1st term, 2017-2018
MWF 1:30-2:20 in W2033
F 10:30-11:20 in W2033
Instructor: Fernando Pineda
Please read ALL of this document carefully.
This course uses the perl programming language to introduce skills and concepts needed to process and interpret data from high-throughput technologies in the biological sciences. The course focuses on generally applicable computer-science concepts rather than statistical analysis concepts. Lectures with live computer demonstrations and hands-on-laboratories will be used to introduce key concepts. These will be reinforced and extended with weekly readings and programming exercises. Exercises and examples will draw heavily from biological sequence analysis, proteomics, genetics and computational biology. Occasional guest lecturers will present case studies. Students will be introduced to the wealth of bioinformatics and computational software-development resources available on the World Wide Web. Students will be introduced to necessary fundamentals in computer science including: (1) pattern matching, parsing and translation (2) data structures, algorithms and complexity, (3) Object-oriented programming (4) programming style and best practices. Applied topics to be covered include: (1) Biological sequence analysis, (2) Perl as middleware (3) how to use unix and perl to manage and process high-throughput datasets and (4) automated interaction with local (e.g. MySQL) and remote (e.g. Genbank) biological databases, (5) High performance computing, (6) parallel processing, (7) simulation.