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140.637.01
Biological Databases and Distributed Computing

Location
East Baltimore
Term
2nd Term
Department
Biostatistics
Credit(s)
3
Academic Year
2012 - 2013
Instruction Method
TBD
Class Time(s)
M, W, F, 1:30 - 2:50pm
Auditors Allowed
Yes, with instructor consent
Available to Undergraduate
No
Grading Restriction
Letter Grade or Pass/Fail
Contact Name
Fernando Pineda
Contact Email
Frequency Schedule
Every Other Year
Next Offered
2024 - 2025
Prerequisite

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

This course will now be offered on alternating odds years (ie, next offered during 2011-12)