Bioinformatics:

1
Bioinformatics  A HHMI Faculty Development
Course

• Physics
• Suzanne Amador Kane
• Biology
• Phil Meneely
• Jenni Punt
• Rob Fairman
• Chemistry
• Rob Scarrow

• Mathematics
• Jeff Tecosky-Feldman
• Curtis Greene
• Computer Science
• John Dougherty
• Funding from HHMI
• Many thanks to Kim Minor

Haverford College May 2002
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Course Goals

• Its unrealistic for us to hire a bioinformatics
  faculty member or teach entirely new courses on
  the subject, so we instead chose to
• Educate faculty about theory behind and use of
  bioinformatics tools
• Stimulate development of research applications
• Stimulate use of bioinformatics in courses
• Get faculty talking across departmental
  boundaries

Haverford College May 2002
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Course Format

• Eleven weekly 1 ½ lectures
• Six 1 ½ hour hands-on computer workshops
• Dinner with instructors in between lecture
  workshop
• Informal homework graded by instructors
• Assigned readings lecture notes
• Follow-up subgroup meetings throughout the spring
  term
• Faculty received one course stipend or release

Haverford College May 2002
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The Instructors

• Greg Grant
• Elisabetta Manduchi
• Warren Ewens
• U. Penn. Center for Bioinformatics
• Guest lecturers
• Jessica Carol Kissinger
• Jonathan Crabtree (both of U.Penn.)
• Stephen Bryant (NIH National Center for
  Biotechnology Information)

Haverford College May 2002
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Course Content Syllabus

• Topics covered
• Statistics
• Sequence alignment
• Gene finding
• Gene expression/DNA microarrays
• Phylogenetic analysis
• Protein structural alignment

• Kim Minor has made a very comprehensive course
  website
• http//www.haverford.edu/biology/genomicscourse/ge
  nomics.htm

Haverford College May 2002
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Textbooks, software, other resources

• We have compiled a list of useful textbooks,
  Powerpoint presentations, and course materials
  from other institutions.
• Lists of and links to these resources are
  available on the course website.

Haverford College May 2002
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Research applications

• Phil Meneely, Curtis Greene Rob Manning will
  perform a phylogenetic analysis of the RCC-1
  protein family this summer with rising junior
  Ethan Roland.
• John Doughertyongoing research with David Barkan
  (HC undergrad) on A Parallel Implementation of
  the Needleman-Wunsch Algorithm for Global Gapped
  Pair-Wise Alignment. (poster presented April
  2002 at Consortium for Computing at Small
  Colleges 7th Annual NE Conference.)
• Jenni Punt will perform a PSI-BLAST analysis of
  CDK2 in order to understand possible targets for
  its unexpected role in programmed cell death

Haverford College May 2002
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Current curricular development

• Bio 100 What is life? Phil Meneely BLAST and
  clustalw used to understand phylogenetic
  relationships of beta globins of humans and other
  mammals.
• Bio 200 Cellular Molecular Biology. Jenni
  Punt DNA Microarray/Gene expression
  examplestumor classification Rob Fairman
  Sample BLAST analysis of a-amylase.
• Physics 320 Intro Biophysics Suzanne Amador
  Kane sequence analysis, DNA chip technology for
  gene expression, protein structual prediction)
• CS392 Parallel Computing J.D. assignment
  implementing a sequential and parallel version
  of the Needleman-Wunsch algorithm for DNA
  sequence alignment.
• Math 218 Probability Statistics Curtis
  Greene dishonest casino example of hidden
  Markov chains probability statistics of
  sequence alignments.

Haverford College May 2002
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Ongoing curricular development

• Bio 303 Protein Structure/Function Rob Fairman
  New modules on PSI-BLAST sequence analysis and
  protein structural alignments (threading
  algorithms)
• Bio 300 PSI-BLAST lab module on anthrax porins
• CS206 Data StructuresJ.D. Assignment on
  phylogeny to provide experience with trees and
  matrices in a bioinformatics context
• Chem 351 Bioinorganic Chemistry Rob Scarrow
  J.D. phylogenetic analysis of metalloproteins
  to understand how the binding of different metals
  has evolved.
• Bioinformatics will be an important part of a new
  biochemistry biophysics Superlab course

Haverford College May 2002
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Conclusions

• The Faculty Development course structure has been
  very successfully applied in Computing across
  the Sciences (Spring 2001) and Bioinformatics
  (Fall, 2001).
• Faculty participation has been strong and
  consistent.
• New research and curricular applications have
  resulted as a consequence.
• The next installment will be a course next spring
  on Science and Society which we hope will draw
  in faculty from other divisions.

Haverford College May 2002
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• Faculty enjoyed the chance to meet and talk
  across disciplinary divisions
• I felt like learning about different teaching
  styles and different approaches to science was
  the most important thing to come out of this
  experience.

Haverford College May 2002
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• Positive outcomes include my understanding of
  bioinformatics, and my appreciation for the use
  of probability and statistics in biology.  I also
  consider the professional relationships forged in
  the lab trying to"BLAST" protein sequences or
  construct SQL queries a positive outcome.
• I knew absolutely NOTHING about bioinformatics
  prior to the course. I've learned a lot about the
  tools and strategies, and the central problems of
  a whole area of inquiry of which I was ignorant.
  This was a terrific way to get to know colleagues
  in the Biology dept. Our collaboration has
  spawned other discussions about ways that the
  Mathematics dept can serve the Biology major.

Haverford College May 2002
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• Mainly, working cohesively with my colleagues
  on bringing bioinformatics into our curriculum.
  It has gotten me to appreciate how we can work
  together as a Department on such goals and to
  articulate the need for expertise in this area
  for the long-term goals of this Department.
• I wanted to find out what all the fuss was
  about.  I had some general ideas about what
  bioinformatics could do and what tools were out
  there, but I'd only used one or two and I wasn't
  sure how they worked. I realized that the things
  that will be most useful to me are things I'd
  already heard of, but I was glad for the
  increased level of under-standing of the
  bioinoformatic tools. It was great to get
  together with other faculty in working toward a
  common intellectual project.

Haverford College May 2002
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• On a more cosmic level, I am now much more
  "available" to offer advice to seniors who are
  thinking about research problems in this area. I
  can imagine it leading to specific mathematical
  projects in the future (for example, studying the
  statistics in Greg and Warren's book).
• I understand the power of PSI-BLAST a lot more
  now. I would never have thought of this research
  project without the course.

Haverford College May 2002
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• Drawbacks
• Time constraints in working out the examples and
  doing background reading
• Time constraints in implementing curricular
  development.
• Requests for more hands-on workshops.
• More application-driven emphasis to math stats
  (less abstraction).

Haverford College May 2002