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140.636.01 Perl for Bioinformatics

1st term
4 credits
Academic Year:
2014 - 2015
East Baltimore
Class Times:
  • M W F,  1:30 - 2:20pm
Lab Times:
  • Friday,  10:30 - 11:30am
Auditors Allowed:
Yes, with instructor consent
Grading Restriction:
Letter Grade or Pass/Fail
Fernando Pineda
Course Instructor:

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


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. Exercises and examples draw heavily from biological sequence analysis as well as real-world problems in proteomics and genetics. Students will 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 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., and
Methods of Assessment:

Student evaluation based on homework and programming project.

Instructor Consent:

Consent required for all students

Consent Note:

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

For consent, contact:

Jointly Offered With: