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CSCE 590I Bioinformatics Algorithms and Data Structures

CSCE 590I Bioinformatics Algorithms and Data Structures. Spring 2003 Instructor: Dr. John Rose January 14, 2002. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures. Purpose of CSCE 590I

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CSCE 590I Bioinformatics Algorithms and Data Structures

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  1. CSCE 590I Bioinformatics Algorithms and Data Structures Spring 2003 Instructor: Dr. John Rose January 14, 2002

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Good Luck! • Enjoy Yourself!! • Work Hard!!! • Don’t Sleep!!!!

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