PERL FOR BIOINFORMATICS Syllabus

140.636.01 | AY 2013-2014 - 1st Term | 4 Credit(s)
MWF 1:30:00 PM
  • Contact Information
    Faculty
    Fernando Pineda
  • Course Learning Objectives

    Upon successfully completing this course, students will be able to:

    • Operate the Perl programming language (including the ability to (1) read and write perl scripts, and (2) download and use perl bioinformatics libraries, e.g. bioperl);
    • Describe programming techniques and styles, e.g. top-down vs bottom-up programming, debugging and object oriented programming;
    • Explain key fundamental concepts from computer science including notions of data structures, algorithms and computational complexity
    • Organize the processing of large amounts of data from high-throughput biology experiments
    • Write automatic scripts that query local and web-based biological databases
    • Search and use the wealth of software development resources available on the web, e.g. cpan.org, sourceforge.net and bioperl.org
  • Course Description
    Uses the PERL programming language to introduce skills and concepts needed to process and interpret data from high-throughput technologies in the biological sciences. Key concepts are introduced and reinforced through lectures with live computer demonstrations, weekly readings, and programming exercises. Excercises and examples draw heavily from biological sequency analysis as welll as real-world problems in proteomics and genetics. Guest lecturers present case studies of PERL and UNIX usage in scientific investigations. Students are introduced to bioinformatics software-development resources available online and to necessary computer science fundamentals.
  • Intended Audience
    Molecular biology students, students in Biostatistics and MMI.
  • Methods of Assessment
    Student evaluation based on homework and programming project.
  • Prerequisites
    Required course for planned degree program (MHS) in bioinformatics.
  • Course Schedule

    Please see the course Session for a full list of dates and items for this course.

    All pertinent course information is available at the course website

  • Academic Ethics Code

    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 the Office of Student Life Services at 410-955-3034 or via email at dss@jhsph.edu.