=$125),andifapprovedapplyforgraduation,selectingtheMS (notPhD)program.

Notethatthereare major financialconsequencesofPhDstudentsobtaininga second MS degreealongtheway.Typically,thiswouldoccurifyourequesttheDBDSMS,andthen addanMSinstatisticsorCS.Generally,youshouldn'tdothis;pleasediscusswiththe StudentServicesattheearliestopportunity.

3.10.14.2. Getting an MS from another program:

SomestudentschoosetopursueanMSinanotherdepartment,typicallyStatisticsorCS, whiletheyareaPhDstudentinDBDS.NotethatyoushouldonlypursueaMSinanother departmentifyouhavenotreceivedanMSfromDBDS. TocompleteaMSinanother departmentstudentsmayusecoursesthatfulfillrequirementsforbothprogramstowards theirMSdegreeandreplacethosecourseswithunrestrictedelectives.Forexample:STATS 200isaDBDSrequirementbutalsofulfillsarequirementfortheSTATSMS.Students pursuingaSTATSMSwouldtakeSTATS200fortheirSTATSMSandreplacethoseunitswith unrestrictedelectivestomeettheDBDSrequirement.StudentsneedtopetitiontheDBDS ExecutiveCommitteetoaddtheoutsideMSandshoulddothisinadvance ofapplyingto theotherdepartment.Thisrequiresplanningahead.PleasesubmittotheExec:

1. Acoverletterfromyouaboutwhythisisacademicallyagoodideaforyou,

2. YourDBDSflowsheetshowinghowyoufitincourseworkfrombothprograms,

3. AletterofsupportfromyourPI.ThisshouldindicatethattheyareawareyourMS couldlengthenthetimetodegree,andthattheymayneedtopaythetuition differentialbetweenregularfull-timetuitionandTGRtuitionifyoutakelonger than

Springquarterof4thyeartoreachTGR.Thiscanvarydependingonwhat fellowshipsandscholarshipssupportyou;pleaseinvolveDBDSStudentsServices earlyinyourplanning.

3.10.15.ApplyingtothePhDprogramwhileenrolledintheMSprogram

TherehavebeencaseswhereastudentalreadyenrolledintheDBDSAcademicMS programhasexpressedaninterestinchangingtothePhDprogram. Wewantto emphasizethattheMSandPhDprogramsareseparatepathways,andMSshouldnotbe viewedasanon-ramptoPhD. IfanMSstudentwishestoapplyforPhD,theywillneedto applythroughthenormalBiosciencesPhDapplication (typicallywithanearlyDecember deadline) andbereviewedalongwithallotherapplicants.

DBDSMSapplicantswillbeevaluatedwiththesamerigorasotherapplicantstothePhD program,and(ifadmitted)willbesubjecttotheexpectations,curriculumandother requirementsofthePhDprogram.

4.Travel

TheofficialStanfordtravelrulesandpoliciesforstudentsaredescribedontheFingate webpage:Fingate-WhenStudentsTravelforStanford.

Onceyouareaffiliatedwithalab,youshouldexpectsometravelsupportfromthatlab, particularlytopresentresearchresultsfromthatlab,sodiscussthiswithyourPI.DBDS canalsoprovidefinancialsupportforconferencetravelforourPhDandfull-timeMS students,includingco-terminalstudentsengagedinresearch.Fundingisobviouslylimited andpriorityisgiventothosewhoareinvitedtopresentorhaveapaperoraposter accepted,aswellasforparticipationinstrategicactivitiessuchastraveltomeetings wherewewanttohaveStanfordDBDSrepresentation(forexample,AMIA,SACNAS, ABRCMS,andtheNLMconference).Asageneralguideline,wehavebudgetedabout$1,300 perstudent.

4.1. NLM Travel Funding and conference

OurNLMtraininggrantsprovidealimitedamountoftravelsupportforstudentsfunded throughthosegrants(includingtotheNLMmeeting).AyearfortheNLMTrainingGrant runsJuly1-June30.Traveldollarsmustbespentduringthegrantyearandcannot carry over.

NLM-supportedstudents must attendtheannualNLMmeeting,usuallyheldinearlyJune. Wewillfundthistravel.TheNLMconferenceincludespostersessionsandresearch presentations,andhavingrigorous,compellingpresentationsbyourtraineeshelps confirmandstrengthenStanford’sreputationaswellasyourvisibilityinthenational informaticscommunity,andpotentiallybenefitsfuturefundingopportunities.

4.2. How to request support for travel

Youneedtorequestsupportfortravelaheadoftime,usingtheproceduredescribed below.Ifyoufirsttravel,andthenrequestpaymentforthetravel,yourrequestwillbe denied.

Co-terminalstudents:ifyouhadapresentationorposteraccepted,letusknow;wemaybe abletosupportyourtravel.

Procedure:

1. SubmitaTravelRequestFormtoDBDSStudentServices.Youshoulddothisahead oftime(weekstomonths,notdays).Failuretosubmitthetravelrequestform beforethetravelwillmeanthatthestudentisresponsiblefortheentirecostofthe trip.

