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140.636.01
Perl for BioInformatics

Location
East Baltimore
Term
1st Term
Department
Biostatistics
Credit(s)
4
Academic Year
2012 - 2013
Instruction Method
TBD
Class Time(s)
M, W, F, 1:30 - 2:20pm
Lab Times
Friday, 10:30 - 11:50am
Available to Undergraduate
No
Grading Restriction
Letter Grade or Pass/Fail
Contact Email
Frequency Schedule
Every Year
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