A Powerpoint Summary - Bioinformatics and Computational Biology

Bioinformatics and Computational BiologyFall 2014BCB Graduate ProgramIntroductionwww.bcb.iastate.edu

Bioinformatics and Computational BiologyStaff IntroductionsKarin Dorman (kdorman@iastate.edu) BCB Program ChairDennis Lavrov (dlavrov@iastate.edu) BCB Associate ChairTrish Stauble (tastaub@iastate.edu) BCB Program Coordinator

Bioinformatics and Computational BiologyProgram OverviewOne of the first Bioinformatics Ph.D. programs in the USWith about 60 Ph.D. students, one of the largest and strongestBioinformatics Ph.D. programs in the USAbout 15 core teaching faculty, but over 70 program-associatedfaculty (from more than 15 departments) with research projects inBCB‘Wet’ and ‘dry’ lab research experiences and mentoring by a majorand co-major professor (each in a different discipline)

Bioinformatics and Computational BiologyMajor Research ThrustsBioinformaticsComputational Molecular BiologyStructural and Functional GenomicsMacromolecular Structure and FunctionMetabolic and Developmental NetworksIntegrative Systems BiologyInformation Integration and Data MiningBiological StatisticsMathematical Biology

Bioinformatics and Computational BiologySources of fundingFirst Year – Research assistantship (RA) provided byprogramAfterward – RA (typically) arranged with major professorTeaching assistantships (typically) arranged with homedepartmentCompetitive fellowships funded by internal as well asexternal sources as available

Bioinformatics and Computational BiologyQuestions on funding?

Bioinformatics and Computational BiologyTraining timelineYear 1. Research rotations, finding a homeYears 1-2. Core CurriculumYear 2. Define dissertation project, additional courseworkYear 2-3. Preliminary examinationYear 5. Ph.D.Progress monitored by the program - interviews withBCB Chair

Bioinformatics and Computational BiologyGetting StartedEach BCB student is advised by a temporary advisorduring the first yearTemporary advisor helps choose courses, andarrange research rotationsKarin Dorman and Dennis Lavrov are the currenttemporary advisors---additional members of theSupervisory Committee may assistAn important choice to make is Track 1 and Track 2

Bioinformatics and Computational BiologyBackground coursework- Track 1 versus 2New students are expected to have a solid undergraduate training in atleast one of the foundation disciplines: biology, mathematics, computerscience, or statisticsNew students often take background courses in computer science,statistics, or biology during the first year to complete their base training.Some students may be prepared for the Core Course curriculum. Inconsultation with their advisor, they will register for the core coursesimmediately and are Track 1. If there are classes a student needs to beprepared for the Core, these students are Track 2.

Bioinformatics and Computational BiologyBackground courseworkComputer ScienceProgramming (Com S 207, 208 or 227, 228)Discrete Mathematics (Com S 330)Database Management Systems (Com S 363)StatisticsStat 341 and/or Stat 430BiologyGenetics (Biol 313)Molecular Cell Biology and Biochemistry (Biol 314)Evolutionary Biology (Biol 315)MathematicsCalculus and Differential Equations (Math 165, 166, 265 )

Bioinformatics and Computational BiologyCore course requirementsI BCB 567 Fundamentals of Genome InformaticsII BCB 568 Advanced Genome InformaticsIII BCB 569 Structural Genome InformaticsIV BCB 570GDCB 511Computational Functional Genomics andSystems BiologyMolecular Genetics

Bioinformatics and Computational BiologyMath 265ComS 207 Biol 313 BBMB 301Stat 341ComS 330 ComS 208 Biol 314Biol 315Stat 430 Bioinformatics I ComS 363Gen 409Bioinformatics II Bioinformatics III Bioinformatics IVGDCB 511Prereq Backgrd Core

Bioinformatics and Computational BiologySample Course plansWell-prepared Students (Track 1)Year 1 Fall SpringBioinformatics I Bioinformatics IIStat 430 GDCB 511 (or Com S 363)RotationsRotationsYear 2 Bioinformatics III Bioinformatics IV(Com S 363)

