Bioinformatics Teaching and Research at DePauw University:

1
Bioinformatics Teaching and Research at DePauw
University Current Activities Future
Plans Greencastle, Indiana 46135

• Current Activities
• Courses
• BIO 290 Genomics Bioinformatics half-unit
  course taught in the Biology Department (see
  syllabus).
• Bioinformatics Lab Modules (primer design, DNA
  sequencing, sequence analyses, tree-building) in
  the BIO 220 Molecular Biology course molecular
  phylogenetics in BIO 250 Microbiology.
• Protein Crystallography enhanced with
  Bioinformatics Proteomics in the Chemistry
  department, for teaching research.
• Rapidly expanding major in Biochemistry
• Computing Cluster development in Computer Science
  department.
• Physical models of Biomolecules developed in the
  Chemistry department.
• Research
• DNA Sequencing, PCR Bioinformatics Lab Facility
  in the Biology Department for teaching research
  projects with students.
• Research by several faculty members working with
  zebra-fish, rotifers, archaebacteria, and
  butterflies on developmental, biochemical, and
  genetic projects

• The DePauw Team
• Caroline Gilson, Prevo Science Library
• Kelly Van Busum, Computer Science
• Bryan Hanson, Chemistry Biochemistry
• Chet Fornari Henning Schneider, Biology
  Biochemistry
• Sergei Markov, Biology

Molecular Genetics Biochemistry
Chemistry Courses
Cell Biology
Microbiology
Molecular Biology
Bioinformatics
The team from DePauw University wishes to
percolate bioinformatics concepts and
applications through a variety of biology,
chemistry, and computer science courses. Six
biology courses (fig.2) ranging from introductory
to upper-level to an existing bioinformatics
course, as well as at least two computer science
courses, and a desired course in chemistry
(fig.3) serve as targets for a plan to develop
collaborative bioinformatics modules and
projects. Information literacy and library
research skills will be a component of all target
courses (fig.1). We hope to clarify and expand
our goals and objectives for incorporating a
variety of specific, concrete bioinformatics
activities into our curriculum from the
discussions and activities at this workshop.
Introductory Biology, Chemistry CS
courses Library Research Skills
Fig. 2 The Percolation Scheme

• ???Future Plans???
• Percolate Bioinformatics in a graded series of
  exercises and projects through the courses in
  Fig.2
• (needs development by means of the Workshop
  projects and talks)
• Create a Bioinformatics Minor?
• Install Accelrys DS Gene Bioinformatics software
  on the server, or a free-ware suite of programs,
  such as Bedrocks WorkBench, BioEdit,
  BioConductor, to create a bioinformatics tool
  box.

• 
  Other Issues
• Why is teaching students to navigate, understand,
  and manipulate huge databases of biochemical
  information an important aspect of a modern,
  effective education in the liberal arts college?
• Some Tentative Goals
• To achieve a better understanding of the
  fundamental concepts in biology and chemistry,
  especially those concepts that show the unity
  lurking within the diversity of form and
  function, from molecules to organisms.
• To acquire literacy in the basic methods and
  applications of both bioinformatics and library
  research skills.
• To enhance discovery of new relationships in the
  analyzed data for creating new concepts, or
  supporting or rejecting existing hypotheses, or
  discovering new drugs from natural products (fig.
  3).
• To underscore the importance and roles of
  computer science and mathematics in developing
  the theoretical basis for effective, reliable,
  and robust bioinformatics tools and applications,
  and to develop new skills in analytical thinking
  (fig. 1).

Fig. 1 Target Student Groups Planned Pedagogies
Fig.3
Biology, Chemistry, Biochemistry Majors
Future Bioinformaticists
Pre-Health Sciences majors minors
Library Research Skills for all Computer
Science Mathematics ina gradient
Bibliography 1. Jerry E. Honts, Evolving
Strategies for the Incorporation of
Bioinformatics within the Undergraduate Cell
Biology Curriculum. Cell Biology Education, vol.
2, 233-247, Winter 2003. 2. David A. Adler and
Darrell Conklin, Bioinformatics. Encyclopedia
of Life Sciences, Macmillan Publishers, 2001,
www.els.net