Biology365:AppliedBioinformatics
Spring,2016
Instructor: VanessaKoelling,Ph.D.
Office:
Thompson257C
OfficeHours:
F,10:00AM-1:00PM,orbyappointment
Email:
vkoelling@pugetsound.edu
Lecture:
TTh,1:00PM-2:20PM,TH311
Lab: T,2:30PM-5:00PM,Th,2:30PM-4:00PM,TH311
RequiredText:
VinceBuffalo.2015.BioinformaticsDataSkills(1stedition).
O’ReillyMedia.
OptionalTexts:
JonathanPevsner.2015.BioinformaticsandFunctionalGenomics
(3rdedition).WileyBlackwell.
StevenHaddockandCaseyDunn.2011.PracticalComputingfor
Biologists(1stedition).SinauerAssociates,Inc.
LectureNotes:
ProvidedonlineafterclassasaPDF.
CourseWebsites:
AMoodlesitewillbeusedtodistributelecturenotes,labsand
othermaterials.http://moodle.pugetsound.edu/
COURSEDESCRIPTIONANDLEARNINGOBJECTIVES
AppliedBioinformaticsisanelectivecoursethatintroducesstudentstotheprinciplesand
practicalapplicationsofbioinformaticsintheanalysisofgenomicdata.Youwilllearnhowto
usebioinformaticssoftwaretoevaluateandanalyzegenomicdatatoanswerquestionsin
molecularandevolutionarygenetics.Whenyoufinishthecourseyoushouldhaveathorough
groundingin:
-whatbioinformaticsisandwhyitisaburgeoningfieldofbiology
-bioinformaticsdataskillsandtoolsthatcanbeappliedtomanybiologicaldatasets
-somemajorquestions/tasks/problemsingenomicsandhowbioinformaticsisusedtosolve
them
Thiscoursewillalsogiveyoutheopportunitytofurtherdevelopyourabilitytoreadprimary
scientificliteratureandcommunicateinwritingandotherforms.
RESPONSIBILITY
Iwillfacilitateaneffectivelearningenvironmentinwhichyoucanexploreapplicationsof
bioinformatics.Noquestionisunreasonable.However,ultimatelyyouareresponsibleforyour
owneducation.Youmustdedicateampleenergyandtimetolearnthematerialonyourown.
Youareresponsibleforobtaininginformationonanyschedulechangesaswellasonclass
materialsyoumaymissduringabsencefromclass.
TIMEREQUIREMENTS
BIO365,Spring2016,V.A.Koelling 1
Pleasebeawarethatassessmentinthiscoursewillbebasedoncomprehensionand
applicationofbiologicalknowledge.Assuch,youwillneedtoplanonSIGNIFICANTadditional
timeoutsideoflecturesothatyoumaymovebeyondsimpleacquisitionofknowledge.
EMAIL
Iwillregularlyuseemailtosendoutannouncements,changesinthesyllabus,reminders
abouttestsorduedates,etc.IwilluseyourPugetSoundemailaddress.Itisyour
responsibilitytocheckthisemailaccountregularlytokeepup-to-datewiththese
announcements.
Iwillrespondtoemailwithin24-48hours.
READINGS
Thisisanupper-divisioncourseinwhichyouareexpectedtoacquirecontentknowledgeof
greaterdepthanddetailthaninlower-divisioncourses;therefore,youareexpectedtodoa
closereadingofthetextbook.Followingeachlecture,itisimportantthatyouintegratethe
informationinthetextwiththatfromlecture.
Youshouldalsoexpectsupplementalreadingassignments(e.g.,newsarticlesorscientific
journalarticles).Assignmentsmaybeassociatedwiththisreadingmaterial.Inallcasesyou
shouldconsiderthereadingmaterialrequiredunlessIstateotherwise.
CLASSPARTICIPATION
Iexpectyourregularattendanceandattentioninclass.Asignificantportionofyourgradewill
bebasedonparticipation.Participationduringclassorlabdiscussionsofprimaryliteratureis
required.Youwillearnpointsbasedonyourparticipationinpaperdiscussionsandyour
completionofin-classactivities.
COMPUTINGRESOURCES
Sinceamajorcomponentofthiscourseinvolvesworkonthecomputer,eachofyouwillhave
accesstoacomputerintheBiologyComputerLabormaybringyourownMaclaptop.Youwill
beactivelyworkingwiththecomputerseachlecture/lab.PClaptopscannoteasilybeused
sincebioinformaticsisprimarilyUnix-based.YouwillalsosetupanaccountwithAmazon
WebServicesforcloudcomputing.Educationcreditsof$100areavailablefromAmazonand
shouldbesufficientforthiscourse.Detailsofhowtoapplyforaneducationcreditandsetup
anaccountwillbecoveredinclass.
