140.637.01 BIOLOGICAL DATABASES AND DISTRIBUTED COMPUTING

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.

Upon successful completion of this course, students will be able to use, specify, develop and publish biological databases with web-based interfaces. Students will learn essential notions of distributed computing on the world-wide-web. This includes the fundamentals of TCP/IP, the client-server model, http protocol, server-side and client-side scripting. The course will present the principals of biological database design using a relational database model and the MySQL database management system. Students will learn SQL, database design, normalization, optimization. Students will learn and apply basic concepts of knowledge modeling and representation using, e.g. ER models, XML schema and ontologies. Guest lectures will provide insights into significant biological database projects such as the Human Protein Reference Database (HPRD) and DRAGON. Students will demonstrate proficiency with a final project, involving the developing of a database-driven application with a web-based interface using CGI and perl.