Stephen Benz
| Andy Nguyen
| Tim Sterne-Weiler
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Sam Boyarsky
| Herbert Lee
| Lauren Lui
|
James Durbin
| Andrew Uzilov
| Lee Slater
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For catalog copy and pre-requisites, see the main page for BME200.
lecture and discussion section (REQUIRED):
Baskin 156
PSB 305 Tues 4-5:45
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.
The course is graded strictly on the Satisfactory/Unsatisfactory scale. Do not register for a letter grade.
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.
| Stephen Benz
| Andy Nguyen
| Tim Sterne-Weiler
|
| Sam Boyarsky
| Herbert Lee
| Lauren Lui
|
| James Durbin
| Andrew Uzilov
| Lee Slater
|
Presentation by CBSE tech staff on computer and cluster use by bioinformatics grad students. Organization of SoE and bioinformatics file systems. Where things are kept, how to get access to cluster computing. How to report problems (email: cluster-admin) powerpoint presentation
Mailing lists:
TA information:
Discussion of Santa Cruz amenities (grocery stores, bike shops, bakeries). Mention of Bike to Work Day (Thurs 4 Oct 2007), Open Studio tours (3 weekends starting 6 Oct 2007), UCSC Farm and Garden fall harvest festival (6 Oct 2007)
Preparing a document with LaTeX.
Using a Makefile and gnumake to run LaTeX, BibTeX, dvips, and
distill (mentioned, but not gone into detail).
Homework assignment: LaTeX assignment
Due 16 Oct 2007.
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
I strongly recommend using LaTeX for thesis proposals and theses. There is a style file available (which I have not checked myself, but which should be a good starting point at least) in http://www.soe.ucsc.edu/~you/notes/ucthesis-ucsc/
Turn in both the .tex source and the printed output by 16 October 2007.
Permissions and user groups. Go through .cshrc file to indicate what things people might want to set up for themselves.
\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 \\
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.
Note: TAs are not allowed to have office hours in shared grad-student space. TA office hours are to be scheduled in Baskin Engineering 314 (scheduler@soe.ucsc.edu handles the scheduling).
Oral presentation. How to design your slides (Powerpoint, keynote, LaTeX+acroread). How to speak loudly.
Choosing a journal. Open-access or subscriber?
Pictures in papers: (use epsfig package), examples. Also examples
of subfigure package.
Some discussion of how to produce posters, mainly design
and where to print: the School of Engineering poster printer and
the Microscopy and Imaging Laboratory in C230 Earth and
Marine Sciences
http://microscopy.ucsc.edu/
Some discussion of design guidelines.
BibTeX: citation databases in LaTeX.
Homework assignment: LaTeX/BibTeX assignment
Due 20 Nov 2007.
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.
"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), 459-4807 (TTY)."
The DRC has provided an updated and comprehensive faculty resource page at: http://www2.ucsc.edu/drc/faculty_staff/faculty_resources.shtml
Homework assignment: Web page assignment Due 4 Dec 07 (last day of class)
Andy Nguyen pointed out that instructions for setting up Soe web pages, turning on directory indexing, and similar stuff is on the SoE FAQ page: http://www.soe.ucsc.edu/administration/computer/faq/cache/41.html
Critiquing the videotape of presentations (they were all pretty good this year---some of the usual problems of looking at the screen too much and moving head so the microphone did not pick up sound).
Lab safety may be a familiar topic to those who came from wet-lab backgrounds, but those who are coming in from the computational side really need to learn this stuff!
Check out the Office Ergonomics page for information about ergonomics. Avoid the wrist and back problems that plague so many computer people! There is a computer workstation self-assessment at http://ehs.ucsc.edu/safety/pubs/ergo/SelfEvaluation.pdf
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| BME 205 home page | Karplus's lab page | UCSC Bioinformatics research |
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
318 Physical Sciences Building