INDEPENDENTPROJECT
Youwillcompleteanindependentprojectinthiscourse.Iwillaskyoutowriteadetailedlab
reportexplainingyourindependentproject.Furtherinstructionsforthisprojectwillbegiven
inclass.
Ifyouneedassistancewithresearchforyourindependentproject,pleaseconsulttheScience
BIO365,Spring2016,V.A.Koelling 2
Librarian.Heisavailableforone-on-onemeetingsandeagertohelpstudentsfindthe
informationtheyneedintheCollinsLibrary.Hiscontactinformationisasfollows:
EliGandour-Rood,ScienceLibrarian
CollinsLibrary,Room1117
Phone:253-879-3678
Email:egandourrood@pugetsound.edu
QUIZZES
Therewillbeshortquizzeseachweekinthisclass.Youwillnothavemid-termorfinalexams.
Iwillnotdiscussaquizorquizgradewithin24hoursofreturningthegradedquiztoyou.If
youwishtodisputethegradeorfurtherdiscusshowtoimproveyourstudyhabits,Iwillbe
happytomeetwithyouafterthe24-hourtimeperiod—onceyouhavethoroughlyread
throughyourquizandthepostedanswerkey.
RegradingPolicy:Ifyoufeeltherehasbeenamistakemadeingradingaquizproblem,you
maysubmititforaregrade.Turninyourquiztomewithawrittenexplanationofwhatyou
thinkiswrong.However,pleasebeawarethatwewillnotrevisithowpointsareassignedfor
questionsthatreceivedpartialcredit.Regradesmustbesubmittedwithinoneweek(7calendar
days)ofthequizbeingreturned.
GRADING(subjecttochangeatdiscretionofinstructoratanytime)
GradingPolicies
o NOMAKE-UPQUIZZESWILLBEGIVEN.However,ifyouaresickorhavesome
othervalidreasonformissingaquiz,pleasecontacttheinstructor.Whilemake-up
quizzesarenotgiven,wemaybeabletoworksomethingout.
o Lateassignmentswillbepenalized10%perdaylate.
o Noextracredit.
GradingScale
A≥94%
A-=90-93.9%
B+=87-89.9%
B=84-86.9%B-=80-83.9%
C+=77-79.9%
C=74-76.9%C-=70-73.9%
D+=67-69.9%
D=64-66.9%D-=60-63.9%
F<60%
Componentsoftheclasswillbeworththefollowingpercentagesofyourtotalgrade:
Participation 50%
Quizzes 15%
PaperDiscussions 15%
IndependentProject 20%
BIO365,Spring2016,V.A.Koelling 3
APPROPRIATEBEHAVIOR
Studentsareexpectedtobehaveinanappropriatemannerwhileattendingthisclass.During
classtimeIexpectyoutobeworkingonmaterialsforthiscourseonly.Pleaseberespectfulto
othersintheclass,especiallyconcerningtheuseofpersonaltechnology:
• Switchyourphonestovibrateorno-ringbeforecomingtoclassandhavethemstowed
inyourbagorpocket
• Noemailortextmessaging
• Youmaynothaveearbudsinatanytimewhileinclass
• Youmaynottouchoruseanyelectronicdevicesinanywayduringanexamorquiz
• Youmaynotleavetheroomduringanexamorquiz
• Computerusewillbeforclassworkonly
STATEMENTCONCERNINGACADEMICMISCONDUCT
AsastudentattheUniversityofPugetSound,youassumetheresponsibilitytoexhibitinyour
academicperformancethequalitiesofhonestyandintegrity.Iwillnottolerateacademic
misconductinanyform,especiallyplagiarism.
Ifyouneedtorefreshyourmemoryaboutthenatureofacademicmisconductanduniversity
policiesonthehandlingofacademicmisconduct,youmaygohere:
http://www.pugetsound.edu/student-life/personal-safety/student-handbook/academichandbook/academic-integrity/
Plagiarismisdefinedaspresentingtheworkofanotherasone'sown.Morethanfour
consecutivewordsfromasourceotherthanthewriterconstitutesplagiarismwhenthe
sourceisnotclearlyidentifiedinappropriatedocumentationformat.
