This course develops the background needed by graduate students pursuing the bioinformatics option or the PhD in Genetics, Bioinformatics, and Computational Biology but not having a computer science background. Fundamentals of computer science discussed and practiced include Linux, data, and the importance of the command line interface; the Perl programming language; program design, implementation, and testing; field-structured, semi-structured, and relational databases; basic data structures, algorithms, and algorithm analysis; and data mining.
Grading for the course is on a 1000-point scale, with the points
distributed as follows:
Homework assignments: 8 at about 50 points each 400
Programming and database assignments: 6 at about 50 points each 300
Exams: 3 at about 100 points each (evenings) 300
A typical homework assignment consists of 2 or 3 problems. All homework must be prepared with LATEX or other word processing system. Homework may be submitted as a stapled printout in class on the date due or may be emailed to the instructor making the assignment as a PDF file prepared by Adobe Distiller. A typical programming or database assignment consists of 2 or 3 programs or database queries to write and test. A programming or database assignment must be prepared with a text editor (vi, pico, or equivalent) and submitted by email to the instructor making the assignment, together with the input and output files from testing. Each assignment is due at 5:00 PM on the due date. No late assignments will be accepted.
The Honor Code applies. All work submitted must be the student's own work. Students may solicit help only from the instructor.
If any student needs special accommodations because of a disability, please contact the instructor during the first week of classes.