Winter 2005 - BME 060

BME 060 - Winter 2005
Programming for Biologists and Biochemists -
Syllabus

Week 1

	Tues, Jan 4th	Thurs, Jan 6th
Schedule	Lecture on biology's digital age	Lecture on data manipulation and computation Begin lab1 assignment, due Jan 18th
Lecture Notes	Introduction [pdf] [ppt]	Building Blocks [pdf] [ppt]
Reading	Tisdall: Chapters 1, 2, 3	Tisdall: Chapters 4

Week 2

	Tues, Jan 11th	Thurs, Jan 13th
Schedule	Lecture on finding and eliminating bugs Continue lab1 assignment	Continue lab1 assignment
Lecture Notes	Debugging [pdf] [ppt]
Reading	Tisdall: Chapter 6, pgs 104-116	Tisdall: Chapter 6, pgs 87-103

Week 3

	Tues, Jan 18th	Thurs, Jan 20th
Schedule	Lecture on subroutines and modular code Finish lab1 assignment Begin lab2 assignment, due Jan 27th (deadline extension: Jan 29th)	Lecture on references and microarrays Continue lab2 assignment
Lecture Notes	Making your code reusable with functions [pdf] [ppt]	References [pdf] [ppt]
Reading	Tisdall: Begin Chapter 8

Week 4

	Tues, Jan 25th	Thurs, Jan 27th
Schedule	Lecture on libraries, and basic pattern matching Continue lab2 assignment	Finish lab2 assignment Begin lab3 assignment, due Feb 8th
Lecture Notes	Building libraries [pdf] [ppt]	Regular Expressions I [pdf] [ppt]
Reading	Tisdall: Chapter 5	Tisdall: Continue Chapter 8

Week 5

	Tues, Feb 1st	Thurs, Feb 3rd
Schedule	Lecture on computing: basic summary of statistics & sorting algorithms Continue lab3 assignment	Lecture on hashes Continue lab3 assignment
Lecture Notes	(no lecture materials)	Hashes [pdf] [ppt]
Reading

Week 6

	Tues, Feb 8th	Thurs, Feb 10th
Schedule	Lecture on misc. UNIX topics Finish lab3 assignment	Begin lab4 assignment, due Feb 17th
Lecture Notes	Communicating with UNIX [pdf] [ppt]
Reading		Tisdall: Finish Chapter 8

Week 7

	Tues, Feb 15th	Thurs, Feb 17th
Schedule	Lecture on regex Continue with lab4 assignment	Lecture on objects and gene networks Finish lab4 assignment
Lecture Notes	Regular Expressions II [pdf] [ppt]	Gene Networks & Objects [pdf] [ppt]
Reading

Week 8

	Tues, Feb 22th	Thurs, Feb 24th
Schedule	Begin lab5 assignment, due Mar 3rd	Lecture on BioPerl Continue lab5 assignment
Lecture Notes		BioPerl I [pdf] [ppt]
Reading		Tisdall: Chapter 12, pgs 294-300

Week 9

	Tues, Mar 1st	Thurs, Mar 3rd
Schedule	Continue lab5 assignment	Finish lab5 assignment Begin lab6 assignment, due Mar 17th
Lecture Notes		BioPerl II [pdf] [ppt]
Reading

Week 10

	Tues, Mar 8th	Thurs, Mar 10th
Schedule	Lab6/BioPerl Workshop Continue lab6 assignment	Lab6/BioPerl Workshop Continue lab6 assignment Instructor / TA Evals
Lecture Notes
Reading

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