UCSC BME 200 Fall 2008

Being a Bioinformatics Grad Student

(Last Update: 08:54 PST 15 December 2008 )
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: PSB 318, W 10:30-11:30 (phone-only: W 10-10:30)
Instructor: Todd Lowe ( lowe@soe.ucsc.edu) http://www.soe.ucsc.edu/~lowe
Office hours: PSB 316, TBA

lecture and discussion section (REQUIRED): 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.

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.


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 so few students, but I have real trouble with names. [Note: "I" here refers to Kevin Karplus—Todd Lowe may have less of a disability here.]

Alex Atkins
home page
Tracy Ballinger
home page
Dan Carlin
home page
Dent Earl
home page
Ted Goldstein
home page
Hyunsung John Kim
home page
Jeff Long
home page
Larry Meyer
home page
Ngan Nguyen
home page
Elinor Velasquez
home page

Tentative schedule of topics

Note: list should be updated throughout the quarter to reflect what really happens.
30 Sept 08

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, itrequest.ucsc.edu) Jorge's presentation

Setting up your PRINTER environment variable correctly: see instructions at http://www.soe.ucsc.edu/administration/computing-support/printing

Mailing lists:

optional mailing list: bioinformatics seminar announcments, jobs, bread-and-tea, ...
See http://www.soe.ucsc.edu/mailman/listinfo/compbio for information about the compbio mailing list and to subscribe.
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.
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.
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.
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
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.
Molecular visualization mailing list.
See http://bioinformatics.org/mailman/listinfo/molvis-list
proteopedia list
Proteopedia users. See http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users for more information about the proteopedia mailing list. Proteopedia itself can be found at proteopedia.org
Bioinformatics education mailing list
See https://bioinformatics.org/mailman/listinfo/bioedu for more information.
Bay Area Bioinformatics

Instructor Checklist for TAs. All TAs need to consult with the instructor they are working for, and discuss the TA responsibilities at the beginning of the quarter. Once both parties agree on what the TA needs to do, they need to sign the checklist. This is a requirement of the job. [I'll provide a link to the checklist when the SoE grad advisers post it.]
Academic integrity: TA responsibilities for detecting, reporting, and enforcing.

Mention of

7 Oct 08
Homework assignment: fellowship application Due Fri 17 Oct 2008.

Discussion of advancement to candidacy and thesis committees.

TA information:

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 21 Oct 2008.

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 21 October 2008.

14 Oct 08
Lab safety and computer ergonomics, Brent Cooley, EHS.
21 Oct 08
Leanne Ravinale Sexual Harrassment/Title IX.

Being a TA: Running discussion sections, workload, TA union and strikes. Forgot to linclude: brief mention of AAUP and their publication Academe, which is available on-line as http://www.aaup.org/AAUP/pubsres/academe/

Who your union rep is:

Trevor Sangrey
UAW Local 2865
310 Locust St., Suite B / Mailbox 2
Santa Cruz, CA  95060

Fax (831) 423-3606

Trevor Sangrey    (FALL 2008)
Office Hours: Friday, 12.30-2.00pm, Communications 202

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).

Discussion of Santa Cruz amenities (e.g., Saturn Cafe). https://twiki.soe.ucsc.edu/twiki/bin/view/LifeAtUCSC/WebHome

28 Oct 08
Intellectual property, patents, and software copyright.

Review of LaTeX assignment. The trick for unaligning the first line was rather ugly:

\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 \\

The main missed point on LaTeX was that several people did not use the \label and \ref commands for creating crossreferences.

Oral presentation (ideas behind 2-minute elevator talk). Tools for designing your slides (Powerpoint, keynote, LaTeX+acroread). Frequent failure of embedded video.

4 Nov 08
How to speak loudly.

Preparing slides (Prosper package in LaTeX).
Pictures in papers: (use epsfig package), examples. Also examples of subfigure package.

How to Write a Scientific Paper by E. Robert Schulman Annals of Improbable Research, Vol. 2, No. 5, pg. 8.
BibTeX: citation databases in LaTeX.
Homework assignment: LaTeX/BibTeX assignment Due 18 Nov 2008.
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.
11 Nov 2008
NO CLASS (Veterna's Day)
18 Nov 2008
  1. 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), 459-4807 (TTY)."

    The DRC has provided an updated and comprehensive faculty resource page at: http://www2.ucsc.edu/drc/faculty_staff/faculty_resources.shtml

  2. Cultural differences in who is included as co-author on a paper. ... Who is an author?
  3. Responsibilities for resarch integrity. All authors at fault for any errors or fraud.
  4. Choosing a journal. Open-access or subscriber?
25 Nov 2008
Videotaping of short oral presentations.
2 Dec 2008
Instructor evaluation.

Critiquing the videotape of presentations.

Tues 9 Dec 2008 12-3 p.m.
Final exam slot (not used)

Topics omitted this year due to being short on lecture slot

  1. How to produce posters, mainly design and where to print: the School of Engineering poster printer (free!) and the Microscopy and Imaging Laboratory in C230 Earth and Marine Sciences http://microscopy.ucsc.edu/ Some discussion of design guidelines.
  2. Setting up a web page, General discussion on presentation of data. Advertising for reading Envisioning Information.

    Homework assignment still due: Web page assignment Due 8 Dec 08 (first day of exam week)

    Instructions for setting up Soe web pages, turning on directory indexing, and similar stuff is on the SoE FAQ page: https://twiki.soe.ucsc.edu/twiki/bin/view/SOEFAQ/WebHome

  3. Permissions and user groups. Go through .cshrc file to indicate what things people might want to set up for themselves.
  4. Writing proposals (thesis proposals, funding applications, ...) (Covered in BME 205.)

    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.)

Useful resources

slug icon to go to Scool of Engineering home page
SoE home
sketch of Kevin Karplus by Abe
Kevin Karplus's home page
Todd Lowe
Todd Lowe's home page
BS, MS, and PhD programs
BME 200 home page Karplus's lab page Lowe'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
318 Physical Sciences Building