BIOLOGICAL DATABASES AND DISTRIBUTED COMPUTING Syllabus

140.637.01 | AY 2013-2014 - 2nd Term | 3 Credit(s)
MWF 1:30:00 PM
  • Contact Information
  • Course Learning Objectives

    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
  • Course 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.

  • Intended Audience

    Students in our proposed MHS program in Bioinformatics; students interested in publishing biological data on the worldwide web.

  • Methods of Assessment

    Grading Policy: Method of student evaluation based on homework and final project

    Grading Restrictions: Letter grade

  • Prerequisites

    140.636, or consent of instructor

  • Academic Ethics Code

    The code, discussed in the Policy and Procedure Memorandum for Students, March 31, 2002, will be adhered to in this class:

    Students enrolled in the Bloomberg School of Public Health of The Johns Hopkins University assume an obligation to conduct themselves in a manner appropriate to the University's mission as an institution of higher education. A student is obligated to refrain from acts which he or she knows, or under the circumstances has reason to know, impair the academic integrity of the University. Violations of academic integrity include, but are not limited to: cheating; plagiarism; knowingly furnishing false information to any agent of the University for inclusion in the academic record; violation of the rights and welfare of animal or human subjects in research; and misconduct as a member of either School or University committees or recognized groups or organizations.

  • Disability Support Services

    If you are a student with a documented disability who requires an academic accommodation, please contact Betty H. Addison in the Office of Student Life Services: baddison@jhsph.edu, 410-955-3034, or 2017 E. Monument Street.