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.
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
, located on the ground floor of Rotary Residence Hall, phone (318) 869-5424.
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 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.
We will follow the textbook for most of the course.
We will also be using additional supplemental material such as
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 3 : Dealing with Databases
- Chapter 4 - 5 : Sequence Alignments
- Chapter 6 : Modeling Motifs
- Chapter 7 - 8 : Evolutionary Processes
- Chapter 15 - 17 : Cells and Organisms
- Chapter 3, 13 - 14 : Protein Structures
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.
There will be two exams, each worth 20% of your final grade.
- Exam 1: March 4th, covering Chapters 1, 3-8
- Exam 2: ???
Your final grade for this course will be based on the Projects, Quizzes, Exams and
Participation described above.
© Mark Goadrich, Centenary College of Louisiana