UCSC BME 220 Home Page
Protein Bioinformatics, Spring 2007
15:23 PDT, 21 May 2007
Handouts and due dates
- Topics and reading list
(by week---appended as the course progresses)
- Intake survey---you must fill this
out to get a permission code.
- Project list
- A project is required for BME 220L---this list gives some ideas.
The only students excused from doing full-size projects are
Ph.D. students who are currently do a lab rotation, or who
have already finished 3 lab rotations. These students are
still expected to do mini-projects. Evaluation weights
for those students will be adjusted appropriately.
Grad students are urged to enter posters for their projects in the Graduate
Research Symposium (Tuesday 22 May 2007, 2-4 p.m.).
Undergraduates are urged to enter their projects in the Undergraduate
Research Symposium (Thursday 7 June 2007).
- Project proposal assignment
- due 13 April 2007
The projects students
actually chose will be put here.
- Homework 1: drawing pictures
- due 20 April 2007
The homework turned in.
- Progress report due 27 April 2007. (no handout)
The progress reports should be drafts of the final report, not
just "I got a lot done this week". We will provide feedback on
the drafts, with suggestions for improvements in both the writing
and the research. The main point of the progress reports is to
teach you to write as work, and not leave it as an after-the-fact
- Homework 2: making a structure prediction
using UCSC local tools
4 7 May 2007
- Progress report due 11 May 2007. (no handout)
- Progress report due 25 May 2007. (no handout)
- Journal club presentations 30 May--8 June.
We have posted a list of papers
from which you may choose a paper. You may also choose a
paper not on the list, but clear it with one of the
instructors first. There will be 2 half-hour presentations
per class, and students will get to choose papers in the order
in which they are presenting (whoever goes first on 30 May has
first choice of paper and so on). Signing up for
presentation slots will happen on 21 May, selecting papers
will happen on 23 May.
Note: a good journal club presentation not only presents
the paper itself, but looks forward and back a bit: what
papers did it cite? who has cited it? has the work been
replaced by newer methods?
- Final report due 8 June 2007. (no handout)
- Poster session 12 June 2007, 4-7.
General Class Information
- Lecture times:
- MWF 2-3:10 PSB 305
- Kevin Karplus
- Phone: +1-831-459-4250
- Office: PSB 318
- Office hours: Mondays 4–5
- Dietlind Gerloff
- Phone: +1-831-459-4833
- Office: PSB 320
- Office hours: TBA
We will each have one open office hour each week, plus a regularly
scheduled meeting with each student enrolled in 220L for 20-30 minutes a
week (mainly to discuss the project, but homework, research, and other
topics are also expected).
There are pictures of the students in the class in the Rogues' Gallery, to help you find out
who might be able to help with homework or class projects. (Also to
help Kevin remember the names of the students in the class.)
Although both professors expect to attend almost all classes, we
have tentatively split the repsonsibility for the class content by
weeks (we may do some trading to handle shorter or longer topics):
We are also keeping a more detailed schedule, with the topics and pointers to
material to read.
|--- ||Apr 4, Kevin ||Apr 6, Kevin|
|Apr 9, Dietlind ||Apr 11, Dietlind ||Apr 13, Dietlind|
|Apr 16, Kevin ||Apr 18, Kevin ||Apr 20, Guest: Martin Paluszewski|
|Apr 23, Dietlind ||Apr 25, Dietlind ||Apr 27, Dietlind|
|Apr 30, Dietlind ||May 2, Dietlind ||May 4, Dietlind|
|May 7, Kevin ||May 9, Kevin ||May 11, Kevin|
|May 14, Kevin ||May 16, Kevin ||May 18, Kevin|
|May 21, Dietlind ||May 23, Dietlind ||May 25, Dietlind|
|--- ||May 30, students ||Jun 1, students|
|Jun 4, students ||Jun 6, students ||Jun 8, students|
- There are no textbooks for BME 220 this quarter, as we will
be working primarily from original literature. You may wish to
have a protein-structure text such as
Introduction to Protein Structure by Branden and Tooze or
Protein Structure and Function by Petsko and Ringe.
(Kevin likes Branden and Tooze better, but Petsko and Ringe were used
for Chem 200B and for BME 220 when Carol Rohl taught it.)
If you are unfamiliar with PDB files and how protein structure
is determined, we highly recommend reading Gale Rhodes's
Crystallography Made Crystal Clear.
- Class format:
- The class will be a mixture of lectures and journal-club
presentations, with somewhat more lecturing than in the past.
Evaluation will be based on participation in class
discussions, on journal-club presentations, and on the term
project done in BME 220L. We will have a poster
session during exam week in place of a final exam.
That poster session will be Tuesday 12 June 4-7 p.m.
All students are expected to present a poster.
- The only official prerequisite for grad students in this course is
either BME 205 (bioinformatics) or CHEM 200B (protein
structure), though it is best to have both. Students lacking
BME 205 may need to choose a project that uses existing tools,
rather than one that requires extensive programming. Students
lacking CHEM 200B should have at least some knowledge of
protein chemistry (at the level of BIOC 100A, for example).
For undergraduates, the prerequisites are BME 205, BIOC
100A, and CMPS 101.
- Roughly 40% of the evaluation will be based on the class project,
20% on in-class presentation of a journal article,
30% on homework,
and 10% on general participation in class discussions
(including reading most of the presented journal articles).
These percentages may need to be adjusted somewhat for
students doing mini-projects or for students who do multiple
- Students will be using the computers set up for
bioinformatics grad students in PSB.
Students can get keys for the doors at the SoE facilities
office (Baskin 217) MTWTF 1–3. The office will have a list of
students in the class. School of Engineering accounts are
obtained by filling out the
my signature on it, and turning it in to the Techstaff office.
(Bioinformatics grad students already
have keys and accounts.)
Other web pages of interest
- WWW resources for biosequence analysis
- URLs for web sites containing biosequence analysis tools, but
not well annotated. This is Kevin's personal list of interesting
sites, but it needs some updating, reorganizing, and annotating.
International Society for Computational Biology
- ISCB is the primary professional organization for
bioinformatics, sponsoring (or co-sponsoring) several conferences
and having PLoS Computational Biology as its official journal.
Membership pays off in reduced conference fees and journal subscriptions.
Disclaimer: both Kevin and Dietlind are on the Board of Directors
Questions about page content should be directed to
University of California, Santa Cruz
Santa Cruz, CA 95064