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FEATURES |
* Department of Biology and
Department of Mathematics and Computer
Science, Wheaton College, Norton, Massachusetts 02766
Submitted June 27, 2002; Revised August 18, 2002; Accepted August 26, 2002
In the first of two National Science Foundation (NSF)–funded workshops, 30 professors of biology and computer science from 18 institutions met at Wheaton College in Norton, Massachusetts, on June 6–7, 2002, to share ideas on how to incorporate genomics research into undergraduate curricula. The participants included nine pairs or trios of biologists and computer scientists, anticipating or already implementing collaborations. In a before-and-after format, the two workshops are intended to encourage experimentation in the classroom (June 2002) followed by reflection on and evaluation of ideas (June 2003).
Interdisciplinary work is the heart of any research in genomics. The magnitude of the data sets and the scale of the problems require the expertise of individuals from both computer science and biology or biochemistry (Brown, 1999; Colwell, 2002). Collaborations in the sciences are common in many research settings but can be difficult to implement in undergraduate classrooms, especially in a relatively new field such as genomics. Biology students need opportunities to ask original questions and participate in algorithm and software design to learn how to set up new projects with programmers. Likewise, programmers entering the field of genomics must have a richer facility with the types of analyses and hypotheses that are useful, and programmers could benefit from interactions with biologists who will be using their programs. Our goals and objectives for this initial workshop targeted these needs and are listed in Table 1.
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OUTCOMES OF THE INITIAL WORKSHOP |
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Confidence
From our perspective, one of the more significant outcomes of the first
workshop was the overwhelming number of participants who left feeling more
confident about their ideas and feeling justified that new teaching models are
needed. The inherently interdisciplinary nature of bioinformatics and genomics
can trigger unease in some departments with faculty who have taught only
within a strict departmental paradigm. Viewing a healthy dose of examples of
innovative models is especially helpful for junior faculty. The workshop
discussion focused on two models, using a radar metaphor, for introducing new
teaching models. One model was to introduce changes subtly by "flying
under the radar."Specifically, several action items were recommended
that do not necessarily need full departmental or institutional approval,
including 1) handling some of your own recruitment and publicity by means of
distributing flyers and creating professional-looking web sites, 2) linking
your course with that of a professor in another department (see Linked
Courses, which follows), 3) infusing genomics content into your syllabus, and
4) advising students to package courses in a less-than–official major
concentration. A number of participants suggested the alternative approach of
"flooding the radar"—that is, lobbying department members,
administrators, alumni, and trustees with the advantages of and the need for
courses and programs in bioinformatics. Participants also noted that most
college publicity departments are eager to send out press releases about even
the most modest research or classroom efforts in genomics.
Compare and Contrast Programs
Although a few participants would have preferred only a small liberal arts
constituency, the workshop purposely featured a faculty with experiences in a
wide range of models, including full programs at large universities (e.g.,
Rensselaer Polytechnic Institute [RPI] and Wright State University), new or
planned majors or concentrations at small colleges (e.g., Colby, Ramapo, and
Trinity Colleges), single dedicated courses in bioinformatics/genomics (e.g.,
Drake University and Williams College), and a series of courses with infused
content (e.g., Dickinson College and Wheaton College). Participants noted that
there are currently three major "flavors" of curriculum design for
bioinformatics or genomics:
A more detailed summary of work at each participating institution is shown in Table 2.
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Infusing Genomics
The participants who are new to bioinformatics/genomics especially
appreciated ideas for infusing genomics content into their existing courses.
Regardless of the size of the institution, faculty in biology in particular
teach the same or similar courses at the undergraduate level (e.g., genetics,
molecular biology, evolution.) The uniform resource locators (URLs) in the
References section point to some of the institutions that are sharing course
materials. Eventually, we envision that some of these materials can help
launch a genomics portal at the upcoming National Science, Mathematics,
Engineering, and Technology Education Digital Library (NSDL).
Linked Courses
One original goal of the workshop was to find pairs of collaborators
(biologists and computer scientists) from the same institution who may want to
experiment with linking their courses. The idea for the workshops stems from
our conviction that undergraduate institutions must do more to prepare
students for a world of interdisciplinary work. For the past 3 yr at Wheaton
College, we have infused genomics content into our respective courses within
an interdisciplinary context by linking our biology and computer science
courses. We define linked courses as two independent courses with certain
shared elements; for example, the professors give reciprocal guest lectures,
students from both classes come together for 4 or more of 12 lab periods,
students collaborate on software specifications and designs, and teams of
computer science and biology students work on a capstone research project. Our
goal of infusion is intended to both complement and extend full programs in
bioinformatics that are beginning to emerge at some colleges and universities.
