CSCE 590I Bioinformatics Algorithms and Data Structures

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CSCE 590I Bioinformatics Algorithms and Data
Structures

• Spring 2003
• Instructor Dr. John Rose
• January 14, 2002

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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.

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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?PID10
  013
• 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.

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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.

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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

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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

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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.

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CSCE 590I Special Topics Bioinformatics
Algorithms and Data Structures

• Course Materials
• Algorithms on Strings, Trees, and Sequencesby
  Dan Gusfield, Cambridge University Press, 1997
  (reprinted in 1999).
• Research papers that Dr. Rose assigns.
• Excerpts from books that Dr. Rose will provide.

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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

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CSCE 590I Special Topics Bioinformatics
Algorithms and Data Structures

• Good Luck!
• Enjoy Yourself!!
• Work Hard!!!
• Dont Sleep!!!!