2. SubmitaStudentCertificateforAuthorizedExpense formsothatthetravel reimbursementwillnotbeconsideredtaxableincometothestudent.

4.3. How to make travel arrangements

Studentsareresponsibleformakingtheirownreservationsforapprovedtravelto conferences.(DBDSStudentServiceswillmakethearrangementsfortheannualNLM InformaticsTrainingConference.)UseEgenciathrough StanfordTravel'sOnlineBooking Tool.Allstudentsareexpectedtoarrangeforthelowest,restrictedfare,usingaUSair carrierundertheFlyAmericaAct.TicketscanbepurchasedwiththeDBDSTravelcardor thestudent'spersonalcreditcard.Ifthestudentusesapersonalcreditcard reimbursementwillbeissuedtothestudentuponcompletionofthetravel. Travel insuranceandseatupgradesarenotcoveredbyDBDStravelfunds.

Studentsshouldcompletetherequiredtravelrequestformsandcertificationaswellas registrationformsformeetingswellinadvance,andattempttoqualifyforearly registrationdiscountswheneverpossible.NormallyonlytheEarlyBirdregistration amountwillbereimbursed.Theregistrationfee,ifitisanapprovedexpense,isoften chargeddirectlytothegrantsupportingthetravelandthereforeisnotaliabilitytothe student.Membershipfeeswillbereimbursedifrequiredforanearlyregistrationdiscount.

Itisalsothestudent'sresponsibilitytoarrangeforlodgingatmostconferences(exceptthe NLMconference).Again,frugalityisencouraged,bothbecausethereisamaximumper diemthattheUniversitywillpayforlivingexpensesawayfromStanford,andbecausethe abilityofotherstudentstotravelinthefuturewilldependoneachstudentworkingto keeptravelcostslow.Studentsshouldordinarilystaytwotoaroom,andshouldnot expectreimbursementforitemssuchasdrycleaning,roomservice,telephonecalls, payper-viewmovies,andothersortsofentertainment.Studentsshouldcarefullyconsider ifacarrentalisreallynecessary.Sincethetravelpoliciescanbeconfusing,pleaseaskthe StudentServicesOfficerforclarification.

IfyouplanothertripsaroundbusinesstravelpleasecheckwithStudentServicesin advanceofyourbookingtodiscussthepotentialcostadjustment.Subsequentchanges couldresultinyoubeingresponsibleforchangefees.

Ifthereisaproblemwiththetravelitinerarysuchascancelledflights,feesforchanging datesortimesoftravel,orchangeofdateoftheconference,youmustcontacttheStudent ServicesOfficeroryouracademicadvisortogetguidanceaboutchangingtheflights and/orhotelandstillmaintaintherequirementsofthetravelguidelines.Failuretoget approvalforthesetypesofchangesmaymeanthatyouwillberesponsibleforthe expenses.

4.4. Receipts

Pleasesavealloriginalreceipts!Itisalmostimpossibletoreimburseyouifwedonot havetheoriginalreceiptsofallexpenses(food,lodging,registration,etc).Yes,pleasekeep yourreceiptsforpurchasesunder$25.Whenpurchasingtheairlineticketonline,the studentMUSTprovideproofofpaymentfortheticket.Ifthereceiptfromthevendordoes notclearlystatehowtheticketwaspaidfor,thestudentneedstoprovideacopyofthe creditcardstatementforproofofpayment.TravelandReimbursementhavestrictrules aboutreimbursementsandtheywillnotreimburseastudentunlesstheyhavethe requiredbackuppaperwork.Ifagroupofstudentsareeatingtogether,itispreferredthat eachstudentreceiveshisorherownbillorthatonestudentpaystheentirebill.Each student'snameshouldbewrittenonthebackofthereceipt.Thiswillnotbecounted againstthestudent'soveralltravelbudgetifonestudentpaysforthewholebillfor8 students,forexample.Studentsareencouragedtotaketurnsateachmeal,however,when payingfortheentirebill.Wedonotreimburseforalcoholicbeverages.

4.5. Reimbursement after you travel

SubmittoDBDSStudentServices:

1. Spreadsheetofdailycosts,includingamounts

2. Electronicorprintofairlinereceipt,includingproofthatyoupaidforit(Copyof creditcardstatement,Expediareceipt,etc.,showingtheamountwithyourname andmethodofpayment.)

3. Boardingpassesfromtheairline(toberevisited,thisisabitdated)

4. Registrationreceipt,includingproofthatyoupaidforit

5. Lodgingreceipt

6. Alloriginalreceiptsforotherpurchases

7. Programoftheconference

Ittakes2weeksforStanfordFinancialstoissuethereimbursementdeposit.Students shouldenrollindirectdepositthrough Axess

Youmaybereimbursedfortheregistrationfeeassoonasitispaid(priortotravel)andyou submittheappropriatedocumentation.Youmaynotbereimbursedfortheother expensesuntilyourreturnfromthetrip.Submitalldocumentationpromptly.If submissioniscompletedmorethan60daysaftertravel,thereimbursementistaxable income.

