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Announcements: Course development is being supported by a grant from NSF.

[Last updated: 12/4/03]

Final 'not-the-final' project proposal. Due 12/16 at 5 pm. Location TBA.

Check back here periodically for updates. If you have a question, send me an email.

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Dr. Eileen Thatcher

Home Page

Office: Darwin 121

v-mail: 664-3058
e-mail: thatcher@sonoma.edu

Office hours:

W 4-5; Th 3-4; or by appt

 

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.
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Site Index | Syllabus | Schedule | Study aids | Computing | Links | Course Materials Home

  Updated 9/4/03 by thatcher@sonoma.edu