COSC 188. Computer Systems (for Computational Biology and Chemistry)
Computational biology is at the core of scientific computation, and both solves real biological problems, and contributes back to computer science. We use and extend computational techniques including statistical methods, provable interleaving strategies, AI techniques, numerical methods, optimization, branch and bound algorithms, expectation/maximization, stochastic labeling and Markov random field paradigms. In this field, computational techniques are central, and the applications present intriguing problems to computer scientists who design algorithms and implement systems. We will develop both upper and lower bounds in the setting of novel algorithms for biophysical problems. For example, to quote Richard Karp, ``The Celera whole-genome shotgun sequencing algorithm is an instance of a general approach to combinatorial problem solving in which constraints on the solution are enforced in an order determined by the strength of the evidence for them. Should this approach be studied within theoretical computer science?" (Keynote address, Computational Systems Bioinformatics Conference, 2003).
Course Director: Donald