Ifyouarefoundtohavecommittedplagiarisminthisclassyouwilllose100pointsor
thevalueoftheassignmentthatwasplagiarized,whicheverisgreater.Inaddition,Iwill
followthestepsforhandlingacademicmisconductoutlinedontheuniversitywebsiteabove.
Ifyoudidnotreceiveinstructiononavoidingplagiarisminyourfreshmanseminarcourses,
pleasetakesometimetocompletethecoursethatthelibraryhassetupforyou.Forthat
course,gohere:http://research.pugetsound.edu/academicintegrity
SPECIALACCOMMODATIONS
Ifyouhaveaphysical,psychological,medicalorlearningdisabilitythatmayimpactyour
coursework,pleasecontactPeggyPerno,DirectoroftheOfficeofAccessibilityand
Accommodations,105Howarth,253.879.3395.Shewilldeterminewithyouwhat
accommodationsarenecessaryandappropriate.Allinformationanddocumentationis
confidential.
CLASSROOMEMERGENCYRESPONSEGUIDANCE
Pleasereviewuniversityemergencypreparednessandresponseprocedurespostedat
www.pugetsound.edu/emergency/.Thereisalinkontheuniversityhomepage.Familiarize
BIO365,Spring2016,V.A.Koelling 4
yourselfwithhallexitdoorsandthedesignatedgatheringareaforyourclassandlaboratory
buildings.
Ifbuildingevacuationbecomesnecessary(e.g.earthquake),meetyourinstructoratthe
designatedgatheringareasoshe/hecanaccountforyourpresence.Thenwaitforfurther
instructions.Donotreturntothebuildingorclassroomuntiladvisedbyauniversity
emergencyresponserepresentative.
Ifconfrontedbyanactofviolence,bepreparedtomakequickdecisionstoprotectyour
safety.Fleetheareabyrunningawayfromthesourceofdangerifyoucansafelydoso.Ifthis
isnotpossible,shelterinplacebysecuringclassroomorlabdoorsandwindows,closing
blinds,andturningoffroomlights.Staylow,awayfromdoorsandwindows,andascloseto
theinteriorhallwaywallsaspossible.Waitforfurtherinstructions.
BIO365,Spring2016,V.A.Koelling 5
Week/dates
Week1
1/19&1/21
Week2
1/26&1/28
Week3
2/2&2/4
Week4
2/9&2/11
Week5
2/16&2/18
Week6
2/23&2/25
Week7
3/1&3/3
Week8
3/8&3/10
Week9
Noclass3/14-3/18
(SpringBreak)
Week10
3/22&3/24
Week11
3/29&3/31
Week12
4/5&4/7
TentativeScheduleforBIO365,Spring2016
SubjecttochangeatanytimeatthediscretionofDr.VanessaKoelling
LectureTopics
IntroductiontoBioinformatics
/Markdown/Unix/Biological
Databases
DNASequencing/Genome
Organization&GenomeProjects
BLAST/AmazonWebServicesCloud
Computing
MoreUnix/Git
Readingfromthe
Textbook
BDSCh.1&2;Pevsner
Ch.2(onMoodle)
Quizzes
PevsnerCh.9,p.377387,&Ch.15(on
Moodle)
PevsnerCh.4;BDSCh.4
Quiz1
PaperDiscussion
BDSCh.3&5
Quiz3
BioinformaticsData&UnixDataTools BDSCh.6&7
Quiz2
IntrotoR
BDSCh.8
Quiz4
PaperDiscussion
Quiz5
WorkingwithRangeData
BDSCh.9
Quiz6
WorkingwithSequence&Alignment
Data
BDSCh.10&11
Quiz7
PaperDiscussion
ShellScripting
BDSCh.12
Quiz8
GenomeAssembly
PevsnerCh.15(on
Quiz9
Moodle)
PevsnerCh.9,p.387-430 Quiz10
(onMoodle)
PaperDiscussion
GenomicVariation(VariantCalling)
BIO365,Spring2016,V.A.Koelling
Week13
4/12&4/14
Week14
4/19&4/21
Week15
4/26&4/30
GeneExpression(RNA-Seq)
Quiz11
IndependentProjects
PevsnerCh.10(on
Moodle)
IndependentProjects
Week16
5/2
Noclass5/5
Week17—FinalExam
Thursday,5/12,12:002:00PM
IndependentProjects
Yourindependentprojectwillbe
dueinplaceofafinalexam.
BIO365,Spring2016,V.A.Koelling
Quiz12