Computing for biomedical scientists

With this course, we hope to provide a foundation for scientists interested in using computers for solving biomedical problems. Computing with biomedical data poses unique challenges with respect to data volume, complexity, and uncertainty in data and in domain knowledge. Students taking this course should come away with a grounding in abstraction for problem decomposition and solution formulation, data modeling, and information management. The latter are key to analysis, development, and proper design of information systems.

Biomedical background and an interest in computing.

Programming will be done in Java®; no prior familiarity with Java is assumed.

Savitch, Walter. Java, An Introduction to Computer Science and Programming. 2nd edition, Prentice Hall, 2000.

McFadden, Fred R., and Jeffrey Hoffer, and Mary B. Prescott. Modern Database Management. 6th edition, Addison-Wesley, 2001.

Aho, Alfred, and Jeffrey Ullman. Foundations of Computer Science. W. H. Freeman & Co., 1995.

van Bemmel, Jan H., and Mark A. Musen Springer-Verlag. Handbook of Medical Informatics. 1997.

Ullman, Jeffrey D. Principles of Database and Knowledge-Base Systems. Vol. 1. W. H. Freeman & Co., 1988.

Relevant papers or readings selected by instructors from: F. Sowa, John. Knowledge Representation: Logical, Philosophical, and Computational Foundations. Brooks/Cole Pub Co., 1999.

There will be weekly homeworks, consisting of programming assignments in Java. Assignments are generally due one week after they are distributed. Assignments submitted up to one week after the due date will get an automatic deduction of 10 points (i.e., if you submit your homework up to a week after the deadline, the maximum score you can receive is 90/100). Assignments submitted between one and two weeks after the deadline will get an automatic deduction of 20 points. Assignments submitted more than 2 weeks after the deadline will receive a score of 0 automatically. Please speak to the instructors if you believe you will need more than 3 weeks to complete an assignment.

The final grade will be based on homeworks (50%), a mid-term exam (20%) and a final project (30%). The midterm exam will be open book, open notes. Your class participation will also be considered in determining your final letter grade.

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