140.636.01
Perl for BioInformatics

Location
East Baltimore
Term
1st Term
Department
Biostatistics
Credit(s)
4
Academic Year
2014 - 2015
Instruction Method
TBD
Class Time(s)
M, W, F, 1:30 - 2:20pm
Lab Times
Friday, 10:30 - 11:30am (01)
Auditors Allowed
Yes, with instructor consent
Available to Undergraduate
No
Grading Restriction
Letter Grade or Pass/Fail
Course Instructor(s)
Fernando Pineda
Contact Name
Fernando Pineda
Contact Email
fernando.pineda@jhu.edu
Frequency Schedule
Every Year
Prerequisite

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

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. 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. cpan.org, sourceforge.net and bioperl.org
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
Consent Contact
fernando.pineda@jhu.edu
Jointly Offered With
Biostatistics
Molecular Microbiology and Immunology