CSCE 590 Bioinformatics Algorithms and Data Structures

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Oct 2, 2013 (3 years and 9 months ago)

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UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Bioinformatics
Algorithms and Data Structures

Spring 2003

Instructor: Dr. John Rose

January 14, 2002

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Purpose of CSCE 590I


Familiarize students with algorithms & data structures
for computational molecular biology


Develop a cadre of bioinformatics researchers in CSE


Contribute to developing a bioinformatics curriculum


This course will eventually become a standard
course offering.

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


CSE at USC is aggressively entering the field of
bioinformatics.


We offer fellowships in computational molecular biology:
http://www.engr.sc.edu/release.asp?PID=10013


We currently collaborate with researchers in Biology,
Statistics, Mathematics, Pharmacy, and Medicine


We need more capable student researchers.


Dr. Rose always has an ulterior motive for anything he
does.

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Ideal Background:
(listed in no particular order)


Biology


Computer Science


Statistics


Biochemistry


Mathematics


In short, bioinformatics is the domain of the
renaissance scholar.

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


CSE students are expected to have adequate STAT and
MATH background but probably not BIOL & CHEM


Basic sequence in molecular biology & genetics


BIOL 302


BIOL 303


BIOL 545


Prerequisites for the above sequence:


BIOL 101 and 102


CHEM 111, 112, 333, and 334


Appropriate labs for listed BIOL and CHEM courses

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Non
-
CSE students are expected to have adequate STAT,
MATH, BIOL & CHEM but probably not CSE.


Basic CSE analytic background


CSCE 350


Transitive closure of CSE prerequisites for CSCE 350


CSCE 145


CSCE 146


CSCE 240


CSCE 245


Appropriate labs for listed CSCE courses

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Expected Background:
(listed in no particular order)


Biology
or


Computer Science
or


Math
or


Statistics
or


Biochemistry


The consequence is that you will have to apply
yourself to wrap your mind around ideas from
other disciplines.

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Course Materials:


Algorithms on Strings, Trees, and Sequences

by Dan Gusfield,
Cambridge University Press
, 1997
(reprinted in 1999).


Research papers that Dr. Rose assigns.


Excerpts from books that Dr. Rose will provide.

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Additional information describing this course can
be found on the course webpage.


This page will be updated regularly to reflect the
developments in this
experimental

course.


Yes, you are part of an experiment!


Now we will look at the class webpage and go
over course topics, grading, cheating policy, etc.
http://www.cse.sc.edu/~rose/590I

UNIVERSITY OF SOUTH CAROLINA

College of Engineering & Information Technology

CSCE 590I Special Topics: Bioinformatics
Algorithms and Data Structures


Good Luck!


Enjoy Yourself!!


Work Hard!!!


Don’t Sleep!!!!