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For catalog copy and pre-requisites, see the main page for BME200.
lecture and discussion section (REQUIRED): Crown 105 Th 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.
Preparing a document with LaTeX
Homework assignment: LaTeX assignment
Due 13 Oct 2005.
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 13 October 2005.
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.
What goes into a paper? Structure, cultural expectations, length, writing style, ... Who is an author? When do you cite?
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.)
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.
Discussion with visitor Jerry Tsai.
Homework assignment: Web page assignment Due 1 Dec 05
general discussion of courses for winter quarter, lab rotations, master's thesis, ...
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!
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| BME 200 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