Computational Techniques in Structural Bioinformatics

 

CS483/CS683    Winter 2012          RCH 209  10:00 – 11:20 TTh

 

 

Instructor:

Forbes Burkowski

DC1309

 


 

 

Assignments Winter 2012:

 

Assignment #1  Due date:  Thursday, Jan. 19

Assignment #2  Due date:  Thursday, Feb.  2       

Assignment #3  Due date:  Thursday, Feb. 16 Starter Script for: Ex.4

Assignment #4   Due date: Tuesday, Mar. 15 Starter Script for: Ex.1 Data Files for Ex. 2.    

Assignment #5  Due date:  Thursday, Mar. 29

 

MIDTERM: Mar. 1 (In class)

 

Project Requirements and Suggestions

 

Some notes related to Assignment #1:  Getting Started with Chimera and Python

 

Office Hours Information

 

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:

Structural Bioinformatics: An Algorithmic Approach

(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:

 

Course Notes

 

Workload

 

•         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 in the final week of classes.

•         You must first submit a project proposal for approval and constructive criticism prior to the end of February.

–        Grad project presentations are to be given on April 3 (an extra class just after the last day of lectures).

–        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 else’s 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.

 

 

 

 

 

 

 

 

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