PBIO / BIOL 4550 / 6550
Bioinformatics Applications
Spring Semester 2008, 3 credits
| Schedule: |
- Lecture: Normally, two 75 minute lectures per week, 9:30 AM, Tuesdays and Thursdays,
room 1501, Plant Sciences.
- Lab: We will have a lab session every-other-Thursday at the normal class time,
although this may change depending upon enrollment.
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| Instructor: |
Russell Malmberg
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| Teaching Assistant: |
Haibao Tang |
| Additional Lecturer: |
Yecheng Huang |
| Course Materials and Lecture Schedule |
 |
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| Course Description |
| The applications and concepts of computational technologies for solving
problems in molecular genetics will be taught. Current programs and the principles
that underlie them will be discussed. Topics include: sequence and structure
databases; sequencing; mapping; sequence alignments (dynamic programming); motifs
and profiles; phylogeny reconstruction; probabilistic approaches (Markov models).
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| Prerequisites |
| Basic genetics or molecular biology, and the willingness to use some simple
algebra and probability.
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| Course Objectives |
| This course is designed for graduate students who wish to learn what
computational technologies exist to solve molecular genetic and genomics problems.
Students should learn what computer applications, including resources that exist
on the internet, are available, and they should also learn some of the basic
algorithms and programming concepts that underlie these programs. The course
should provide students with enough information that they will know how to use
these technologies to analyze their own genetic and sequence data, what options
are available. Students will learn enough of the underlying computational
algorithms to be able understand what current research in bioinformatics is
trying to accomplish.
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| Grades: |
| Student grades will be based on homework assignments and take home problems sets.
Additionally, graduate students will be required to write a report in the form
of a web page that will be demonstrated in class. For details, see:
Grading Points.
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| Computers: |
| Some computers will be available during the computer lab, but otherwise
students will need to have their own access to computers and the internet
through other means.
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What is Bioinformatics?
"The definition of bioinformatics is not univerally agreed upon. Generally speaking,
we define it as the creation and development of advanced information and computational
technologies for problems in biology, usually molecular biology. As such, it deals
with methods for storing, retrieving and analyzing biological data, such as nucleic
acid (DNA/RNA) and protein sequences, structures, functions, pathways and interactions.
Some people construe bioinformatics more narrowly, and include only those issues
dealing with the management of genome project sequencing data. Others construe
bioinformatics more broadly and include all areas of computational biology, including
population modeling and numerical simulations."
Quotation from Doug Brutlag
This course owes much of its organization and inspiration to Doug Brutlag's
and Lee Kozar's Computational
Molecular Biology course.