4.6. Local Travel

StanfordpolicyisthatconferenceorothertraveltoSanFrancisco,SanJoseorotherlocal citieslessthan50milesfromStanforddoesnotqualifyforovernightstayorfor reimbursablemeals.Studentsmaybereimbursedformileageandparkingortrain fare withareceipt.ConsultwiththeStudentServicesOfficerbeforeyoutravelifyouhave questionsaboutreimbursementpolicy.Wearenotabletoreimbursestudentsforgas mileagetotheannualDBDSretreat.Weencouragecarpooling.

4.7. Foreign travel

ContactDBDSStudentServices.Inmostcases,permissionisgivenifthestudent purchasestheairfarefromanapprovedAmericancarrierortheirforeignpartner.Referto theFlyAmericaAlliancesPolicybeforebookingaflight.

5.Timeaway

5.1.

Leave of absence

Theleaveofabsencepolicyisdescribedin 5.3.1LeavesofAbsence:Policy|Graduate AcademicPoliciesandProcedures

Pleasenotethatitisthestudent’sresponsibilitytoreviewVadenHealthand CardinalCare Insurancepoliciesduringaleaveofabsence. BesuretocontactVaden’sInsuranceand ReferralOfficeforguidanceaboutcoverageinadvance,ifatallpossible. Currentpolicies fromtheVadenHealthwebsite(asofAugust2024)are:

• AstudentwhoisgrantedaLeaveofAbsenceinAutumnforwhichtheeffectivedate oftheleaveispriortothefirstdayofclasswillnotbechargedtuitionorany associatedfeesforthequarter.Uponreversalofthetuition,thestudent’seligibility forenrollmentinCardinalCarewillbecancelledretroactivetoSeptember1.(The student’seligibilityforenrollmentinCardinalCarewillresumewhentheyreturn andtuitionisreinstated.)

• AstudentwhoisgrantedaLeaveofAbsenceinAutumnforwhichtheeffectivedate oftheleaveisonorafterthefirstdayofclassbutbeforethetermwithdrawal deadlinewillbecharged(prorated)tuitionandassociatedfeesforthequarter.If enrolledinCardinalCare,thestudentwillremainenrolledthroughtheendofthe planyear(August31)andapplicablefeeswillapply.

• AstudentwhoisenrolledinCardinalCareasofAutumnquarter,andwhois grantedaLeaveofAbsenceforasubsequentquarter(i.e.,Winter,Spring,or

Summer)willremainenrolledinandcoveredbyCardinalCarethroughtheendof theplanyear(August31)andapplicablefees(chargedWinterandSpringquarters only)willapply.

• AstudentwhoseinitialquarterofentryisWinterorSpring,andwhois subsequentlygrantedaLeaveofAbsence,willbesubjecttothesameguiding principlesasastudentwhoentersinAutumn,i.e.,iftheeffectivedateoftheleave ispriortothefirstdayofclass,tuitionandanyassociatedfeesforthequarterwill bereversed.Uponreversalofthetuition,thestudent’seligibilityforenrollmentin CardinalCarewillbecancelledretroactivetothestartoftheapplicablecoverage period(December1forWinterentrystudentsandApril1forSpringentrystudents). Iftheeffectivedateoftheleaveisonorafterthefirstdayofclassbutbeforethe respectivetermwithdrawaldeadline,thestudentwillbecharged(prorated)tuition andassociatedfeesforthequarter.IfenrolledinCardinalCare,thestudentwill remainenrolledthroughtheendoftheplanyear(August31)andapplicablefees willapply.

Thesepoliciesaresubjecttochangeeachyear,sowehighlyrecommendthatyougo directlytotheVadenHealthwebsiteforthelatestinformation.

5.2. Family leave

Thepregnancy,childbirth,andadoptionpolicyisdescribedin 5.9.1Pregnancy,Childbirth andAdoption:Policy|GraduateAcademicPoliciesandProcedures

5.3. Internships

Internshipscanbeagreatlearningopportunity,butalsocancausedelaysinyourresearch orpotentialconflictsofinterest.Notethattherearesometimeconstraints,soyouneedto planahead.

• InternshipsforPhDstudentsarerecommendedduringthe3rdand/or4thyear.In general,theDBDSGraduateProgramExecutiveCommitteehasaverystrong preferencethatinternshipshappenafteryoupasstheQualifyingExam,inorderto ensurethatyoupasstheExambyendofsecondyear,andtoensurethatyouhave sufficientscientificknowledgeandmaturitytogetthemostoutofyourinternship.

• InternshipsforMSstudentsarehighlyencouragedduringthesummerfollowing thefirstyear.

• CareerResourcescanbefoundontheStanfordSchoolofMedicine BioSciCareers website.

