UCSC BME 100 Fall 2001
Intro to Bioinformatics
Assignments
(Last Update:
14:59 PST 20 November 2001
)
Reading assignments
The following list of reading assignments is tentative, and may have
to be adjusted to fit the order of presentation better. Additional
readings will almost certainly be assigned.
In Developing Bioinformatics Computer Skills read
| Pages | By |
| 1 - 21 | Fri 21 Sept |
| 22 - 44 | Mon 24 Sept |
| 329 - 350 | Fri 28 Sept |
| 159 - 169 | Mon 1 Oct |
| 169 - 190 | Fri 5 Oct |
| 133 - 158 | Fri 12 Oct |
| 191 - 214 | Fri 19 Oct |
| 215 - 229 | Fri 26 Oct |
| 268 - 293 | Fri 2 Nov |
Chapters we won't cover, but that you may find interesting include
3--5, 13--14. I'm not yet sure about the second half of Chapter 9 nor
about Chapter 11.
In Programming PERL read as much as you can stomach---at least
Chpater 1 by 28 Sept. Refer to the book frequently to learn more
concepts as you need them.
Pencil-and-paper exercises
Some of the algorithms are best understood by working through small
examples by hand, and there may be other short write-up questions to
further your understanding of the material.
- assignment Paper 1
- DUE Monday 29 Oct 2001.
PERL programming assignments
PERL is an ugly, but handy, programming language. Bioinformaticians
are expectd to know it (some love it, some hate it, but they all have
to know it). Programming exercises will be designed to be typical of
the sorts of things PERL gets used for in bioinformatics, and will be
evaluated on the basis of
- how clean the code is,
- how well it is documented,
- how easy it would be to modify,
- how good its error handling is, and
- whether it accomplishes the assigned task.
You'll want to keep your Programming Perl book handy as you
work on the programming assignments. As a general rule, it is best to
sketch out how you will structure the program, then look up any Perl
constructs that you might need, then write the program. When looking
for the constructs you need you may stumble across Perl techniques
that allow you to restructure and simplify the program---it is best to
do that before you have locked yourself in with a lot of detailed
coding.
- assignment PERL 1
- Due Monday 1 Oct 2001.
- assignment PERL 2
- Due Monday 8 Oct 2001.(Slipped to Wed, because of CATS unreliability.)
- assignment PERL 3
- Due Monday 15 Oct 2001. (Slipped to Tues, because of power failure.)
- assignment PERL 4
- Due Friday 2 Nov 2001.
- assignment PERL 5
- Due Wednesday 20 Nov 2001.
Bioinformatic assignments
We will have several assignments to perform typical bioinformatics
tasks on real data. Generally, we will provide some of the data to
you, but you will have to go to the Web for more. Early exercises
will rely on pre-existing tools (mainly on the Web), but later
exercises may require you to write special-purpose tools of your own.
These exercises will be evaluated based on
- the quality of your English writeup,
- what information you managed to find,
- what analyses you made,
- what programs you wrote (when appropriate), and
- what conclusions you reached.
- asssignment Web 1
- Due Monday 22 Oct 2001.
- asssignment Web 2
- Due Monday 12 Nov 2001.
- asssignment Web 3
- Due Monday 3 Dec 2001.
SoE home
UCSC Bioinformatics Home Page
BME 100 home page
Questions about page content should be directed to
Kevin Karplus
Computer Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250