Graduate Bioinformatics: Molecular Systematics -- CBMG 688O

Spring 20112

2-3 credits

Molecular Systematics is a graduate course in bioinformatics that addresses the use of phylogenetic methods for the analysis of biological sequence data. Taken for 2 credits CBMG688O satisfies the CBMG program module requirement.

Prerequisites: Biochemistry, Genetics, Evolution, and Systematics/Taxonomy are recommended.

Schedule: Lecture MW 4-6 pm in PLS 1184

Instructor: Charles F. Delwiche, 2108 Biosciences Research Building. Tel: 301-405-8286.

Office Hours: MW 2-3 p.m.

Textbook: Recommended: Felsenstein, Joseph. 2004. Inferring Phylogenies. Sinauer Associates, Inc., Sunderland MA.

Supplementary Reading: Recommended and required reading assignments are given with each lecture.

Course project: Students taking CBMG688O for 3 credits will complete a molecular phylogenetic analysis addressing an issue of interest to them, or an experimental study of a substantial theoretical issue in molecular phylogenetic analysis. You may work with your own data, or with data from the literature, but all analyses, including the alignment and the final write-up, should be your own work and uniquely performed for this course.

Web Sites: http://elms.umd.edu/ (for class participants only) and http://www.life.umd.edu/labs/delwiche/MolSyst.html (public).

Lab: No laboratory is associated with the course, but there may be occasional computer practica.

Grading (2 credits):

Grading (3 credits):

Grading will use the letter grade +/- system, and will be based on the cumulative point total.Guaranteed grades are as follows: A, 90%; B, 80%; C, 70%; D, 60%. Students who finish the semester with at least as many points as the minimum indicated for a guaranteed grade will receive at least that letter grade. Depending upon the performance of the class, the minimum percentage required for any given grade may be adjusted downward. The grade of A+ will be given to exceptional students, A- to students at the lower end of the "A" range, B+ to students at the upper end of the "B" range, etc.

The midterm and term project (for CBMG 688O) will be graded for point value. All other exercises will be graded S (satisfactory) or U (unsatisfactory). Students with more than one unsatisfactory assignment will have their grade reduced by one full grade point. Students with more than two unsatisfactory assignments will not pass the class.

Students are expected to participate in class discussions. All assignments are mandatory, and must be completed at the scheduled time, subject to standard university guidelines. Makeup assignments as allowed by the University must be requested (in writing) within one week of the missed exercise. At the instructor's discretion, the format of any assignment, including makeup assigments, may be changed, although they will always be at the same level of difficulty. Note that makeup assignments may the form of an oral exam.