• Talktoyourresearchandacademicadvisorstoseeifaninternshipmakessense givenyourstatusintheprogram.Alsoconsiderwhatperiodoftimeandits relationshiptoyourDBDSmilestonestominimizedelaysinyourprogress.

• WhileinternshipsshouldberelatedtoBiomedicalDataScience,makesurethatthe specificareaofproposedinternshipresearchisdistinctfromyourStanford research,sothattherearenointellectualpropertyissues,suchaswhoownsyour workproductandwhetheritispublishable.Thisissuecanleadtoverylarge problems.Thetopicoftheinternshipprojectshouldbereviewedbyyourprimary researchadvisor,whowillbeabletoevaluateforpotentialoverlap.Askyour researchadvisortosendanemailtotheDBDSstudentservicesofficersupporting yourplanatleast1fullquarterbeforethestartoftheinternship.Thisisimportant togettingapprovalfromyourfundingsource.

• NotifytheDBDSStudentServicesOfficerwellinadvanceyourplans.

• IfyouareonanNIHtraininggrant,youwillhavetogooffthegrantforthetimeyou areaway,andpermissionwillneedtobeobtainedinadvancefromtheNLMorNIH. Thismaytakemorethan1quarter,sobesttoaskforpermissionwiththestudent servicesofficerASAP.TheNLMallowsthisforonlyonesummerduringyourdegree program.YoumightbeeligibletoextendyourNLMsupportforoneextraquarterif youdoaninternship,withpriorapproval.

• Ifyouaresupportedonanyothertypeoffellowshiporgrant,suchastheNSF,SGF, NDSEG,etc.,youneedtoverifytherulesforinternships.

• YoucannotreceivepaymentfromtheinternshipandyourStanfordsourcesforthe sametimeperiod.Youaretakingabreakfromfull-timeregistrationintheDBDS programandwillnotbefundedbytheDBDSprogramwhileparticipatingina fulltimeinternship.InternshipsmayaffectyourUniversitybenefits,suchashealth insuranceandVadenservices.Internationalstudents:seethenextsection.

• Ifyourproposedinternshipisnotduringsummerquarter,thenyouneedtomake specialarrangements.Pleaseseethesectionabouttakingaleaveofabsence.

5.3.1.SpecialNotesforInternationalStudents

InternationalstudentswithinternshipsintheUSneedtosignupforCurricularPractical Training(BIOMEDIN390A,BorC)andreceiveauthorizationthroughBechtelInternational Centertomaintaintheirvisastatus.Carefullyreadandfollowtheinstructionsat: CurricularPracticalTraining(CPT)|BechtelInternationalCenter

Specialcase:WhenaTGRstudentengagesinsummerCurricularPracticalTraining,they mustenrollforatleastoneunitinthedesignatedCPTcourse(BIOMEDIN390A,BorC)and shouldnotenrollinTGRorpayTGRtuition. BechtelInternationalCenterapprovesthe student’sCPTrequestandnotifiestheRegistrar’sOffice,whothentemporarilydeactivates theTGRtuitiongroupfortuitionassessmentpurposes,sotuitionischargedforonlyone unit.

Internationalstudentswhohavealreadycompletedallcourse/unitrequirementsfortheir degreearenoteligibleforcurricularpracticaltraining.CPTmaynotbeusedasareasonfor delayinggraduation.Internationalstudentswhoareofferedinternships outsideoftheUS

willneedtoallowsignificantleadtimetoconsultwithBechtelandmultipleembassies. Theconditionsforvisasandinternshipswilldependonindividualtreatiessignedbetween nations.

***WARNING*** WorkingwithoutaCPTendorsedI-20isaseriousviolationofyourlegal statuswhichcouldforfeityourabilitytoremainintheU.S.andbaryouinthefuturefrom re-entrytotheU.S.

6.Externalemployment

Pastexperienceswithourprogramhavetaughtusthatexternalworkcommitments, especiallyinareasthatoverlapwithresearchinterestsinthelab,essentiallyalwaysleadto problems,especiallywithrespecttointellectualproperty.Suchinvolvementsarenotin yourbestinterest,andtheycansignificantlydelaythecompletionofyourtraining.

Ifyoudotakepart-timeorhourlypositionsoutsidetheuniversity,youarerequiredto informtheDBDSExec.Amaximumofeighthoursperweekisallowedforoutsidework. Failuretogetapprovalbeforedoingworkoffcampusisacauseforconcernabout progress towardsdegree.Studentsmustregisterforallquartersandbeoncampus,unless specificallyapprovedotherwise.

TheUniversityrestrictsstudentsonfellowshipstonomorethan8-10hoursperweekof on-campusassistantships(suchasapaidTeachingAssistantshipinadifferent department).Internationalstudentsalsohavestrictlimitsonworkhours pleasecheck withtheStudentServicesOfficerorBechtelInternationalCenter.

7.Finances

7.1.

