Course Numbers: BMME 8053, OCMB 9911, MEVS 5606
The primary goal of this course is to introduce the student to the field of bioinformatics and the skills needed to manipulate datasets from biological studies. Computer exercises will include working in the UNIX/LINUX environment, interpretation of DNA sequence analyses, and gaining a familiarity with online bioinformatics resources. There will be an emphasis on hands on practice through the guidance of the instructor.
At the conclusion of this course the student will be:
- be able to locate appropriate online databases for accessing genomic data and metadata.
- be able to recognize and describe file formats used for bioinformatics.
- be able to propose the appropriate bioinformatics analysis for a project.
- be able to assess the analytical strengths and weaknesses of published studies.
- be able to use UNIX and Perl to efficiently extract data from tab delimited text files.
*These are directly related to the Program Learning Outcomes for Marine Biology, Coastal Zone Management and Marine Environmental Science.
- The student will need a computer with privileges to install software. Use of an Apple is recommended. If the student has a PC, it will need to have Cygwin to allow access to a UNIX interface. Cygwin is free and instructions for installing Cygwin will be provided in the course.
- The NCBI Handbook. McEntyre and Ostell. Available free online at https://www.ncbi.nlm.nih.gov/books/NBK21101/
- Genomes. TA Brown. Available free online at http://www.ncib.nlm.nih.gov/books/NBK21134
- Beginning Perl. Cozens. Available free online at https://www.perl.org/books/beginning-perl/
- Weekly reading assignments and instructional videos will provided during the course.
Fall 2016 Syllabus