140.636.01 PERL FOR BIOINFORMATICS

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.

Upon successful completion of this course, students will have: 1) a working knowledge of 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) an understanding of programming techniques and styles, e.g. top-down vs bottom-up programming, debugging and object oriented programming; 3) an understanding of key fundamental concepts from computer science including notions of data structures, algorithms and computational complexity; 4) the ability to organize the processing of large amounts of data from high-throughput biology experiments; 5) the ability to write automatic scripts that query local and web-based biological databases; and 6) the ability to search and use the wealth of software development resources available on the web, e.g. cpan.org, sourceforge.net, and bioperl.org.