Bioinformatics and Computational BiologySample Course plansStudents Missing Computer Science Prerequisites, but withstrong Biology background (Track 2)Year 1 Fall SpringCom S 207 Com S 208Stat 430 GDCB 511Rotations Com S 330RotationsYear 2 Fall SpringBioinformatics I Bioinformatics IICom S 363 Bioinformatics IVYear 3Bioinformatics III

Bioinformatics and Computational BiologySample Course plansStudents Missing Biology Prerequisites, but with strongComputer Science background (Track 2)Year 1 Fall SpringBiol 313 Biol 314BBMB 301 GDCB 511Stat 430 RotationsRotationsYear 2 Bioinformatics I Bioinformatics IIBioinformatics III Bioinformatics IVBiol 315

Bioinformatics and Computational BiologyQuestions on Training Timelineor Coursework?

Bioinformatics and Computational BiologyFinding a homeTake Faculty Research Seminar (BCB 691)Arrange Research RotationsChoose Major and Co-major ProfessorsYour major professor’s department becomes your homedepartment.Major and co-major professors are responsible forresearch supervision, mentoring, and assistantshipsupport.

Bioinformatics and Computational BiologyArrange Research Rotations– Rotations include ‘wet’ and ‘dry’ lab researchexperiences– Goal of rotations is to help identify major and comajorprofessors (each in a different discipline)*– Rotations will be completed with submission ofevaluation form

Bioinformatics and Computational BiologyResearch Rotation opportunities available with thefollowing faculty:• Steven Cannon -Agronomy and USDA ARS• Michael Cho - Biomedical Sciences• Julie Dickerson – Electrical and Computer Engr.• Drena Dobbs – GDCB• Karin Dorman - Statistics

Bioinformatics and Computational BiologyMore Research Rotation opportunities availablewith following faculty:• Xun Gu - Genetics, Development and Cell Biology• Eric Henderson - Genetics, Development and Cell Biology• Robert Jernigan – Biochemistry, Biophysics and Molec Biol• Dennis Lavrov – EEOB• Allen Miller – Plant Pathology and Microbiology

Bioinformatics and Computational BiologyAnd More -- Research Rotation opportunitiesavailable with following faculty:• Basil Nikolau – BBMB• Tom Peterson Genetics Development and Cell Biology• Donald Sakaguchi Genetics Development and Cell Biology• Patrick Schnable, Agronomy• Taner Sen Genetics Development and Cell Biology• Guang Song, Computer Science• Eric Underbakke, BBMB

Bioinformatics and Computational BiologyAnd More -- Research Rotation opportunities:• Nicole Valenzuela - Ecology, Evolution and OrganismalBiology• Erik Vollbrecht - Genetics Development and Cell Biology• Roger Wise – Plant Pathology and Microbiology• Eve Wurtele - GDCB

Bioinformatics and Computational BiologyResearch Rotation TimetableDeadline for submitting Rotation Planning form Sept 23Approximate dates for rotations:Rotation #1 Sept 25 – Nov 20Rotation #2 Nov 27 – Feb 5Rotation #3 Feb 12 – Apr 9There is time for a 4 th rotation: April 16 – May 28Deadline for final lab decision May 15Deadline for filing Home Department form May 30

Bioinformatics and Computational BiologyQuestions on research rotations and finding a home?

Bioinformatics and Computational BiologyResearch and DissertationResearch RotationsThesis proposal and Preliminary ExaminationResearch and journal and conference publicationsPh.D. ThesisThesis Defense

Bioinformatics and Computational BiologyAdditional training opportunitiesParticipation in scientific conferences and symposiaInternshipsInternational experiences

Bioinformatics and Computational BiologyQuestions on Training Requirements?

Bioinformatics and Computational BiologyResourcesL.H. Baker Center for Bioinformatics and Biological StatisticsOrganizes faculty researchProvides computer infrastructureHome to computer support staffOrganizes campus-wide seminars and workshopsISU Library – Heather Lewin, Science & Technology Librarianhttp://instr.iastate.libguides.com/bcb

Bioinformatics and Computational BiologyBCB program resourcesBCBLabThis student led group coordinates many BCB activities and researchopportunities. Get involved and benefit ! Sweta Roy is the currentpresident of the organization.BCB OfficeTrish can and does answer a lot of questions - I can help as wellRead through the BCB Graduate Student HandbookUse the on-line version: www.bcb.iastate.edu/Handbook.html