UCSC BME 200 Fall 2006
Being a Bioinformatics Grad Student
(Last Update:
08:11 PDT 2 July 2007
)
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: M3:30-4:30 PSB 318
lecture and discussion section (REQUIRED):
PSB 305 Th 4-5:45 (Not Baskin 169 as scheduled by the Registrar)
Do not take BME 200 for a letter grade!
The lectures and discussions will cover topics specific to
bioinformatics, including such things as lab safety and cultural
differences between the academic cultures of biology and computer
science, as well as more general graduate student stuff, such as how
to write a research paper, avoiding sexual harassment, fellowships,
library usage, LaTeX, ...
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.
Requirements to pass
There will be a small number of written assignments for this class:
a LaTeX exercise, a library/BibTeX exercise, writing a fellowship or
grant proposal, and a web page exercise.
The course is graded strictly on the Satisfactory/Unsatisfactory scale.
Do not register for a letter grade.
-
The attendance requirement:
You must attend the 7 of the 10 class sessions (and all 10 would be preferable).
- You must turn in all four assignments,
and do passing work on at least three.
Texts
Required:
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.
Rogues' Gallery
Who is in the class this year. I'm trying to learn the names of this
year's students. I'm hoping to have them all straight within 10
weeks. That doesn't sound very challenging with only 9 students, but
I have real trouble with names.
John Archie
| Miriam Bellows
| Jonathan Magasin
| Daniel Sam
|
Chris Szeto
| Shyamini Vasili
| Marcos Woehrmann
| Zeng Zhu
|
Tentative schedule of topics
Note: list should be updated throughout the quarter to reflect what
really happens.
- 21 Sept 06
-
Administrivia.
Mailing lists:
- compbio
- optional mailing list: bioinformatics seminar announcments, jobs, bread-and-tea, ...
compbio is now a mailman-maintained list!
See http://www.soe.ucsc.edu/mailman/listinfo/compbio
for information about the compbio mailing list.
- binf-grads
- automatic, can't unsubscribe: official announcements from the department.
- grads, grad-news, ...
- See the
http://www.soe.ucsc.edu/advising/graduate/grademail.html web
page for more information about these School of Engineering mailing lists.
- genecats
- For developers of the genome browser, and comparative genomics
research results.
See http://www.soe.ucsc.edu/mailman/listinfo/genecats
for information about the genecats mailing list.
- netdogs
- An informal group of grad students interested in tools for
dealing with protein networks.
See http://www.soe.ucsc.edu/mailman/listinfo/netdogs
for more information.
- mcdseminars
- Announcements of the topics for seminars in the Monday+Friday
Molecular, Cell, and Developmental Biology series (12:30 in Nat Sci
Annex 101)
http://lists.pbsci.ucsc.edu/mailman/listinfo/mcdseminars
- pdb-l
- Users mailing list for the Protein Data Bank. Often has
questions about tools and interpretation of protein models,
resulting in tutorial replies.
See https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l
for more information.
- molvis-list
- Molecular visualization mailing list.
See http://bioinformatics.org/mailman/listinfo/molvis-list
- bioedu
- Bioinformatics education mailing list
See https://bioinformatics.org/mailman/listinfo/bioedu
for more information.
Organization of SoE and bioinformatics file systems.
Where things are kept, how to get access to cluster computing,
- 28 Sept 06
-
Permissions and user groups.
Go through .cshrc file to indicate what things people might want to
set up for themselves.
Using a Makefile and gnumake to run LaTeX, BibTeX, dvips, and distill.
Preparing a document with LaTeX
Homework assignment: LaTeX assignment
Due 12 Oct 2006.
The purpose of this assignment is to develop some preliminary facility
with LaTeX, particularly with math equations and tables.
You are to try to duplicate (approximately) the 2-page paper in
latex-assign.pdf
There are some examples of a basic LaTeX paper in example.tex and the corresponding output example.pdf. You can use "make" to do the
repeated calls to latex with the Makefile
Turn in both the .tex source and the printed output by 12 October 2006.
- 5 Oct 06
- Lab safety (with some ergonomics) Brent Cooley, EHS
Homework assignment:
fellowship application
Due 19/20 Oct 2006.
- 12 Oct 06
-
Being a TA: Running discussion sections, workload, TA union and strikes.
Brief mention of AAUP and their publication Academe,
which is available on-line as
http://www.aaup.org/publications/Academe/
Academic integrity: TA responsibilities for detecting, reporting,
and enforcing.
Expectations of a GSR.
Cultural differences in who is included as co-author on a paper.
... Who is an author? When do you cite?
- 19 Oct 06
-
- Review of LaTeX assignment.
The trick for unaligning the first line was rather ugly:
\begin{eqnarray}
\hbox to 5pt{$E(c^2) =$ \hskip 0pt minus 1fill} & & \nonumber\\
&=& \lambda^{-2} \int_{-\infty}^{\infty} {y^2\over(1+e^{y})(1+e^{-y})} dy \\
- Funding opportunities. Writing a fellowship application.
-
Oral presentation. How to design your slides (Powerpoint,
keynote, LaTeX+acroread). How to speak loudly.
- 26 Oct 06
- Pictures in papers: (use epsfig package), examples. Also examples
of subfigure package.
Some discussion of how to produce posters (not design, just tools
and where to print: the Microscopy and Imaging Laboratory in C230 Earth and
Marine Sciences
http://microscopy.ucsc.edu/
BibTeX: citation databases in LaTeX.
Homework assignment: LaTeX/BibTeX assignment
Due 16 Nov 2006.
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.
- 2 Nov 06
-
- Rita Walker Sexual Harrassment/Title IX.
- Classroom accomodations for disabilities
The Dean for Undergraduate Education (William Ladusaw) recommends
incorporating the following paragraph into all syllabi:
"If you qualify for classroom accommodations because of a disability,
please submit your Accommodation Authorization from the Disability
Resource Center (DRC) to me during my office hours in a timely manner,
preferably within the first two weeks of the quarter. Contact DRC at
459-2089 (voice), 459-4806 (TTY)."
The DRC has provided an updated and comprehensive faculty resource page at:
http://www2.ucsc.edu/drc/faculty_staff/faculty_resources.shtml
-
Poster presentation. How to prepare and print a poster, design guidelines.
- Writing proposals (thesis proposals, funding applications, ...)
Funding sources.
Example of a great thesis proposal by Rachel Karchin.
(Postscript file
Portable Document Format file;
both only available from Baskin School of Engineering computers.)
- 9 Nov 06
- Videotaping of short oral presentations.
- 16 Nov 06
-
Setting up a web page,
General discussion on presentation of data.
Advertising for reading Envisioning Information.
Homework assignment:
Web page assignment
Due 1 Dec 06 (last day of class)
- 23 Nov 06
- Thanksgiving---no class
- 30 Nov 06
- Instructor evaluation.
Karplus maybe out of town for CASP meeting.
We can have a guest lecturer (faculty, senior grad student, ...?).
- Wed 6 Dec 06 8am-11am
- Final exam slot (not used)
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