Fellowship Stipends

Studentsonfellowships(NLM,SGF,SIGF,NRSA,NSF,etc.)receivestipendpaymentsatthe beginningofeachquarterfortheentirequarter.Ifyouarelivingincampushousing,the systemissetuptoautomaticallysubtractthehousingfeesfromthestipendamount. Stipendsforlivingexpensesusuallyaretaxablebutincometaxesarenotwithheld.

7.2. Assistantships (Salary)

Studentsbeingpaidonanytypeofassistantship,usuallyaResearchAssistantshipfunded bythePI,orstudentspaidonanyothertypeofhourlyappointmentthatrequires submissionofhourlytimesheets,arepaidonthesamescheduleasthestaffandfaculty: workcompletedonthe1st-15thwillbepaidonthe22ndofthemonth,andwork completedonthe15ththroughtheendofthemonthwillbepaidonthe7thofthenext month.

• TheI-9formmustbecompletedbeforeassistantshipcheckscanbegin.Reachout toaStudentServicesOfficerforinformationonwheretogotocompletethis mandatorypaperwork.

• Pleasenotethathousingandotherfeesarenotautomaticallydeductedfromyour salary.

• YoursalaryistaxableandtaxeswillbewithheldasyourequestontheW-4TaxData form,submittedthroughAxess.

Switchingbetweenthetwopaymentsystemsrequirescarefulbudgeting.Forexample: Switchingfromafellowship(SGF,NLM)stipendtoanassistantshipsalary:Ifthefellowship endsafterSummerQuarter,andyouhaveanRAappointmentforFallQuarter,you will receiveyourSummerstipendpaymentatthebeginningofthatquarterinJune.Youwill notreceiveyourfirstpaycheckuntilOctober22,astheFallQuarterdoesnotbeginuntil October1(inPayrollterms),andyouarepaidforthefirsthalfofthemonth(October1-15) onOctober22ndandforthesecondhalfofthemonth(October16-31)thefollowing monthonNovember7th.

7.3. Direct Deposit

Fellowshipstipendsandassistantshipspaymentsarebesthandledthroughdirectdeposit toyourbankaccount.Tosetupyourdirectdeposit,logintoAxessandfollowthese directions:https://studentservices.stanford.edu/my-finances/refunds-and-direct-deposits

7.4. Holds

Checksandothertypesofpaymentstothestudentwillnotbeissuedifthestudenthas unpaidfeesfrompreviousquarters(housing,activityfee,etc.),hasnotsubmittedthe federalemploymenteligibilityform(I-9foremployeePayrollonly),federaland statetax withholdingcertificate,andpatentagreementform(SU-18,doneonlineinAxess). Outstandingbillsfromthelibrary,University,orVadenHealthCenterwillalsoresultin holds.Holdsmustbeclearedwiththeoriginatingofficebeforestipend checkswillbe issued.Pleasepayyourhousingandothermiscellaneousfees. IfyouowemoneyfortuitionorhealthinsuranceandreceivefundingfromDBDS,please seeStudentServicesOfficer.Ifanotherdepartmentisresponsibleforyourfunding,please contacttheappropriatedepartment.TheDBDSStudentServicesOfficerishappytohelpin thosesituationstoo.CheckyouraccountinAxessoften!PleaseseeStudentServices Officerifyouneedhelpresolvinganyissues.

7.5. Taxes

Unfortunately,DBDSStudentServicescannotgivetaxadvice.Herearesomeuseful resources.

• Starthere:1098-TFAQ's&Resources|StudentFinancialServices

• AccordingtothissiteyoudoNOThavetopayincometaxesonVadenHealth ServicesFee,HealthInsurance,orRequiredFees(suchas1styearstudent DocumentFeeorASSUFee).

• Stanfordissuesanannualtuitionstatement,IRSForm1098-T,toprovide informationnecessaryforstudentsorparentstoclaimeducationaltaxcredits (http://www.irs.gov/uac/Tax-Benefits-for-Education:-Information-Center).Ithas cometoourattentionthatsomeonlineaccountingprograms(i.e.,TurboTax) inappropriatelyrefertoForm1098-Tasanincomeform.Usingthe1098-Tformto determineincomeratherthanclaimeducationaltaxcreditscancause misunderstandinganderrors.DoNOTusethe1098-Tformtodetermine fellowship/scholarshipincome.

• InternationalstudentsmaycontactBechtelInternationalCenter

• Also,IRSwebsite:http://www.irs.gov/

8.Graduation

8.1.

Graduation Photo

AllPhDstudentsshouldhavetheirphotographtakenbeforetheydefendtheirthesis. FulltimeacademicMSstudentsshouldhavephotostakenthequarterbefore graduation. StudentServiceswillreachouttograduatingstudentswithalistofphotographersandthe DBDSprogramwillpayforthephotographysessionandprint. Theportraitsittingshould bearound$250-$300plustax/shippingfees(tobesenttotheDBDSoffice)for(2)5x7 professionalportraitsinblackandwhite.

