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Course Catalog

140.636.01 PERL FOR BIOINFORMATICS

Department: Biostatistics
Term: 1st term
Credits: 4 credits
Contact: Fernando Pineda
Academic Year: 2014 - 2015
Course Instructor:
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. Introduces key concepts, which are reinforced through lectures with live computer demonstrations, weekly readings, and programming exercises. Excercises and examples draw heavily from biological sequence analysis as welll as real-world problems in proteomics and genetics. Students learn how to use a High Performance Compute Cluster and also how to create their own servers in the Amazon cloud. Guest lecturers present case studies of PERL and Linux usage in scientific investigations. Introduces students to bioinformatics software-development resources available online, and to necessary computer science fundamentals.

Learning Objective(s):
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

Methods of Assessment: Student evaluation based on homework and programming project.
Location: East Baltimore
Class Times:
  • Monday 1:30 - 2:20
  • Wednesday 1:30 - 2:20
  • Friday 1:30 - 2:20
Lab Times:
  • Friday 10:30 - 11:30
Enrollment Minimum: 5
Instructor Consent: Consent required for all students

All students should confirm with instructor that they have the necessary prerequisites to take the course

For consent, contact: fernando.pineda@jhu.edu
Prerequisite:

Students should be comfortable using a command line interface and have some experience programming in some other language.

Auditors Allowed: Yes, with instructor consent
Grading Restriction: Letter Grade or Pass/Fail
Jointly Offered With: