Introduction
This new course focuses on bioinformatics, a rapidly
evolving field integrating computation and biology,
especially focused on information relating to DNA and
protein sequences.
Format: Lecture/discussion will be based on
selected readings and short presentations on selected topics
by students and faculty. There will be presentations by
faculty and others on research problems and applications in
a variety of fields, including but not limited to molecular
parasitology, genomics, molecular biology, environmental
genetics, protein modeling, and gene expression. Many of
these presentations will be associated with computer lab
problems and projects. Problem-based computer lab
instruction will focus on web-based bioinformatics,
integrating databases and application programs.
The course is divided into six units preceded by an
introduction to problem-based learning as applied in this
course and a pre-module exercise. The pre-module exercise is
ungraded and is designed to assess necessary background and
readiness for the course. It is linked to several web-based
tutorials useful for preparation and/or review on basic
support topics, such as molecular biology and statistics.
Each of the units focuses on a general topic with discussion
and activities related to the topic.
General topics: Types of databases and search
strategies, genomics, molecular genetics, phylogenetics,
protein structure prediction, and metabolic pathways.
Prerequisites: For biology majors:
Completion of the lower-division core in Biology or
equivalent; one course in statistics strongly recommended.
Open to non-majors with consent of instructor. [This
course would particularly be of interest to majors in
chemistry, computer science, and math with an interest in
biological applications.]
Texts
Recommended: This year we are recommending the
following texts. I only expect that you select and use one
of these or an equivalent book. Reading will support the
exercises and projects that are the core of the course.
Selection of a suitable book will be discussed at the first
class meeting.
Gibas & Jambeck, Developing
Bioinformatics Computer Skills, 2001, O'Reilly.
Baxevanis & Ouellette, Bioinformatics: A
Practical Guide to the Analysis of Genes and Proteins
(2nd ed.), 2001, John Wiley & Sons, Inc.
Mount, Bioinformatics: Sequence and Genome
Analysis, 2001, Cold Spring Harbor Laboratory
Press.
Westhead, Parish & Twyman, Instant Notes:
Bioinformatics, 2002, BIOS Scientific Publishers
Ltd.
Campbell & Heyer, Discovering Genomics,
Proteomics & Bioinformatics, 2003, Benjamin
Cummings.
Claverie & Notredame, Bioinformatics for
Dummies, 2003, For Dummies.
Readings are listed on the Course Materials web
pages.
For your convenience, on-line links to the bookstore and
elsewhere are available on my home
page.
.
|