SeetheStudentServicesOfficerforadditionalinformationandtoprovideyournameas youwantittoappearonthebrassplate.

HCPMSandCoterminalMSstudentswillhavetheirnamesaddedtoplaquesaswell. PleaseinformtheStudentServicesSpecialisthowyouwouldlikeyournametoappearon thebrassplate.

8.2. Degree Conferral

Inordertohaveyourdegreeconferred,youmusthavecompletedalloftheUniversityand Departmentrequirements,andsubmittedallworkbeforethedeadlines.TheUniversity imposesrequirementssuchasresidency,submissionofofficialscoresandtranscripts, paymentoffees,andreturnoflibrarybooks,thattheDBDSprogramhasnocontrolover andsometimesnoknowledgeof.Youshouldmakesurethatthesehavebeenaddressed.

ChecklistitemsforDegreeConferral:

• OfficiallyapplytograduateinAxessbythe applicationtograduatedeadline

• Provideuswithanupdated courseflowsheet(whichgetsreviewedafterthe applicationtograduatedeadlinepasses)

• Provideuswithyourmilestonedates,specificallywhenyoucompletedyour(2)TA requirementsandthesisresearchinprogressmeetingdate

• Forwardanydepartmentalapprovedcoursewaivercommunications

• RunyourunofficialtranscriptandcheckforanyoutstandingGNRsorIncompletes. Contactyourprofessorstoupdate.

• RemindfacultyandTAsthatyouaregraduatingattheendofthequarterandtoget yourgradesinASAPsothatyoucanbeclearedforgraduation.

8.3. Notice of Intention to Graduate

YoumustfileaNoticeofIntentiontoGraduate(“applytograduate”)throughAXESSforthe quarteryoucompletethedegreerequirements.Ifyoudonotfinishintime,youwillneed toannultheinitialIntentiontoGraduateandsubmitanewoneforthequarterinwhich youintendtofinish.PleaserefertotheUniversitycalendarfordeadlines.Thereareno exceptionsformisseddeadlines.ThisisaUniversityrule.ThedeadlinesarelistedinAXESS andontheacademiccalendar.

8.4. Graduation Quarter

Ifyouhavecompletedeverythingexceptfordepositingthereport,thesisordissertation, youmaysubmitthatandgraduatewhileregisteredforaGraduationQuarteryourverylast quarter.ThisGraduationQuarteroptionisonlyavailableforonequarter. Youmustbean ActivestudentregisteredthequarterpriortothisoronanapprovedLeaveofAbsenceand youmusthavefiledTGRpapersanddefendedyourthesisbeforethis.Youwillstillneedto fileanIntentiontoGraduateforthatlastquarterinAXESS.Asmalltuitionfeewillbe chargedandyouwillbeconsideredafull-timestudentforvariousadministrative purposes.Yourdegreewillnotbeconferreduntiltheofficialconferraldateforthatfinal GraduationQuarter.

8.5. Commencement

DBDSstudentsfromalldegreeprogramsareencouragedtoparticipateinMedicalSchool Commencement,whichiscoordinatedbytheOfficeofStudentServicesintheSchoolof Medicine.IfyoucompleteyourdegreeinJuneorinapreviousquarterduringthat academicyear,youwillbeencouragedtoattendtheceremony.

9.Changelog

• 2017September:entirelynewformatwithheavilyrevisedcontent,including descriptionofWrittenQualifyingExaminationforPhDstudents.

• 2017October:updateddescriptionofinternationaltravel.

• 2017November:addednotethatyourPIshouldapproveofyouapplyingto taketheinformaticscontentpartofthewrittenqualifyingexam.

• 2018January:addedBiomedicalDataSciencesuitemailcode.Minortextual changestosectiononwrittenquals.

• 2018February:addedtextaboutpreparingslidesforpreproposalandthesis proposaldefense.

• 2018April:removedmostofthetextaboutthePhDQualifyingExambecause thattextandthecorrespondingcontentoutlinesareavailableinaBoxfolder.

• 2018April:addedtextaboutnotingsourceoffigures/tablesinyourslides.

• 2018May:replacedoldThesisProposalDefense+FinalTalkwithThesis Defense.

• 2018May:clarifiedergonomicsequipmentsection.

• 2018October:rewrotetheProgressReportsectiontoreflectcurrent(greatly simplified)procedure.

• 2019May:MinorupdatestoFlowsheet/ProgramProposalInstructions

• 2019August/September:UpdatedstaleURLs.ClarifiedWaiverprocess.Updated computingenvironmentsection.ClarifiedTArequirement.ClarifiedQuals section.AddedasectiononfundingsupportforMSstudents.Expandedthe studentssectionincludinglinks fornewstudentsandinformationaboutthe retreatandorientation.Updatedemergencyinformation.

• 2019November:ClarifiedadvisorchangeprocedureperCGAPrequirements. UpdatedQualsprocedurefor2019-20.AddedsectiononapplyingtothePhD programwhileintheMSprogram

• 2020January-March:PhDfundingplanclarification.Travelclarifications. ReorderedportionsofSection2.Addedwellnessresources.FurtherQuals clarifications.Temporaryreferencetodocumentrelatedtopublic-healthcrisis situation.

