Lec01-intro

Lec01-intro - CMSC 423: Introduction & Biology Basics...

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Unformatted text preview: CMSC 423: Introduction & Biology Basics August 31, 2010 Carl Kingsford Center for Bioinformatics and Computational Biology What does biology have to do with computers? • Huge amount of data: too much to analyze by hand • Requires clever algorithms to: • Fnd interesting patterns • store / search / compare • predict missing or hard-to-observe features (like protein structure or evolutionary relationships) • Nearly all molecular biology is now “computational biology”: biologists depend on computer scientists every day. Algorithmic Techniques & Data Structures • Dynamic programming • Divide and conquer • Branch and bound • Linear programming • Gibbs sampling / expectation maximization • Hidden Markov Models • Burroughs-Wheeler transform • SufFx arrays / sufFx trees Very general algorithmic techniques Techniques widely used in string / sequence algorithms. Course work & Evaluation • 2 exams during the semester: • Sept 30, 2010 • Nov. 11, 2010 • These dates are fxed. Exams are non- cumulative. • 2nd exam will cover material since the frst exam. • Each 20% oF the grade. • Comprehensive fnal (30%) : • Tuesday, Dec 14, 2010 • 8am - 10am. • Covers everything in the class • Several homework assignments. • 10% oF your grade • Neatness counts • Programming project: • 20% oF your grade. • Mostly in the second “halF” oF the semester. Administrative Details • TA: Emre Sefer • TA ofFce hours: TBD • Instructor ofFce hours: Mondays 2:30-3:30pm, or by appointment, in CBCB 3113. • Grades will be posted on: http://grades.cs.umd.edu • More details on syllabus handout. • Homeworks are due at the start of class on their due dates. No late homeworks will be accepted. • You can discuss homeworks with your classmates. • You must list the names of the people with whom you collaborated at the top of the homework. • You must write up homeworks solutions on your own . • Late programming assignments will lose 10% per day, up to 5 days, after which they will not be accepted. Tentative Course Topics & Outline • Sequence search & comparison • Dynamic programming • Local / global alignments • Aligning multiple sequences • RNA folding • SufFx trees / sufFx arrays • Burroughs-Wheeler Transform • Hidden Markov Models • ¡or gene Fnding • ¡or sequence pattern Fnding • Expectation Maximization for pattern Fnding • Gene Expression & Clustering • Phylogenetics • Algorithms for building trees • Genome Rearrangements • Protein Structure • Secondary structure prediction • Threading for structure prediction • Side-chain positioning • Spatial biology • Mouse brain structure • Genome shape Before midterm #1 Before midterm #2 Before Fnal E. coli Christos Savva ( Microscopy & Imaging Center ) and Thomas Wood (Dept. of Chemical Engineering) at Texas A&M University....
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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Lec01-intro - CMSC 423: Introduction & Biology Basics...

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