Spotlight: Bioinformatics

News flash! Bioinformatics (CS 378, Interim 2004) approved for NST-B on Wednesday, 11/12/03!

This course breaks the mold in lots of ways: the three profs (Biology, CS, and a Bioinformatics specialist visitor); counting towards three majors and two concentrations; and now a NST-B course taught outside of Biology, with Biology’s encouragement. To study the ways that CS research can work together with Biology research to solve fascinating applied problems, one has to learn new Biology as well as new CS.

See below for more information.

When biologists ask questions that require computer scientists to answer, the result is Bioinformatics. For example, now that the patterns of DNA (genomes) have been determined for various organisms, retrieving that data in useful ways, and analyzing it (e.g., comparing two genomes, or detecting individual genes within a genome) calls for some interesting Computer Science. Furthermore, the inspiration goes both ways: the results of CS techniques make it possible to ask further questions and pursue new lines of Biology research. Furthermore, biological results produced by this fruitful collaboration have great relevance in society, e.g., helping to determine genetic causes of cancer or factors in the spread of organism-borne diseases such as tuberculosis.

We will offer a first course in this exciting new interdisciplinary field during January Interim 2004. Biology, CS, and mathematics students are encouraged to take this course, which has prerequisites ]crsref([CS1])[ and either ]crsref([SD])[ or Biology 125, or permission of instructor; students with biology background will be given extra help in CS, and students with CS background will be given extra help in Biology. The course counts for no less than three majors—Biology, CS, or Mathematics (satisfies the “applied” requirement)—and two concentrations—CS and Molecular Biology.

Read on for a catalog description and further details about the Interim course.

Interim catalog description for Bioinformatics course

CS 378, Bioinformatics, Interim 2004

Bioinformatics brings biologists and computer scientists together to work on problems that intrigue both groups. For example, analyzing biological genome data requires specialized algorithms that interest computer scientists; and the results from those algorithms provide new directions for further study in biology.

This course provides an introduction to the field of bioinformatics. Topics will include sequences of DNA and RNA and the “central dogma;” comparing sequences, predicting sequences, predicting species; computational techniques such as substitution matrices, sequence databases, dynamic programming; and bioinformatics tools such as FASTA and BLAST. Programming in Perl language will be introduced and used in the course. Besides presentations on bioinformatics, breakout sessions will give additional CS background to biology students, and additional biology background to CS students. Coursework will include team projects in interdisciplinary groups of four.

Prerequisites: Computer Science 172 and either Biology 125 or Computer Science 272, or permission of instructor.

Counts for Computer Science Major, Biology Major, Mathematics Major, Computer Science Concentration, and Molecular Biology Concentration.

Earlier announcement of Bioinformatics course

Special Opportunity for Interim 2004in

CS 378 — Professors Trilling, Allen, and RutherfordBioinformatics is a new and fast-developing field that lies at the intersection of computer science, biology, and mathematics. Since the unraveling of DNA in 1953, molecular biology has witnessed a tremendous increase in the ability to sequence and manipulate biomolecular sequences and thus generate enormous amounts of data. The need to process this data has created new problems. In particular, the sheer size and complexity of this DNA-related data has required computer scientists to create tools, techniques, and structures to store, search, analyze, and transform the data in ways that support asking important biological questions. New databases are needed to store all this data and to record changes in the understanding of molecular sequences as they are studied. Computer Scientists face tremendous challenges in how to design data bases and algorithms for biologists to mine these data accurately and quickly. The shear number of questions one could ask about the data makes this an exciting and challenging task for all involved.

The Interim course, Computer Science 378, Bioinformatics, will address central problems arising from the need to store, access, transform, utilize DNA-related data. The course is intended for sophomores, juniors, and seniors majoring, concentrating, interested in biology, biochemistry, computer science, and mathematics. We hope that a good mix of students from a variety of backgrounds will enroll. Bioinformatics is intrinsically an interdisciplinary area where different viewpoints, different contributions, different expertise are welcomed, encouraged, needed. Consequently, we would like to have interdisciplinary groups of students in the course. Everyone will benefit from such a blend. Bioinformatics is changing how medicine is done, how to do research in biology, how to structure, transform, access databases. It already constitutes crucial knowledge for many areas of study.

A trio of professors will be responsible for the course: (1) Laurent Trilling, a computer scientist from the Computer Science and Applied Mathematics Institute in Grenoble, France; (2) Professor Richard Allen, a longtime member of the CS faculty at St. Olaf; and (3) Professor Rob Rutherford, a new faculty member in the Biology whose primary interests are in bioinformatics. So we have a lot of teaching resources to ensure that all students from all backgrounds will find lots of help in understanding the multiple facets of the course and in succeeding academically.

Prerequisite: Computer Science 172. If you have not taken Computer Science 172 (Introduction to Computer Science), you can take it next fall. Even though the Interim course has a high course number, we are committed to making the course a success if you have taken CS 172 and have a high interested and commitment to learning about bioinformatics.