“Bioinformatics is the most democratic of scientific disciplines. One does not need a lot of equipment or big grants. One only needs a computer, access to the Internet, and some interesting questions.”
Thanos Lykidis, invited seminar at Hiram College, 2004
Symposium on Chromohalobacter salexigens Genome
Bioinformatics arises from the interaction of biology, computer science, math, and statistics. It deals with the staggering amount of biological information, mainly in the form of DNA and protein sequences, and tries to find ways to organize, sort, compare, and decode these sequences to find underlying similarities and patterns that are biologically relevant. This course will help students become comfortable thinking about problems and arriving at solutions both as biologists and computer scientists. The course will cover computational methods for the study of biological sequence data: analysis of genome content and organization, techniques for searching sequence databases, pair-wise and multiple sequence alignments, methods for finding fractured patterns, phylogenetic methods, and protein structure prediction and modeling. Each of the problems will be analyzed both from the biologist's and the computer scientist's point of view. Students will have the opportunity to analyze biological data, to experiment with available bioinformatics tools, and to program in Perl to solve bioinformatics problems.
The goals of this course are: (1) to introduce you to the exciting interdisciplinary field of bioinformatics, the scope of the currently available tools, and the depth of the problems it tries to tackle, (2) to give you multiple opportunities to hone your problem solving skills in general and to develop specific skills in handling bioinformatics data, identifying problems, and figuring out the best way to arrive at a solution, and (3) to give you multiple opportunities to make significant contributions to ongoing research projects using your newly developed skills, your curiosity, and your passion for learning.
Jonathan Pevsner. Bioinformatics and Functional Genomics, 2nd Edition, 2009. (ISBN: 978-0-470-08585-1)
Familiarity with using computer applications. BIOL 334 recommended.
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| Paper Discussions/Homework | 10% |
| Participation | 10% |
| Midterm Exam | 20% |
| Project Phase One | 15% |
| Project Phase Two | 15% |
| Project Presentation (part of final exam) | 5% |
| Best Area | 5% |
| Final Exam | 20% |
Make-up tests will be allowed for excused absences only.
Unless specified otherwise, all work should be your own work! It should be completed in accordance with the PC Honor Code. Answers that are very similar will become evidence of too much collaboration and, therefore, a violation of the Honor Code. Your answers should be distinctive enough from another student's answers.
No more than 8 classes missed, excused or not excused. Anyone with 9 absences will lose a letter grade for the final grade for the course. Any absences after the 9th will also result in losing a letter grade on the final grade for the course. If you come late to a class, it is your responsibility to inform the instructor after the class to avoid being counted as absent. The instructor reserves the right to count three (3) tardies as one (1) absence.