BioInformatics at FSU - whose job is it and why it

needs to be done.Steve ThompsonSteve Thompson

Florida State University School of Florida State University School of Computational Science and Computational Science and

Information Technology (Information Technology (CSITCSIT) / ) / BioInfo 4UBioInfo 4U

OverviewWhat is bioinformatics , genomics, What is bioinformatics , genomics,

sequence analysis, computational sequence analysis, computational molecular biology . . .molecular biology . . .Reverse Biochemistry & Evolution.Reverse Biochemistry & Evolution.Database growthDatabase growth & cpu power. & cpu power.

Show and tell, very brief survey.Show and tell, very brief survey.NCBI’s NCBI’s BLASTBLAST & Entrez, & Entrez, GCG’sGCG’s SeqLab, SeqLab,

phylogenetics . . .phylogenetics . . .

High quality training is essential!High quality training is essential!Why: our graduates need to be competitive Why: our graduates need to be competitive

on the world biotechnology market.on the world biotechnology market.

CSIT’s role in all of this; out-reach.CSIT’s role in all of this; out-reach.

Florida State University’s ad hoc BioInformatics Planning Committee:

Lawrence DennisLawrence Dennis Physics/CSITPhysics/CSIT dennisl@csit.fsu.edudennisl@csit.fsu.eduRoss EllingtonRoss Ellington IMB/BiologyIMB/Biology elling@bio.fsu.eduelling@bio.fsu.eduLei LiLei Li StatisticsStatistics lilei@stat.fsu.edulilei@stat.fsu.eduNarayanan PerumalNarayanan Perumal Information Management SciencesInformation Management Sciences

nperumal@cob.fsu.edunperumal@cob.fsu.eduJack QuineJack Quine IMB/MathematicsIMB/Mathematics

quine@math.fsu.eduquine@math.fsu.eduQ.X. Amy SangQ.X. Amy Sang Biochemistry/ChemistryBiochemistry/Chemistry

sang@chem.fsu.edusang@chem.fsu.eduBruce SmithBruce Smith Biology/Information StudiesBiology/Information Studies

bsmith@bio.fsu.edubsmith@bio.fsu.eduDeWitt SumnersDeWitt Sumners MathematicsMathematics sumners@math.fsu.edusumners@math.fsu.eduTrisha SpearsTrisha Spears BiologyBiology spears@bio.fsu.eduspears@bio.fsu.eduScott SteppanScott Steppan BiologyBiology steppan@bio.fsu.edusteppan@bio.fsu.eduDavid SwoffordDavid Swofford Smithsonian Institute soon to be Biology/CSITSmithsonian Institute soon to be Biology/CSIT

swofford@lms.si.eduswofford@lms.si.eduSteve ThompsonSteve Thompson CSIT/BiologyCSIT/Biology stevet@bio.fsu.edustevet@bio.fsu.eduJoseph TravisJoseph Travis Biology/CSITBiology/CSIT travis@neuro.fsu.edutravis@neuro.fsu.eduJames WilgenbuschJames Wilgenbusch Smithsonian Institute soon to be Biology/CSIT Smithsonian Institute soon to be Biology/CSIT

jim@lms.si.edujim@lms.si.edu

ObjectivesThe university tripartite mission: Education, The university tripartite mission: Education,

Research, and Service.Research, and Service.

Research: CSIT is hiring 20-30 new faculty Research: CSIT is hiring 20-30 new faculty overall, of this 6-8 will be in comp’ bio’. overall, of this 6-8 will be in comp’ bio’.

David Swofford (PAUP*) is the first!David Swofford (PAUP*) is the first!

Service: CSIT assistance in consultation, systems Service: CSIT assistance in consultation, systems administration, and hardware access.administration, and hardware access.

Contact CSIT (Contact CSIT (http://www.http://www.csitcsit..fsufsu..eduedu//) for general ) for general questions; me (questions; me (stevetstevet@bio.@bio.fsufsu..eduedu) for specific ) for specific bioinformatics assistance and/or collaboration.bioinformatics assistance and/or collaboration.

FOR MORE INFO...

EducationSix Major Proposal Foci: Six Major Proposal Foci:

WorkshopsWorkshops — continue and expand GCG SeqLab — continue and expand GCG SeqLab series; each session offered twice per semester.series; each session offered twice per semester.

