1. Sonoma State University
Integrating Bioinformatics tools/problems into Upper level Computer Science Courses
B. Ravikumar
Sonoma State University
Rohnert Park CA 94952

2. Almost in every upper-level course, it is possible to include:
Upper-level courses:
Almost in every upper-level course, it is possible to include:
AI, Database, Theory of Computation, Software Engg, Algorithm Design, Parallel and Distributed Processing etc.
We will discuss sample projects in the following two courses:
Software Engineering
Algorithm Design and Analysis

3. Software Engineering Course
focus on specification, design and testing
specification: concerned with what software we want to build
design: identify the modules and features to be built
testing: create test plan, test cases for unit testing, intgration testing etc.
A complex software like Bio-workbench is a good example to introduce various aspects of large-scale software design

4. Example software design projects:
Create a new layer on top of biology work-bench for compositional tasks, for example suppose we want software tool that takes the output of Blast and plots the result using a 3-d viewer.
Create tools to convert protein/DNA data between different formats. 3.

5. Algorithm Design and Analysis
HIV problem space: From the HIV data, create a model that suggests mutation probabilities. Can we classify patients based on the probability of mutations?
Tools: bayesian statistics, maximum likelihood estimate, hidden Markov models etc.

6. Algorithm Design and Analysis
Problem 2: Extend BLAST to handle tandem repeats.
Step 1: identify tandem repeatsand remove.
Step 2: call BLAST on the cleaned sequence.
Is it possible to do it directly?
Tools needed: dynamic programming, finite automaton

7. Algorithm Design and Analysis
Problem 3: Given a receptor site in a protein, what is the largest volume of a molecule (sphere) that can fit at this site?
Computational geometry problem: given a set of spheres, and a point x, what is the largest sphere centered at x that does not intersect any other spheres?
Tools: Voronoi diagram

8. Algorithm Design and Analysis
4 Knot drawing recognizer: With tablet PC, we can input data from a pen based interface. Develop a program that takes a standard knot diagram drawn with a pen, and recognize the 3d model of the knot.
(on-going project.)