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Course Catalog

140.636.01 PERL FOR BIOINFORMATICS

Department:
Biostatistics
Term:
1st term
Credits:
4 credits
Academic Year:
2013 - 2014
Location:
East Baltimore
Class Times:
  • M W F,  1:30 - 2:20pm
Lab Times:
  • Friday,  10:30 - 11:50am
Grading Restriction:
Letter Grade or Pass/Fail
Course Instructor:

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Prerequisite:

Required course for planned degree program (MHS) in bioinformatics.

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.

Learning Objectives:

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

  1. 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);
  2. Describe programming techniques and styles, e.g. top-down vs bottom-up programming, debugging and object oriented programming;
  3. Explain key fundamental concepts from computer science including notions of data structures, algorithms and computational complexity
  4. Organize the processing of large amounts of data from high-throughput biology experiments
  5. Write automatic scripts that query local and web-based biological databases
  6. Search and use the wealth of software development resources available on the web, e.g. cpan.org, sourceforge.net and bioperl.org
Methods of Assessment:

Student evaluation based on homework and programming project.

Instructor Consent:

Consent required for all students

For consent, contact:

fpineda@jhsph.edu

Jointly Offered With: