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BioInformatics at FSU - whose job is it and why it needs to be done.

BioInformatics at FSU - whose job is it and why it needs to be done. Steve Thompson Florida State University School of Computational Science and Information Technology ( CSIT ) / BioInfo 4U. Overview. What is bioinformatics , genomics, sequence analysis, computational molecular biology . . .

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BioInformatics at FSU - whose job is it and why it needs to be done.

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  1. BioInformatics at FSU - whose job is it and why it needs to be done. Steve Thompson Florida State University School of Computational Science and Information Technology (CSIT) / BioInfo 4U

  2. Overview What is bioinformatics , genomics, sequence analysis, computational molecular biology . . . Reverse Biochemistry & Evolution. Database growth & cpu power. Show and tell, very brief survey. NCBI’s BLAST & Entrez, GCG’sSeqLab, phylogenetics . . . High quality training is essential! Why: our graduates need to be competitive on the world biotechnology market. CSIT’s role in all of this; out-reach.

  3. Florida State University’s ad hoc BioInformatics Planning Committee: Lawrence Dennis Physics/CSIT dennisl@csit.fsu.edu Ross Ellington IMB/Biology elling@bio.fsu.edu Lei Li Statistics lilei@stat.fsu.edu Narayanan Perumal Information Management Sciences nperumal@cob.fsu.edu Jack Quine IMB/Mathematics quine@math.fsu.edu Q.X. Amy Sang Biochemistry/Chemistry sang@chem.fsu.edu Bruce Smith Biology/Information Studies bsmith@bio.fsu.edu DeWitt Sumners Mathematics sumners@math.fsu.edu Trisha Spears Biology spears@bio.fsu.edu Scott Steppan Biology steppan@bio.fsu.edu David Swofford Smithsonian Institute soon to be Biology/CSIT swofford@lms.si.edu Steve Thompson CSIT/Biology stevet@bio.fsu.edu Joseph Travis Biology/CSIT travis@neuro.fsu.edu James Wilgenbusch Smithsonian Institute soon to be Biology/CSIT jim@lms.si.edu

  4. Objectives The university tripartite mission: Education, Research, and Service. Research: CSIT is hiring 20-30 new faculty overall, of this 6-8 will be in comp’ bio’. David Swofford (PAUP*) is the first! Service: CSIT assistance in consultation, systems administration, and hardware access. Contact CSIT (http://www.csit.fsu.edu/) for general questions; me (stevet@bio.fsu.edu) for specific bioinformatics assistance and/or collaboration. FOR MORE INFO...

  5. Education Six Major Proposal Foci: Workshops — continue and expand GCG SeqLab series; each session offered twice per semester. Modules — incorporate across the curricula within existing courses, interdisciplinary by nature. Graduate Course — practical, project-oriented approach. Collaborate with proposed Math course. Undergraduate Genomics Course — survey, practical WWW techniques, implications, & ethics. Computational Molecular Biology Program — in association and cooperation with students’ present major department. Pros and Cons . . . Summer Short Course — long-range. Participants from world-wide disparate disciplines learning bioinformatics techniques and theory.

  6. GCG SeqLab Workshop Series Presently four different sessions: Intro to SeqLab & Multiple Sequence Analysis and its supplement Rational Primer Design Database Searching & Pairwise Comparisons — Significance Molecular Evolutionary Phylogenetics http://bio.fsu.edu/~stevet/workshop.html FOR MORE INFO...

  7. Modules in Existing Courses Cooperate with extant programs to incorporate bioinformatics into their existing curricula. Key is cooperation & necessity. Many different courses across many different departments, even across different colleges. Identify potential courses from the General Catalog and approach individual instructors and chairs.

  8. Graduate Course team-taught; lecture + lab; pragmatic, real-world approach. Theory + practical applications Potential collaboration with proposed course in Mathematics Computational Biology Program Washington State University’s Biochemistry 578 model.

  9. Undergraduate Course Genomics team-taught; lecture + lab also, but . . . Survey course. Emphasis on basics of theory, Web based resources, implications/ramifications, & ethics of genomics research.

  10. Computational Biology Program Coordinated by CSIT in association with student’s major department. Undergraduate and/or Graduate? Pros and Cons . . . Avoid duplication of effort. Candidate department collaborations.

  11. Summer Short Course Long-range plan — May 2002? Broad spectrum — both instructors and students from many different disciplines and world-wide distribution. One or two weeks? On-campus room & board support. To be undertaken this course will need the potential to achieve an exceptional world-wide reputation!

  12. Comparable Programs Washington State University had one of the first; still rare, but more all the time. Biocomputing education URL’s: http://iscb.org/univ.html http://linkage.rockefeller.edu/wli/bioinfocourse/ http://bozeman.genome.washington.edu/compbio http://www.csc.liv.ac.uk/~martyn/biosystems http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html http://130.88.90.2:8900 http://www.snarkware.org/bioedusoft/

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