Teaching: Curriculum Samples

Biology 301: Computational Biology, offered sporadically in winter and then canceled from program offerings (co-taught with Dr. Dutton)

Course Evolution Statement

Since Winter 2001 (the first year this then-new course was offered), this Biology Degree elective has been taught three times - with Dr. Dutton teaching the first half (morphological traits, phylogenetics, and databases) and me teaching the second (molecular bioinformatics, structure, and phylogenetics). Although we originally hoped to allow majors to take this course instead of traditional 100-level Computer Science course requirements for some degrees, we received somewhat negative feedback in response to this idea - despite the fact that basic computer science courses remain a moving target that still do not serve our needs. This - combined with what is challenging material - likely kept our numbers low (i.e. 4-6 students), prompting us to explore other options for delivering this important material in 2004/5. Specifically, Dr. Dutton added a computer-based phylogenetics lab component to his Evolution course and I improved bioinformatics lab components in General Microbiology and Molecular Biology. Consequently, we both agreed to eliminate Biology 301 from the program.

Course Materials Evolution Statement

Although my course content coverage has changed minimally, we regularly altered texts (owing to the severe lack of traditional sources on this topic at the time) and I frequently revised software and websites for each new offering. By the end, I provided reserve readings or hand-outs from 4 equally valuable resources: Molecular Evolution: A Phylogenetic Approach (Page), Bioinformatics: A Practical Guide to the Analysis of Genes & Proteins (Baxevanis), Bioinformatics for Dummies (Claverie), Brock Biology of Microorganisms (Madigan). While I continued to use the National Center for Biotechnology Information (NCBI) website and its several databases (both DNA and protein), I expanded lecture and lab coverage to include the burgeoning field of genomics (albeit focused on smaller and more well-organized microbial genomes). I also fully dropped the use of cumbersome stand-alone software packages like SeqPup and ClustalW in favor of using the comprehensive and program-oriented bioinformatics website called DNA Workbench (a free site that allowed users to create temporary accounts and analyze data on-line). Developing all new procedures for this resource involved a significant allocation of time - although I was able to add interesting new exercises covering DNA fingerprinting using restriction enzyme prediction programs (which were also available through the Workbench). Both Dr. Dutton and I continued to use the stand-alone (but not free) phylogenetics software package, PAUP - which my NSF/MO funding supported.

Provided Curricula Samples

Owing to the ultimate demise of this course, I have only included a manuscript (linked here) that effectively summarizes all versions of this course. This manuscript was based entirely on an extremely well-received poster (A Bioinformatics Course Emphasizing Molecular Microbial Diversity, by D. P. Lodge, S.M. Boomer, B.E. Dutton) presented by me at the 2004 ASM General Meeting in New Orleans. Although the final manuscript was submitted to Microbiology Education (ASM Press) in 2004, it was rejected in favor of other manuscripts that employed sexier disease-oriented applications (e.g. HIV or Influenzavirus) and contained more assessment. Nevertheless, I continue to post this manuscript on my professional website where it still receives moderate email interest. Also, a sub-section of this manuscript and poster - based on General Microbiology adaptations, was published in 2005 and this reference can be found in the Research/Publications section: Boomer, S.M., K.L. Shipley, B.E. Dutton, D.P. Lodge. A Laboratory Class Exploring Microbial Diversity and Evolution Using On-Line Databases, the Biology Workbench, and Phylogenetics Software. MicrobeLibrary Curriculum Resources (ASM On-Line Education).