HI 5007 Data Structures and Algorithms in Biomedicine

Concepts and implementation of basic data structures including stacks, queues, lists, hash tables, trees, heaps, and graphs. Concepts and implementation of algorithms for sorting and searching. Basic concepts of analysis and comparison of algorithms.

This course builds on prerequisite skills of basic computer program development and limited functional knowledge of an object-oriented or procedural programming language. The concept of an algorithm is developed through examples of algorithms and implementation of algorithms. Abstract data types are defined and students are required to create ADTs in support of algorithm implementation. Programming projects are used to more fully develop concepts and practices of object-oriented programming and software engineering applied in the context of problems of medical information processing and management.

HI 5005 Data Structures for Bioinformatics is a one-semester graduate level course that examines the process of using an object-oriented programming (OOP) language to building computer applications in support of health care and/or life science practice or research. Students learn modern principles of program design and implementation that enable rapid application development through reusable code modules. Students are exposed to fundamental data structures used to implement algorithms as computer programs. The course examines the structure of well-known algorithms, paying careful attention to differentiate between algorithms and programs that implement algorithms. A brief overview of the analysis of algorithms for computability is undertaken. Students develop applications of limited scope to implement algorithms in support of health care or life science processes that arise from practice and/or research. The applications will illustrate the OOP principles of encapsulation, inheritance, and polymorphism. Python (2.4.3) is the current course programming language. It was chosen because of it’s prevalence of use in the bioinformatics community and because it is open source software.

Prerequisites

Information Technology for Biomedicine, consent of instructor.  Course prerequisite may be waived by instructor depending on student background.

Requirements:
1.    Every student must have access to course information delivered via the Internet.
2.    Each student is responsible for completing assigned readings, exercises, homework assignments, exams, collaborative web-based activities, and group projects.
3.    Students complete numerous assignments, many of which require the use of the computer. It is assumed that a student has his/her own computer on which the necessary software can be installed.
4.    The course is delivered via the Web, so there is no required class attendance, but there are deadlines by which certain amounts of content must be covered and activities and assignments completed.
5.    While the class is not scheduled to meet face-to-face three hours each week; the material covered does require a time commitment from the student. There is a general “rule-of-thumb” that pursuing 1 hour of college credit during a regular semester requires a student to spend 1 hour per week in the classroom plus a minimum of 3 more hours per week outside of class studying, working on projects, doing research, etc. This means a student in HI 5005 should budget about 12 hours per week to spend on the course material.