ModulesModules — incorporate across the curricula within — incorporate across the curricula within existing courses, interdisciplinary by nature.existing courses, interdisciplinary by nature.

Graduate CourseGraduate Course — practical, project-oriented — practical, project-oriented approach. Collaborate with proposed Math course. approach. Collaborate with proposed Math course.

Undergraduate Genomics CourseUndergraduate Genomics Course — survey, — survey, practical WWW techniques, implications, & ethics.practical WWW techniques, implications, & ethics.

Computational Molecular Biology ProgramComputational Molecular Biology Program — — in association and cooperation with students’ in association and cooperation with students’ present major department. Pros and Cons . . .present major department. Pros and Cons . . .

Summer Short CourseSummer Short Course — long-range. — long-range. Participants from world-wide disparate disciplines Participants from world-wide disparate disciplines learning bioinformatics techniques and theory. learning bioinformatics techniques and theory.

GCG SeqLab Workshop Series

Presently four different sessions:Presently four different sessions:

Intro to Intro to SeqLabSeqLab & Multiple Sequence Analysis & Multiple Sequence Analysis and its supplementand its supplement

Rational Primer DesignRational Primer Design

Database Searching &Database Searching & Pairwise Pairwise Comparisons — Significance Comparisons — Significance

Molecular Evolutionary Molecular Evolutionary PhylogeneticsPhylogenetics

http://bio.http://bio.fsufsu..eduedu/~/~stevetstevet/workshop.html/workshop.html

FOR MORE INFO...

Modules in Existing CoursesCooperate with extant programs to Cooperate with extant programs to

incorporate bioinformatics into their incorporate bioinformatics into their existing curricula.existing curricula.

Key is cooperation & necessity.Key is cooperation & necessity.

Many different courses across many Many different courses across many different departments, even across different departments, even across different colleges.different colleges.

Identify potential courses from the Identify potential courses from the General Catalog and approach General Catalog and approach individual instructors and chairs.individual instructors and chairs.

Graduate Course

team-taught; lecture + lab; pragmatic, team-taught; lecture + lab; pragmatic, real-world approach.real-world approach.

Theory + practical applicationsTheory + practical applications

Potential collaboration with Potential collaboration with proposed course in Mathematics proposed course in Mathematics Computational Biology ProgramComputational Biology Program

Washington State University’s BiocWashington State University’s Biochemistry 578hemistry 578

model. model.

Undergraduate Course

GenomicsGenomics

team-taught; lecture + lab also,team-taught; lecture + lab also,

but . . .but . . .

Survey course.Survey course.

Emphasis on basics of theory, Emphasis on basics of theory, Web based resources, Web based resources, implications/ramifications, & implications/ramifications, & ethics of genomics research.ethics of genomics research.

Computational Biology Program

Coordinated by CSIT in association Coordinated by CSIT in association with student’s major department.with student’s major department.

Undergraduate and/or Graduate?Undergraduate and/or Graduate?

Pros and Cons . . .Pros and Cons . . .

Avoid duplication of effort.Avoid duplication of effort.

Candidate department collaborations.Candidate department collaborations.

Summer Short Course

Long-range plan — May 2002?Long-range plan — May 2002?Broad spectrum — both instructors and Broad spectrum — both instructors and

students from many different students from many different disciplines and world-wide disciplines and world-wide distribution.distribution.

One or two weeks?One or two weeks?On-campus room & board support.On-campus room & board support.To be undertaken this course will need To be undertaken this course will need

the potential to achieve an the potential to achieve an exceptional world-wide reputation!exceptional world-wide reputation!

Comparable ProgramsWashington State University had one of the Washington State University had one of the

first; still rare, but more all the time.first; still rare, but more all the time.

Biocomputing education URL’s:Biocomputing education URL’s:http://http://iscbiscb.org/.org/univuniv.html.html

http://linkage.rockefeller.edu/wli/bioinfocourse/http://linkage.rockefeller.edu/wli/bioinfocourse/

http://bozeman.genome.washington.edu/compbio http://bozeman.genome.washington.edu/compbio

http://www.csc.liv.ac.uk/~martyn/biosystemshttp://www.csc.liv.ac.uk/~martyn/biosystems

http://www.techfak.uni-bielefeld.de/bcd/Curric/http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.htmlsyllabi.html

http://130.88.90.2:8900http://130.88.90.2:8900

http://www.snarkware.org/bioedusoft/http://www.snarkware.org/bioedusoft/