• 2020Spring:ClarifiedNIHpublicaccesspolicy.Addedlinksandresources. Rearrangedafewsections(e.g.onmailinglists)forformatting.Expanded discussionofTArequirementsandtypes.AddeddetailsforHCPprogramand switchingpolicy

• 2020August.SlightlymodifiedtheAcademicMSdescriptiontoreflectthetextin ExploreDegreesaboutresearchrotationsandtherequiredresearchpaper. Removeddescriptionoffundingforinternationalstudentsbecauseitisonly relevantduringapplicationprocess.

• 2020September.Revertedthecurriculumdescriptiontoremove“BMI-relevant” andreplacewith“Unrestricted”.Cleaneduptheemaillists.Addtoexplanation of50%RAship.FixeddescriptionofadviceonQuals.Clarifiednoneedto completeresearchprojectifstudenttransfersoutoftheAcademicMSprogram. Updateddescriptionofcurrentcoursewaiverproceduretoremoverequirement ofapprovalofacademicadvisor.

• 2020October.AddedlinktoOfficeofAccessibleEducation(OAE).

• 2021May.RemovedWalkthroughINFOforgraduation.

• 2021August.AddedinfoonInternshipsandaddinganMSdegree

• 2021September.Lotsofminorwordingchanges.Clarifiedroleofco-advisors, anddoctoraldissertationreadingcommittee.

• 2021November:Clarifysecond-yearcommitteemeetingforPhDstudents.

• 2022:Oct/NovUpdates:

• Section1.4computeresourcelinkshaveallbeenupdated

• Section2.3HowtostayupdatedonBMI/DBDSeventsnewsection

• Section2.4Howtoreserveaconferenceroom

• Section2.12CardinalPrintinstructions

• Section3.1TuesdaytalkschangedtoMondaytalks

• Section3.2MoreclarificationonCo-Advisors

• Section3.4WaiversandExceptions–clarificationie52unitsofformalcoursework required

• Section3.7.1TAshipsitem#1addedtohelpclarifyexpectations;alsoremovedmention ofTAreviewsbeingattachedtostudentrecords

• Section3.9.2RemovedmentionofMSprogressreports3.9.2,whicharenolonger required.

• Section3.9.5MentionedtheGoogledocwithpotentialresearchopportunities

• Section3.10.1AddedareminderthatfortheCS/Stats/Math/Engelectivesthatyoucan havenomorethan9unitsincoursesbelowthe200level.

• Section3.10.3MentionedtheGoogledocwithpotentialresearchopportunities

• Section 5.3Internships–addedverbiageforMSstudents

• Section8.1GraduationPhotos–updatedinformation

• Also:Updatedmanylinks,andafewtypos

• OnallDocumentchangedBMItoDBDS;BMIExecutiveCommitteechangedtoDBDS GraduateProgramExecutiveCommittee;BiomedicalInformaticschangedto BiomedicalDataScience

AsofOctober2023,thefollowingchangesweremade:

• Changed“bmi::ethics”to“dbds::ethics”

• ChangedallmentionsofBMIorBiomedicalInformaticstoDBDSorBiomedicalData Science

• Section1.4:UpdatedComputeClusterinfoonNeroandCarina

• Section2paragraph2:Updatedinformationregardingannualretreat

• Section2.5Newbulletatbeginning.Toreachstudentservicespleaseusethefollowing email:dbds-studentservices@stanford.edu. AlsoupdatednewDBDSlistservs

• Section3.2ResearchAdvisorsandCoadvisorsUpdated

• Section3.4AddedtransferunitpoliciesforPhDStudents

• Section3.6:Updatedchartwithdegreeprogramsandannualto-do’s

• Section3.9.4:Updatetoclarifythattheresearchadvisorherecanbeprimary, secondary,oradvisingfaculty

• Section3.10.7.1:addedinformationonNSFGraduateResearchFellowship;updated NRSAFellowshipsdatesforcycle2and3

• Section3.10.8Rewrittentoclarifyoralandwrittenquals

• Section3.10.9UpdatedinfoinPre-ProposalTalk(nowcalled“ResearchinProgress” Talk)

• Section5.1MoreinfoaboutLeaveofAbsenceandimplicationsonCardinalCarehealth insurancecoverage

AsofSeptember2024,thefollowingchangesweremade:

• Section1.4(afterchartisadded)–updatedcomputeofferings

• Section1.4Updatedinformationandincludedchart

• Section2.3Addedlinksinceitwasmissing

• Section3.2LinktoAdvisingFacultywasincorrect,nowfixed

• Section3.10.1Removed“IfyouwereadmittedbeforeAugust1,2016,youmayfollowthis curriculum,ortheoldcurriculum,listedonthe DBDSwebsite.”

