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 Computing for Biomedical Scientists  posted by  duggu   on 11/27/2007  Add Courseware to favorites Add To Favorites  
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Ogunyemi, Omolola, Qing Zeng, and Aziz Boxwala, HST.952 Computing for Biomedical Scientists, Fall 2002. (Massachusetts Institute of Technology: MIT OpenCourseWare), (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA

Object oriented programming.

Object oriented programming. (Image by Prof. Ogunyemi.)

Course Highlights

This course features a comprehensive set of assignments, lecture notes and project background information.

Course Description

This course introduces abstraction as an important mechanism for problem decomposition and solution formulation in the biomedical domain, and examines computer representation, storage, retrieval, and manipulation of biomedical data. As part of the course, we will briefly examine the effect of programming paradigm choice on problem-solving approaches, and introduce data structures and algorithms. We will also examine knowledge representation schemes for capturing biomedical domain complexity and principles of data modeling for efficient storage and retrieval. The final project involves building a medical information system that encompasses the different concepts taught in the course.

Computer science basics covered in the first part of the course are integral to understanding topics covered in the latter part, and for completing the assigned homework.

Technical Requirements

Any number of development tools can be used to compile and run the .java files found on this course site. Please refer to the course materials for any specific instructions or recommendations.
File decompression software, such as Winzip® or StuffIt®, is required to open the .zip files found on this course site.

Java® is a trademark or registered trademark of Sun Microsystems, Inc. in the United States and other countries.
WinZip® is a registered trademark of WinZip Computing, Inc.
StuffIt® is a trademark of Aladdin Systems, Inc.


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.
Textbooks (Required)
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.
Supplementary Texts/Readings
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.
Assignments, Exams and Grading
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.
Java® is a trademark or registered trademark of Sun Microsystems, Inc. in the United States and other countries.



Part 1: Introduction to Computing

  LEC #       TOPICS    
  1       Course Overview    
  2       Algorithms and Object Oriented Programming    
  3       Java® Constructs    
  4       Built-in Operators, Built-in Java® Classes, and Classes, Objects & Methods    
  5       Recursion and Iteration, Imperative & Declarative Programming, Abstract Data Types (ADTs), Arrays, and Classes, Object & Methods (continued)    
  6       Designing Methods, Wrapper Classes, Arrays, Packages, Inheritance, Derived Classes, and Dynamic Binding    
  7       Information Hiding, Exceptions    
  8       Vectors, Streams, Input and Output    
  9       Searching and Sorting    
  10       Time Complexity of Algorithms    
  11       Review Session    

Part 2: Data and Knowledge Representation

  LEC #       TOPICS    
  12       Logic and Medical Ontology    
  13       Boolean Algebra and Predicate Knowledge    
  14       Ontology and Data Model    
  15       Medical Vocabulary Representation and Survey of Medical Coding Systems    
  16       Medical Coding Systems (continued) and UMLS    
  17       Major KR Schemes    
  18       Process    

Part 3: Data Management, Querying and Retrieval

  LEC #       TOPICS    
  19       Nature of Data    
  20       Data Models    
  21       Maintaining Integrity of Data    
  22       Implementing a Relational Database    
  23       Overview of Object-oriented Data Management    
  24       Modeling for Analytical Processing of Data    
  25       No Lecture, Final Project Due    


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