Wheaton College Norton, Massachusetts
Wheaton College
Genomics

Academics

Example

An Example of "Linked" Courses

Linking “Cell Evolution” (BIO 317) and “Algorithms” (COMP 215)

Linking two courses assumes a range of teaching options for faculty, from sharing one programming assignment to collaborating in multiple labs, homeworks, and final projects throughout the semester. The following table shows an example of how faculty might manage the points of contact between two linked courses, in this case the biology and computer science professors were linking “Cell Evolution” and “Algorithms.” An underlying assumption in our plan is that new exciting research questions will be answered by new software (or at least modifications to existing software). Our personal research collaboration and classroom experiences to date have convinced us that successful collaborations emerge over time, not, for example, in one or two isolated laboratory sessions. Thus, we intend to develop materials that bring students from both disciplines together in class and lab and then later in follow-ups outside of lab, for example, in a joint homework assignment, in modifications to a programming assignment, design of an experiment in genomics, or preparations for final project presentations.

  • Linking the courses “Cell Evolution” and “Algorithms”
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    Approximate timeline during the semester

    (14-week semester)

    Type of Collaboration
    Course Materials Developed
    Biology Computer Science

    Week 2

    Guest lecture

    by biology professor

    “DNA 101” - an introductory lecture for computer science students along with a demonstration of DNA extraction “in the manner of Julia Childs”

    Week 2 or 3

    Genomics Lab1 - Biology and computer science students share initial joint lab; work in BIO-CS teams ..... followed-up with homework BLASTing the Flagellar Genes - an intro to NCBI, BLAST and PubMed database
    Joint Homework & BLAST Homework

    Week 3

    initial genomics programming assignment -- DNA data and string algorithms Motif Finder - an intro to DNA (*.fna) files and protein table (*.ptt) files; software to find all locations of a user-entered motif

    Week 3

    Guest lecture

    by computer science professor

    Explanation of DNA data files, the algorithm in the Motif Finder software, and potential tweaks to suggest to the programmer

    Week 4

    Genomics Lab2
    Software demonstration of v1.0 leading to a design for v2.0

    Tweaking Motif Finder - demos of software; biologists suggest changes to programmers for (new) added functionality

    Week 6

    Genomics Lab3

    Towards innovative and creative searches in DNA

    Introduction to pattern matching with regular expressions and Perl for both biologists and computer scientists

    Week 8

    second genomics programming assignment: recursion, recurrence relations, and dynamic programming IsPal - finding “palindromes” or inverted repeats with potential mismatched base pairs: comparing algorithms O(2 N ) vs. O(N 2 )

    Week 10

    Genomics Lab4

    ... followed-up by informal

    out-of-class work on projects

    Planning for final projects - review of general specifications (e.g., triplet repeat diseases), suggested timeline, and coordination of team day-timers

    Near end of the semester

    Final oral presentations Bio-CS teams give talks.
    Summary of planned development of course materials as viewed within an example of points of contact between “Cell Evolution” and “Algorithms”

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