• Section3.10.2 Addedthechartherethatiscurrentlyinsection10.5aftertheverbiage aboutinformaloverviewofmilestones. Addedanotere"Seethesubsequentsectionsfor moreinformationontheMilestones,Progressreport,IDPetc."

• Section3.10.2(aftermilestonechartandverbiageisadded)

• Section3.10.5Addedlinktostudentprogressreportform

• Section3.10.5newsectionregardingtheannualDBDSProgressreporthasbeenadded.

• Section3.10.7.1–afterthisisupdatedwithnewdates,amounts,andconfirmallinfo

• Section3.10.7.1UpdatedthelinkanddatestoNSFapplicationdeadlines

• Section3.10.9Addedlinksinceitwasmissing

• Section3.10.9LinktoResearch-In-ProgressGuidelineswasbroken,nowfixed

• Section3.10.10Added“Pleaseseethemilestoneschartinsection3.10.2onthetimingand expectationsformeetingwithyourDissertationReadingcommittee.Notethatstudents mustmeetwiththereadingcommittee2xperyearintheyfifthyearandbeyond.”

• Section3.10.11Addednewrequirementforthefinalthesisdrafttoalsobesenttoreading committeeforanyfinalinput,especiallywhenoralcommitteehasdifferentmembersinit.

• Section3.10.12.1.AddedclassroombookinginstructionsforThesisDefenses

• Section3.10.15–ClarificationforMSstudentsinterestedinapplyingtoPhDprogram

• Section4.0travel(increasedto$1300theavailablefundingfortraveltoaconferenceper student)

• Section5.1UpdatedVadenHealthInsurancesection.Addedtwonewbulletpointsto updatethepolicy.

• Section7.2 AddedPayrolllinkfortimingsofSalaryappointmentspans

• Section8.1Increasegraduationphotobudget

• Section8.2Addedadegreeconferralchecklist

• Allthebrokenlinksthroughoutthehandbookhavebeenfixedandverified

DBDS Handbook 2024/25

BiomedicalDataScienceGraduateProgram

StudentHandbook

Table of Contents

1.IntroductionandoverviewofStanfordresources

1.5. NLM/NIH

2.Forstudents

2.1 How to get a computer

2.2 How to get ergonomic equipment

2.3 How to stay updated on DBDS events

2.4 How to reserve a conference room

2.5 How to send DBDS email

2.6 How to submit a help request

2.7 Personal wellness

2.11 How to receive and send US Mail

2.12 How to use Cardinal Print

LearntouseCardinalPrint

Ensureyouhavetherequiredprintdriver

Gethelporreportanissue

3.AcademicsandResearch

Monday Talks: Research in progress/journal club

3.2. Advisors

3.3. Course registration

Studylist

GradingbasisandminimumGPA

Units

3.3.4.Cross-listedcourses

3.4. Waivers and Transfer Units

3.5. Course flowsheet

3.6. Annual Flowsheet Review with your Advisor (Annually)

Degreeprogram,status Todo

3.7. Teaching Assistant (TA) requirements and guidelines

3.7.1.TAGuidelines

3.8. Publishing a paper and NIH Public Access Policy

3.8.1.ReviewofPublicationsbyStanfordfaculty

3.8.2.NIHPublicAccessPolicyandPMCIDs

3.8.3.Issuesaboutauthorship

3.9. MS degree

3.9.2.Milestones

HCPMSDetails

3.9.4.AcademicMSresearchrotationandresearchpaper(Practicum)

3.9.5.FundingSupportforMSstudents

3.9.6.TerminalGraduateRegistrationandPart-TimeEnrollment

3.10 PhD Degree

Researchrotations

3.10.4.GraduateStudentTrackingSystem

3.10.5.AnnualProgressReport

3.10.6.IndividualDevelopmentPlan(IDP)

3.10.7.Fundingsupportandfinances

Whatyoushoulddo CycleII

CycleIII

3.10.8.QualifyingExamination(Quals)

3.10.9.ResearchinProgressTalk

3.10.10.SettingyourDoctoralDissertationReadingCommittee

3.10.11.UniversityOralExamination(DissertationDefense)

OldThesisProposalDefense(enteredPhDprogrambeforeJuly 1,2018)

Thesis Proposal Defense (University Oral Examination)

3.10.12.2. Final talk:

3.10.13.Submittingyourdissertation

3.10.14.

3.10.15.ApplyingtothePhDprogramwhileenrolledintheMSprogram

4.Travel

4.1. NLM Travel Funding and conference

4.2. How to request support for travel

4.3. How to make travel arrangements

4.4. Receipts

4.5. Reimbursement after you travel

4.6. Local Travel

4.7. Foreign travel

5.Timeaway

Leave of absence

5.2. Family leave

5.3. Internships

5.3.1.SpecialNotesforInternationalStudents

6.Externalemployment

7.Finances

Fellowship Stipends

7.2. Assistantships (Salary)

7.3. Direct Deposit

7.4. Holds