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Course Catalog

140.637.01 BIOLOGICAL DATABASES AND DISTRIBUTED COMPUTING

Department: Biostatistics
Term: 2nd term
Credits: 3 credits
Contact: Fernando Pineda
Academic Year: 2014 - 2015
Course Instructor:
Description:

Provides students with the principles and skills required to implement biological databases and their web-based interfaces. Presents essential notions of distributed computing on the worldwide web. Includes the fundamentals of TCP/IP, client-server model, http protocol, server-side and client-side scripting with CGI and PHP and Javascript. Presents the principles of biological database design using relational and object-oriented database models and management systems (e.g. MySQL and Zope). Topics include SQL, database design, normalization, optimization and ER modeling. Discusses biological database interoperability, with e.g. XML, XML schema, and ontologies (i.e. GO). Guest lectures provide insights into significant biological database projects such as the Human Protein Reference Database (HPRD) and DRAGON. As a final project, students develop and publish a database-driven web-based application for a biological application.

Learning Objective(s):
Upon successfully completing this course, students will be able to:
Use, specify, develop and publish biological databases with web-based interfaces
Describe essential notions of distributed computing on the world-wide-web
Explain the fundamentals of TCP/IP, the client-server model, http protocol, server-side and client-side scripting
Describe the principals of biological database design using a relational database model and the MySQL database management system
Operate SQL, database design, normalization, optimization
Apply basic concepts of discuss modeling and representation using, e.g. ER models, XML schema and ontologies
Discuss significant biological database projects such as the Human Protein Reference Database (HPRD) and DRAGON

Methods of Assessment: Method of student evaluation based on homework and final project
Location: East Baltimore
Class Times:
  • Monday 1:30 - 2:50
  • Wednesday 1:30 - 2:50
  • Friday 1:30 - 2:50
Enrollment Minimum: 5
Instructor Consent: No consent required
Prerequisite:

140.636, or consent of instructor

Auditors Allowed: Yes, with instructor consent
Grading Restriction: Letter Grade or Pass/Fail
Jointly Offered With:
Frequency Schedule: Every Other Year
Next Offered: 2015-2016