Computational
Techniques in Structural Bioinformatics
CS483/CS683 Winter 2015
Instructor:
Forbes Burkowski
DC1309
Assignments
Winter 2015:
Assignment #5 Due date: Thurs. Apr. 2 Delaunay
Starter Script
Some notes related to Assignment
#1: Getting
Started with Chimera and Python
Overview
The magic that is life ultimately takes place on the
surfaces of biomolecules. Biochemical interactions
at the active site of a protein surface are involved in both the normal
reactions that support life processes and the contrived reactions that
constitute therapeutic intervention via drugs.
In both situations, the biochemist and the bioinformatician
must take on the challenge of working with large collections of high
dimensional data dealing with three-dimensional structures.
The main
emphasis of the course will be the application of computational approaches to problems
in structural bioinformatics. This
includes algorithms for database storage and retrieval of biomolecular
structures and the geometric algorithms that help us analyze and model both
macromolecular chains and the surfaces that they form.
Text:
Computational
and Visualization Techniques for Structural Bioinformatics Using Chimera
(Hardcover)
Author: Forbes Burkowski
Website for the text:
www.structural-bioinformatics.com
Some additional reference texts will be mentioned in the first set of
slides.
Copies of all transparencies used in
class will be made available:
Workload
- 3 hours of lectures
per week
There will be five assignments corresponding to
various major topics of the course.
Marking scheme CS483. Assignments 30%, Midterm 30%,
Project 40%.
Marking scheme CS683 Any 4 of the 5 Assignments: 25%, Midterm: 25%, Project: 50%.
The project will
include a 30 minute class presentation.
You must first
submit a project proposal for approval and constructive criticism prior to the
end of February. This proposal will be
part of Assignment 3.
Note: To pass CS483/683, the weighted average of the
Midterm and Project must be more than 50%.
If this average is below 50%, then that average becomes the final grade
(project or assignments are not included in the final grade).
Academic Honesty
The usual penalties for academic dishonesty will
apply: -100% on an assignment if there is evidence of copying or plagiarism.
So that there are no future
misunderstandings, please read the following:
In any program you write, each line of code should
come from your effort only.
If you are writing text that is part of the
assignment, each sentence that you write
will fall into one of the following categories:
1. The sentence is
expressed in your own words and expresses your own ideas.
2. The sentence is expressed
in your own words but the ideas or concepts are from somebody else.
In
this case you must supply a reference at the end of your document and a pointer
to that reference must be associated with that sentence (for example, the
pointer is either within the sentence or immediately after the paragraph if the
entire paragraph contains your sentences but are describing someone elses
ideas.
3. The sentence is copied
from work done by somebody else.
In
this case you must use indentation and quotation marks to clearly specify the
limits of the copied material. You must
then provide a pointer to a reference as described in the previous point.
.