Seminar in Computer Science (Section 31119):
Fundamental Models and Algorithms in Bioinformatics

CSCI B490 Fall 2015

Time & Location:    Mon, Wed 1:00p - 2:15p (Credits: 3.0); Lindley Hall (LH) 008
Instructors:    Volker Brendel (205C Simon Hall; Tel.: 855-7074); Guest lectures: Daniel Standage (Brendel group)
Email:     VB, vbrendel@indiana.edu; DS, daniel.standage@gmail.com
WWW:     https://brendelgroup.org/
Office Hours:     Mon, Wed after class and by appointment.
Grades:    will be determined as described below.
Schedule:     https://brendelgroup.org/teaching/2015/FMAB15Fschedule.php
Computing Resources:     You will have access to networked computer terminals in class and will need such basic access outside of the classroom for assignments.

version of this syllabus

Synopsis

Biology has become one of the primary application domains of computer science and informatics approaches. The term "Bioinformatics" covers a wide spectrum of data management and processing associated with large-scale, high-throughput biological data generation. This class will focus on biomolecular sequence data (DNA and protein) that underpin much of modern biology, including for example genetics; ecology, evolution, and population biology; and structural biology. Applications in medicine and biotechnology are changing the world we live in. Many of the data analysis problems in the field have been mapped to tractable mathematical models amenable to algorithmic solutions. The course will cover fundamental models and algorithms in bioinformatics, with emphasis on the general principles involved in the modeling and algorithmic approaches. The course should be of interest to you if one or more of the following apply to you: (1) You are curious and would like to learn about a "hot topic"; (2) You want to expand your range of options for graduate school; (3) You are considering a high-paying job in the biotechnology sector.

Prerequisites

This class is directed primarily at upper level undergraduates in Computer Science and Informatics, although students of Mathematics, Statistics, or Biology may find the course accessible and of interest. Although there are no formal prerequisites for the course, some basic calculus and statistics knowledge will be necessary and will be reviewed as required by students' background. Relevant biological concepts will be introduced as needed. Some classes will be taught as a computer lab. Students will need to be familiar with basic computer operational skills, including some programming language knowledge. Class messages and materials, including assignments, will be shared through our Oncourse site in addition to these web pages, and students are required to regularly check these relevant communication channels. IU is committed to Creating a Positive Environment for teaching and learning. If you have any concerns or suggestions, please let the instructor know.

Assignments

The class material will be organized into six topics (chapters), each occupying four class periods over a two-week section. For each topic, the first class period will be devoted to a lecture-based introduction to the topic. Relevant reading material will be assigned as homework. The second period will begin with an ungraded comprehension quiz concerning the reading material and then go into problem solving. The homework assignment for this period will be a programming task. The third period will be a programming laboratory in which the homework code will be discussed, exchanged, and tested. The forth period will consist of a written test (quiz). Each quiz will count 20 points towards the grade in the class.

Grading

Grades will be based on a 100-point scale, derived as the total of the five best scores from the six quizzes and a written final (which will also count 20 points). Absences during quizzes or the final will be counted as zeros (and presumably discarded in calculating the final score).

Text book

The class is based on a draft textbook "Fundamental Models and Algorithms in Bioinformatics", V. Brendel (Indiana University) & K. Dorman (Iowa State University). Excerpts of the draft will be made available to the students as PDFs.