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

2. Course Goals It’s 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

3. 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

4. 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

5. Course Content & Syllabus Kim Minor has made a very comprehensive course website:course website http://www.haverford.edu/biology/genomicscourse/genomics.htm Topics covered: Statistics Sequence alignment Gene finding Gene expression/DNA microarrays Phylogenetic analysis Protein structural alignment Haverford College May 2002

6. 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.course website Haverford College May 2002

7. 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 Dougherty—ongoing 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 7 th 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

8. 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 examples—tumor classification; Rob Fairman: Sample BLAST analysis of  -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

9. 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 Structures—J.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

10. 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

11. 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

12. “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

13. “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

14. “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

15. 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