UCSC BME 200 Fall 2004
Being a Bioinformatics Grad Student
(Last Update:
17:50 PST 9 November 2004
)
This is a required course for graduate students in bioinformatics.
For catalog copy and pre-requisites, see the
main page for BME200.
Who, When, and Where:
Instructor: Kevin Karplus (
karplus@soe.ucsc.edu) http://www.soe.ucsc.edu/~karplus
Office hours: Not chosen yet 315B Baskin Engineering
Lectures: Th 4-5 Media Theater M110
(first half of CMPS 200 and CMPE 200)
Discussion section (REQUIRED):
Tues 4-5:10 Baskin Engineering 169
Do not take BME 200 for a letter grade!
The lecture sessions on Thursdays meet at the same time and place as
CMPE 200 and CMPS 200—all School of Engineering graduate students
get the same general training. See the CMPE 200 and CMPS 200 web
site for more information.
The required discussion sections on Tuesdays will cover topics
specific to bioinformatics, including such things as cultural
differences between the academic cultures of biology and computer
science and lab safety.
All new grad students should plan on taking 280B this quarter, since
it will be a series of introductory lectures by faculty who can accept
grad students into their labs for lab rotation projects.
Here are a couple of pictures of this year's BME200 class (click
for larger image):
Requirements to pass
There will be a small number of written assignments for this class:
a LaTeX exercise, a library/BibTeX exercise, an exercise in teaching or
ethics, and writing a fellowship or grant proposal.
The course is graded strictly on the Satisfactory/Unsatisfactory scale.
Do not register for a letter grade.
The requirements for passing BME 200 are a little different from
the requirements for CMPS/CMPE200.
-
The attendance requirement is modified:
You must attend the first half of 7 of the 9 Thursday lectures,
plus you must attend 8 of the 10 Tuesday discussion sections.
- You must do passing work on all three assignments.
(Fourth assignment canceled.)
Note: the due
date for the fellowship assignment and the details of the assignment
are different for BME 200, as we want you to do the assignment early
enough to get feedback before submitting fellowship applications for
real. I may modify some of the other assignments also (they haven't
been written yet for CMPS/CMPE200, so I don't know whether
modification will be needed).
Texts
Required:
- TA handbook: A practical reference for Graduate Student Teachers
Division of Graduate Studies, UCSC, 2003?
- LaTeX User's Guide and Reference Manual
Leslie Lamport
Optional:
Academic Integrity
Anyone caught cheating in the class will be punished severely—most
likely failed in the class and possibly thrown out of grad school.
Cheating
includes any attempt to claim someone else's work as your own.
Plagiarism in any form (including close paraphrasing) will be
considered cheating. Use of any source without proper citation will
be considered cheating.
Collaboration without explicit written acknowledgment will be
considered cheating.
Collaboration on some assignments with explicit written acknowledgment
is encouraged—guidelines for the extent of reasonable collaboration
will be given in class.
Tentative schedule of topics
The schedule for the whole-SoE 200 course is at
http://www.soe.ucsc.edu/classes/cmps200/Fall04/200schedule.html
Note: list should be updated throughout the quarter to reflect what
really happens.
- Tues 28 Sept
- Discussion sections.
TA union and strikes.
Brief mention of AAUP and their publication Academe,
which is available on-line as
http://www.aaup.org/publications/Academe/
Writing a fellowship application.
Homework assignment:
LaTeX assignment
Due 14 Oct 2004.
Homework assignment:
fellowship application
Due 20 Oct 2004.
- Tues 5 Oct
- Funding sources for research
How the /projects/compbio directories are organized.
Permissions and user groups.
Our bioinformatics BibTeX database.
- Tues 12 Oct
- What does a good thesis/grant proposal look like?
Example of a great thesis proposal by Rachel Karchin.
(Postscript file
Portable Document Format file;
both only available from Baskin School of Engineering computers.)
- Tues 19 0ct
- Environmental Health and Safety. Lab Safety presentation.
Brent Cooley
- Tues 26 Oct
- Running an undergrad lab using Instructional Computing labs.
Oral presentations, how to prepare and present them.
- Tues 2 Nov
- Practice speaking loudly (outdoors) for presentations.
Homework assignment:
library search and BibTeX
assignment
Due 18 Nov 2004.
David Bernick has provided a list of possible
topics—you can come up with your own.
Incidentally, it would be a good idea to use the
existing database in
/projects/compbio/papers/tex/all.bib, by using
setenv BIBINPUTS .:/projects/compbio/papers/tex::
in your .cshrc file, and saying
\bibliography{all,my}
to include both your file my.bib and /projects/compbio/papers/tex/all.bib
in your search for bibliography entries.
- Tues 9 Nov
- General discussion or presentation of data.
Advertising for reading How to Solve It
and Envisioning Information.
- Tues 16 Nov
- Topic to be chosen. Perhaps paper writing—different styles and cultures.
Perhaps refereeing of papers or continuing education.
- Tues 23 Nov
- Ethics issues
Homework assignment: ethics paper
canceled
- Tues 30 Nov (my birthday!)
- Topic to be chosen.
Topics originally intended for the course, but now unlikely to be covered:
- Library research and on-line resources for bioinformatics.
This will be covered by a longer presentation in BME 100, so would
be redundant to cover in BME 200 this quarter.
There is also a more generic presentation in the CMPS/CMPE200 lecture,
which students attended.
Useful resources
Questions about page content should be directed to
Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
