UCSCBaskin School of Engineering  
General Information Events, News & Organizations Degrees & Departments Research Classes Admissions & Advising People & Jobs Administration

BME 060 logo
BME 060 - Winter 2007
Programming for Biologists and Biochemists -
Syllabus



Week 1
  Mon Wed Fri, Jan 5
Activity
Lab: UNIX Skills
Location
College 8, Acad 101
Reading
Tisdall Chap 1-2
Notes
TA-led exercise

 

 

Week 2
  Mon, Jan 8 Wed, Jan 10 Fri, Jan 12
Activity
Lab: UNIX Skills
Lecture 1: Code building blocks [PPT]
Lecture 2: Flow of Control [PPT]
Location
College 8, Acad 101
College 8, Acad 101
Physical Sciences, 305
Reading
Tisdall Chap 3-4
Tisdall Chap 5
Notes
Begin Lab 1
Lab 1 Deadline Extended!

 


Week 3
  Mon, Jan 15 Wed, Jan 17 Fri, Jan 19
Activity
MLK Holiday, no class
Lab
Lecture 3: Subroutines & Variables [PPT]
Location
 
Social Sciences I Mac Lab
Physical Sciences, 305
Reading
 
Tisdall Chap 6, pgs 104-116
Rest of Tisdall Chap 6
Appendix B, pgs 330-333
Notes
Lab 1 Due.
Begin Lab 2.
Quiz 1.

 

 

Week 4
  Mon, Jan 22 Wed, Jan 24 Fri, Jan 26
Activity
Lecture 4: References [PPT]
Lab
Lecture 5: Libraries [PPT]
Location
PSB 305
Soc Sci I Mac Lab
PSB 305
Reading
Chap 9. Appendix B pg 320-1
Notes
Lab 2 Due.

 

 

 

Week 5
  Mon, Jan 29 Wed, Jan 31 Fri, Feb 2
Activity
Lecture 6: Libraries & Stats & Sort [PPT]
Lab
Lecture 7: Search & Hashes [PPT]
Reading
Pgs 320-1, Chap 8: Pgs 149-158
Notes

Code developed in class:

search_url.pl: Call it with the syntax:
search_url.pl URL PAT
and it retrieves a page at the URL and returns lines from the page with the given pattern matching PAT.

search_text.pl: Called with:
search_text.pl PAT < FILE
and it returns lines that match the pattern PAT in the file FILE. Recall that the less-than symbol "<" sends the file into the standard input.

libText.pm: A library that currently contains one function that finds matching lines in a given string. Both the above Perl scripts use libText.pm.

Begin Lab 3.

 

 

 

Week 6
  Mon, Feb 5 Wed, Feb 7 Fri, Feb 9
Activity
Lecture 8: Regular Expressions I & Recursion [PPT]
Lab
Lecture 9: Regular Expressions II [ppt]
Reading
Chap 9.
App B: Pgs 334-40
Notes
Continue Lab 3
Lab 3 Due.
Memoized fibonacci code.
Slow version: fib-slow.pl
Fast version: fib-fast.pl

 

 

 

Week 7
  Mon, Feb 12 Wed, Feb 14 Fri, Feb 16
Activity

Lecture 10: Regular Expressions III [PPT]

Lab
Lecture 11: Calling & Parsing External Programs in Perl [PPT]
Reading
Chaps 10 & 12 (294-300)
Notes
We wrote a little program, called dup.pl, that uses the s/// operator to duplicate any text inside double quotes. It also changes the double quotes to single quotes.
Begin Lab 4

 

 

 

Week 8
  Mon, Feb 19 Wed, Feb 21 Fri, Feb 23
Activity

Presidents Day - no class

Lab
Lecture 12: Organizing work flow with make. [PPT]
Reading
Notes
Continue Lab 4.
Lab 4 Due. (due date extended)

 

 

 

Week 9
  Mon, Feb 26 Wed, Feb 28 Fri, Mar 2
Activity

Lecture 13: Object-oriented programming [PPT]

Lab
Lecture 14: BioPerl I [PPT]
Reading

BioPerl Tutorial (Sections III.3 and III.4)
Tisdall: Chapter 12, pgs 294-300

perldoc perltoot [HTML] [PDF]
Notes
Lab 4 Due
Begin Lab 5.

 

 

 

Week 10
  Mon, Mar 5 Wed, Mar 7 Fri, Mar 9
Activity

Lecture 15: BioPerl II [PPT]

Lab
Lecture 16: BioPerl III [PPT]
Reading
Notes
Continue Lab 5

 

 



Week 11
  Mon, Mar 12 Wed, Mar 14
Activity

Sequence Alignment & BLAST [PPT]

Optional Lab
Reading
Notes
Lab 5 due.
Lab 5 due.

 

 

 

Final Projects and Cummulative Quiz
  Tue, Mar 20
Activity

Cummulative Quiz and 10min research projects

Reading
Notes
7:30-10:30 PM
PSB 305