CSE 308: Bioinformatics: Issues and Algorithms (3)

Instructor: Daniel Lopresti

 

Current Catalog Description

Computational problems and their associated algorithms arising from the creation, analysis, and management of bioinformatics data.  Genetic sequence comparison and alignment, physical mapping, genome sequencing and assembly, clustering of DNA microarray results in gene expression studies, computation of genomic rearrangements and evolutionary trees.  Credit will not be given for both CSE 308 and CSE 408.  No prior background in biology is assumed.  Prerequisite: CSE 17 or permission of the instructor.

Textbooks

"An Introdution to Bioinformatics Algoithms", Neil C. Jones and Pavel A. Pevzner, MIT Press, ISBN 0-262-10106-8

"Exploring Bioinformatics: A Project-Based Approach", Caroline St. Clair and Jonathan E. Visick, Jones & Bartlett, ISBN 978-0763758295. (EB).

Course Outcomes     

Students will have:

1.    Ability to write computer programs in Perl to analyze bioinformatics data.

2.    Ability to choose appropriate algorithms and data structures when programming solutions to bioinformatics problems.

3.    Ability to communicate technical material relating to bioinformatics algorithms and applications.

4.    Ability to recognize moral and ethical issues arising from creation of software for bioinformatics applications.

    

Relationship between Course Outcomes and Program Outcomes   

CSE 308 substantially supports the following program outcomes:

A. An ability to apply knowledge of computing and mathematics appropriate to the discipline

J.  An ability to apply mathematical foundations, algorithmic principles, and computer science theory in the modeling and design of computer-based systems in a way that demonstrates comprehension of the tradefoffs involved in design choices

CSE 308 provides modest support to the following program outcomes:

B.  An ability to analyze a problem and identify and define the computing requirements appropriate to its solution

E.  An understanding of professional, ethical, legal, security, and social issues and responsibilities

 

Prerequisites by Topic

1. Top-down design

2. Basic data structure

 

Major Topics Covered in the Course

         1. Intro to molecular biology

         2. Intro to algorithms and complexity

         3. Programming in Perl

         4. The DNA physical mapping problem and its solution

         5. The genome rearrangement problem and its solution

         6. Techniques for sequence comparison and alignment

         7. Genome sequencing and assembly

         8. Genetic pattern matching

         9. DNA microarray analysis and clustering techniques

        10. Evolutionary tree construction

        11. RNA and protein structure prediction

        12. Bioethics

Assessment Plan for the Course

The students are given five substantial homework assignments, some of which include programming problems.  Written homework questions account for 20% of their course grade and programming problems account for another 20%.  They also maintain a “lab notebook” which records their observations when performing Web Exploration projects assigned from their Exploring Bioinformatics textbook.  This accounts for 10% of their course grade.  Students are also required to write a final 15-page research paper on a bioinformatics topic relating to the course, and to give a 15-minute talk on this work during the final week of the course.  This final paper/project accounts for 50% of their course grade.

How Data in the Course are Used to Assess Program Outcomes (unless adequately covered already in the assessment discussion under Criterion 4)

Each semester I include the above data from the assessment plan for the course in my self-assessment of the course. This report is reviewed, in turn, by the Curriculum Committee.