|
The following linked resources will open in a new browser window.
This work is licensed under a Creative Commons License.
TEACHING TOGETHER (Bio-CS team teaching)
"DNA" (BIO/COMP 242) Syllabus
"DNA" Sequence Analysis Programming Specifications
New Book
Perl for Exploring DNA (Oxford University Press, 2007)
INFUSING Genomics into a Computer Science course
NEW: Presented at SIGCSE '08 -- Portland, OR in March 2008.
The best way to get started integrating Bioinformatics/Genomics into your
computer science courses is to infuse one or two new programming assignments
into an existing course. Below is a link to two programming assignments tested
in our Algorithms course (the third course in our majors sequence). The first
leads students down a runtime garden path as they (attempt to) find repeats
in microbial genomes using an elegant but exponential algorithm. Included with
the programming specification are three homework assignments to encourage students
to explore the recursive solution, including work with recurrence relations,
using Maple's rsolve() to arrive at a closed form, and play with Excel to
compare various computations of the amount of work involved. The second
follow-up assignment finds students solving the same problem but this time with a quadratic
dynamic prorgramming algorithm.
Finding Inverted Repeats (DNA palindromes ) Recursively
Finding Inverted Repeats with Dynamic Programming
LINKING Biology and Computer Science Courses
 |
Partial support for this work was provided by the National Science Foundation's Course, Curriculum and Laboratory Improvement program (CCLI-EMD) under grant NSF DUE 0340761 |
| |
|
Example of linking BIO 211 and COMP 215 |
Course Materials (all .zip downloads)
Pre-Post Student Course Evaluations
Suggested Readings
Suggested readings and discipline-specific questions for homework/discussion
Sample Guest Lectures
Tips and materials for lecturing in the "other" course
Collaborative (Shared) Labs
Three BLAST labs for BIO-CS pairs of students from various semesters:
(i) Flagella genes, (ii) Huntingtin genes, and (iii) Seven Transmembrane proteins
CS students demo new software; BIO students ask for more ...
Example Programming Assignments
Motif Finder -- could be used in almost any programming course, e.g., CS1
isPal -- finding palindromes (inverted repeats), application of recursion
experiments in sorting, use of qsort
More Programming Assignments
Motif Finder -- use of dynamic memory allocation in C/C++
Top-10 motifs -- use of hash tables
Team Project Specifications
Sample Project: "Finding Triplet Repeats" (separate specs for BIO and CS)
Timeline, Topics, Goals, and Challenges of your Interrelated Projects
Helps: A Biologist's Introductory Guide to Interpreting Raw Data concerning DNA Motifs
Helps: Editing FNA files to find Genes: Locating Intergenic Regions for a Favorite Gene
Final Presentations
A sample team-talk given by the BIO and CS professors.
A list of BIO-CS student final talk titles from a given semester.
A sample grading key the professors used to grade the final oral presentations.
|
