CSC 277 - Bioinformatics

Course Details

Textbook

Understanding Bioinformatics by Marketa Zvelebil, Jeremy O. Baum 2007 Find this text on Amazon

Overview

This course explores computational methods for analyzing and understanding the large quantities of information now available in the growing fields of genomics, proteomics and systems biology. It complements practical experience of current bioinformatics systems with a deep understanding of their algorithmic underpinnings. Topics include aligning pairwise and multiple sequences, constructing phylogenies, searching strings, modeling motifs, clustering microarray data, inferring regulatory networks, and modeling biological systems.

Disabilities

Centenary assures students with disabilities equal opportunity to reach the same level of achievement as other students. Strict confidentiality will be maintained on students with disabilities. Services for students with disabilities are available through the Counseling Center, located on the ground floor of Rotary Residence Hall, phone (318) 869-5424.

Honor Code

All students are bound by the Honor System. The Honor System is applicable to all academic work. See the Centenary College Handbook for the complete Honor Code. All code you write and turn in for a grade is understood to be pledged. You may discuss topics with other students and tutors, but all code you write must be your own, and you must be able to explain to me how it works. In this course, it is a violation of the honor code to look at code from previous semesters or in other students' directories.

Extensions

Extensions and rescheduling for labs, projects, exams and quizzes are only given when circumstances beyond your control (e.g. being sick, choir or sports travel) prevent you from completing a project on time. You must notify me either by email or phone of your circumstances well in advance of the due date. No extensions are given for requests made within three days of the due date.

Quizzes and Participation

You are encouraged to attend class and participate in discussions every day. Sporadically throughout the semester, there will be short quizzes covering material from the previous class. These quizzes will serve as records of your attendance, and in total they will comprise 5% of your final grade. Active participation in class discussions will comprise another 5% of your final grade. This will be awarded for answering questions, asking questions, presenting material, etc.

You will be expected to sign up for a Twitter account and use it regularly to post status updates about the class and your progress in labs and projects with the #csc277 hashtag.

• Quiz 1

Syllabus

We will follow the textbook for most of the course. We will also be using additional supplemental material such as relevant web-pages and background material for the lab assignments. Readings will be assigned before material will be covered in class. You are expected to review the material and come to class prepared. As readings are assigned, they will be posted here.

• Chapter 1 : The Nucleic Acid World
• Chapter 2 : Protein Structure
• Chapter 3 : Dealing with Databases
• Chapter 4 - 5 : Sequence Alignments
  • Alignment Lecture
  • Affine Gaps
  • Star and Tree Multiple Alignment
• Chapter 6 : Modeling Motifs
  • HMMs
  • HMM Applications
• Chapter 7 - 8 : Evolutionary Processes
  • UPGMA
  • UPGMA 2
  • Neighbor Joining

Projects

You will have seven projects in this course, one about every 2 weeks, for a total of 50% of your final grade. These projects will cover concepts we have discussed in class and will be due approximately one week after they are assigned.

You may work with a partner on these projects. You may discuss concepts and ideas with your other classmates, but the code you turn in must be your own. You will be graded not only on correctness, but also technique, documentation and evaluation of your solution. Further details on the grading standards and handin instructions for each project will be given when they are assigned.

• Project 1: The Central Dogma

• Project 2: Bioinformatics Scavenger Hunt

• Project 3: Pairwise Alignment

• Project 4: Hidden Markov Models

• Project 5: Microarray Clustering

• Project 6: Gene Regulatory Networks

Exams

There will be two exams, each worth 20% of your final grade.

• Exam 1: March 5th

• Exam 2: April 29th 12-3pm

Grading

Your final grade for this course will be based on the Projects, Quizzes, Exams and Participation described above.

Grading Scale 90-100 A 80-89 B 70-79 C 60-69 D 0-59 F

Weights Projects 50% Quizzes 5% Participation 5% Exam 1 20% Exam 2 20%

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© Mark Goadrich, Centenary College of Louisiana