UCSC BME 100 Fall 2003
Intro to Bioinformatics
Assignments
(Last Update:
10:07 PST 10 November 2003
)
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 Programming PERL read as much as you can stomach---at least
Chapter 1 by 29 Sept. Refer to the book frequently to learn more
concepts as you need them.
In Biological Sequence Analysis, here is a rough schedule for
the reading
| Sections | Read by |
| 1.1--1.4 | 29 Sept |
| 11.1--11.6 | 1 Oct |
| 2.1--2.9 | 8 Oct |
| 3.1--3.6 | 15 Oct |
| 5.1--5.8 | 22 Oct |
| 6.1--6.5 | 29 Oct |
| 7.1--7.6 | 12 Nov |
Results of homeworks
The individual papers will be handed back to students as soon as
possible after grading. Histograms of the scores will be posted in
http://www.soe.ucsc.edu/~karplus/bme100/f03/
Because there are enough students in each group to avoid individually
identifying students, the histograms are further labeled by student
class (undergrad, grad, or concurrent enrollment). Currently the
grads are doing better than the undergrads (with significant overlap)
and the concurrent enrollment students are split between the top and
bottom of the grad-student range.
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.
We'll also have an assignment to write a graduate fellowship
application---a skill every senior and grad student should practice!
Due dates are tentative until the assignment itself is released:
- assignment Paper 1 (model kit)
- Due Wed 15 Oct 2003 (in class).
- assignment Paper 2 (fellowship application)
- Due Wed 29 Oct 2003 (in class).
- assignment Paper 3 (web and literature search)
- Due Wed 3 Dec 2003 (in class).
PERL programming assignments
PERL is an ugly, but handy, programming language. Bioinformaticians
are expected 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.
Due dates are tentative until the assignment itself is released:
- assignment PERL 1
- Due Wed 1 Oct 2003 (midnight). Mask out lower-case in FASTA.
- assignment PERL 2
- Due Wed 8 Oct 2003 (midnight). Plot proline fraction of windows.
- assignment PERL 3
- Due Wed 15 Oct Oct 2003 (midnight). Perl module for
handling sets of IDs.
- assignment PERL 4
- Due Wed 22 Oct 2003 (midnight). Markov chains.
- assignment PERL 5
- Due Wed 5 Nov 2003 (midnight)
- assignment PERL 6
- Due Wed 19 Nov 2003 (midnight)
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