Humberto Ortiz Zuazaga will be teaching an introductory graduate course in bioinformatics Spring 2009 in UPR-RRP. Topics covered will include biological sequences, programming in python, UNIX, sequence alignments, sequence phylogeny, sequence database searches, gene prediction, and whole genome analysis, including transcriptome and microarray analysis, gene clustering and application of statistics to gene profiling data.
We will emphasize the fundamental theory behind the analysis, and also present practical problems and their solutions. The course will use open-source bioinformatics tools, and show how to construct such tools using biopython, a set of libraries for bioinformatics in the python programming language.
The course is designed for graduate and advanced undergraduate students in biology. A basic knowlege of molecular biology is assumed. Students from other disciplines are invited to participate, but will have to make up the background.
3 hours per week, 3 credits
None
Introduce students to fundamental concepts in bioinformatics, programming, and algorithm design. After completing the course, students should be able to select tools and programs to solve bioinformatic problems and participate in their development.
Class will meet Tuesdays and Thursdays, 1:00 - 2:20 PM in UPR-RRP, Julio Garcia Diaz building, room JGD-215.
The proposed schedule of lectures, subject to change:
| Lectures | Topic |
| 1 | Introduction: History of Bioinformatics |
| 1 | Ethical Issues in Bioinformatics |
| 2 | Sequences: Nucleic Acids and Proteins |
| 2 | Collecting and Storing Sequences |
| 2 | Computer platforms used in sequence analysis |
| 2 | Sequence features, Promoters, etc. |
| 2 | Gene order |
| 3 | Pairwise and Multiple Sequence Analysis |
| 2 | Database Searching for Similar Sequences |
| 1 | First Partial Exam |
| 3 | Phylogeny |
| 1 | Functional Genomics: Microarrays |
| 3 | Statistical Methods for Analysis of Microarray Data |
| 3 | Gene Clustering Analysis |
| 3 | Defining Gene Regulatory Networks: Reverse Engineering |
| 1 | Second Partial Exam |
The professor will discuss each topic, students will complete a practical excercise for each bioinformatic technique discussed in class.
A custom CD-ROM containing software to be used in the coursework will be distributed to students (see http://bioknoppix.hpcf.upr.edu). A website with all the course lectures and supplemental materials and references will be available on the HPCf Moodle http://moodle.hpcf.upr.edu
Students will be scored on two partial exams and 10 assigned works. Participation in class will account for an additional grade.
An Introduction to Bioinformatics Algorithms Neil C. Jones and Pavel A. Pevzner ISBN-10: 0-262-10106-8 ISBN-13: 978-0-262-10106-6
Most recent change: 2009/1/22 at 08:43
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