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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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