For most colleges, especially small liberal arts colleges such as ours, the
infusion of genomics in linked courses will reach far more students than a new
major would. The suite of courses for a bioinformatics major would attract an
extremely small number of students, some of whom would be likely to switch out
of already small and rigorous programs such as biochemistry. In the pilot
iterations of our linking model at Wheaton (Algorithms and Genetics;
Algorithms and Cell Evolution), we reached 100% of the computer science majors
of a given class year (Algorithms is a required course) and approximately 70%
of all majors in the biological sciences (biology, biochemistry, environmental
science, and psychobiology).
Collection of Resources
Our genomics web site at Wheaton College (see References) will organize and
collect links to sites providing pedagogical ideas on linked teaching and
student collaborations, suggested homework and projects, and sources of
bioinformatic and algorithmic content, including pointers to forthcoming
textbooks (e.g., Campbell and Heyer,
2003; Krane and Raymer,
2003) and rich web sites of links (e.g.,
Bagga, 2002).
Communication Across the Disciplinary Boundaries
Forming interdisciplinary partnerships and teaching models is nontrivial,
as evidenced in this suggestion to biologists who want to approach a computer
scientist:
Wrong way: "Want to work on bioinformatics with me?" Right way: "I hear you are an expert in pattern matching. Could you help me solve....?"
Table 3, based on both formal discussions and informal discussions during the workshop, summarizes some of the differences between the two disciplines. These differences are often at the core of communication problems. Discussions began at Workshop I and are anticipated to continue into Workshop II as the participants experiment with ways to help both students and colleagues cross those boundaries.
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Also, although many computer scientists could probably summarize what biologists do for research, the reverse is usually not true. Biologists often think of their computer science colleagues as resources for building web pages or troubleshooting commercial software packages. Computer science research might appear to biologists to be an odd subset of mathematics because so many computer scientists are still housed within mathematics departments, especially at small colleges. Therefore, biologists (both professors and their students) may underestimate the degree to which their computer science colleagues might enjoy the opportunity to apply their problem-solving and tool-building expertise to a large, meaningful data set such as a genome.
At Wheaton College, we have found it valuable to model and deconstruct for our students some of the working parts of our (LeBlanc and Dyer's) research collaborations in genomics. Our class discussions on communication differences can facilitate interdisciplinary work and help to prepare students for the realities of working in teams at their future jobs. Our research has led to several publications with students (e.g., LeBlanc et al., 2000), poster presentations (e.g., LeBlanc et al., 2002), and a web site where we host our tools (see Wheaton College Genomics Group URL in References).
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SUMMARY |
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The pursuit of answers to these and other emerging questions is part of our relentless effort to bring genomics to undergraduate biology and computer science students.
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ACKNOWLEDGMENTS |
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Corresponding author. E-mail address:
bdyer{at}wheatoncollege.edu.
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REFERENCES |
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TOPOUTCOMES OF THE INITIAL...SUMMARYREFERENCESRELEVANT WEB SITES |
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Campbell, A.M., and Heyer, L.J. (2003).Discovering Genomics, Proteomics, and Bioinformatics , San Francisco: Benjamin Cummings.
Colwell, R. (2002, April). NSF director: "New bioscientist" will be future of genomics [Interview]. Genome Technol. (20), 72.
Krane, D.E., and Raymer, M.L. (2003).Fundamental Concepts of Bioinformatics , San Francisco: Benjamin Cummings.
LeBlanc, M., Aspeslagh, G., Buggia, N., and Dyer, B.
(2000). An annotated catalogue of inverted repeats of
Caenorhabditis elegans Chromosome III with observations concerning
odd/even biases and conserved motifs. Genome Res.
10(9),1381
-1392.
LeBlanc, M., Baron, M., Christoforou, A., Doolittle, N., Kimball, M., Villa, A., Williams, G., and Dyer, B. (2002). The DNA motif lexicon—cataloguing and annotating genomes. Presented at the 14th International Genome Sequencing and Analysis Conference (TIGR), Boston.
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This article has been cited by other articles:
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  A. M. Campbell Public Access for Teaching Genomics, Proteomics, and Bioinformatics CBE Life Sci Educ, June 1, 2003; 2(2): 98 - 111. [Abstract] [Full Text] [PDF]
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