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, homework, 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.” The underlying belief in this plan is that new and exciting research questions will be answered by new software (or 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, the intention is 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.

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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”