For catalog copy and pre-requisites, see the main page for BME200.

Who, When, and Where:

Lectures: F 2-3:10 changed to Merrill 102 (Same as CMPS 200 and CMPE 200)

Discussion section (REQUIRED): changed to Soc Sci 2 Room 137 Fridays 12:30-1:40 Tues 12-1:45 Porter 241

Because of repeated miscommunication with staff, the Registrar did not have BME 200 on the books by 22 Sept 2003. It should be available after the first day of class (Friday 26 Sept). Do not take BME 200 for a letter grade!

The lecture sessions on Fridays 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 sites for more information.

The required discussion sections on Fridays 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 is a picture of some of the new grads at the Wednesday orientation session.

Texts

• TA handbook: A practical reference for Graduate Student Teachers Division of Graduate Studies, UCSC, 2003
• LaTeX User's Guide and Reference Manual Leslie Lamport

• How to solve it G. Polya

Evaluation

The course is graded strictly on the Satisfactory/Unsatisfactory scale. Do not register for a letter grade.

Academic Integrity

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

Tues 30 Sept

Discussion sections. How the /projects/compbio directories are organized. Permissions and user groups. Our bioinformatics BibTeX database.

Tues 7 Oct

Running an undergrad lab using Instructional Computing labs. TA union and strikes. Writing a fellowship application. Homework assignment: fellowship application Due 29 Oct 2003.

Fri 10 Oct

What does a good thesis/grant proposal look like? Brief mention of AAUP and their publication Academe, which is available on-line as http://www.aaup.org/publications/Academe/ Homework assignment: LaTeX assignment Due 24 Oct 2003.

Fri 17 0ct

Environmental Health and Safety. Lab Safety presentation. Brent Cooley

Fri 24 Oct

Funding sources for research

Fri 31 Oct Halloween

Paper writing---different styles and cultures. Advertising for reading How to Solve It

Fri 7 Nov

Oral presentations, how to prepare and present them.

Fri 14 Nov Guest Lecture

Kevin will be out of town. Jim Kent will speak on "Ins and Outs of the Genome Browser and Database."

Fri 21 Nov

General discussion (literature search, lifecycle of a paper). Practice speaking loudly (outdoors) for presentations.

Fri 5 Dec

Ethics issues

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 was a more generic presentation in the CMPS/CMPE200 lecture, which students attended.

Useful resources

• The CMP 200 newsgroup [Note: almost nothing appeared on the newsgroup.]
• Martine's slides from the presentation on giving conference and seminar talks.
• A 5 Step plan for better journal writing.
• Environmental Health and Safety web site.

  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!

• Ethan Miller's presentation on security

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• Phoenix Eagleshadow maintains a list of fellowship opportunities for the CBSE (useful for non-bioinformatics people too).
• Here is on that is missing from Phoenix's list (as of 26 Sept 2003): http://ucsystembiotech.ucdavis.edu/funding.cfm
• Community of Science webpage. This page has information about finding grants and fellowships.

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• UCSC list of journals for which we have electronic subscriptions

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• http://www.soe.ucsc.edu/~charlie/presentations/taTalk2003/ Charlie McDowell's 3-Oct-2003 presentation on using CATS for teaching. This has some useful pointers to where to find information.
• From Wesley Mackey's lecture on CATS computing:
  Instructional Computing Homepage
  CATS' Unix help page: for help on AFS and other ATHENA-related stuff
• The online CATS Support Center
• Online CATS guide to Managing class-course lockers for instructors and TAs

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• The Baskin Center Policy about Cheating (postscript).
• UCSC Policy on Academic Dishonesty.
• UCSC Policy on Research Integrity.
• The Center for Teaching Excellence which offers midquarter TA feedback and videotaping for improving your teaching abilities.
• A guideline for creating class web pages in SOE.
• Advice for dealing with difficult situations/students:
  • Disruptive Students
  • Distressed Students
  
  You should consult the instructor of your course if you encounter these types of problems as a TA.
• Teaching Assistant Contract The contract was copied from http://atyourservice.ucop.edu/employees/policies/local_contracts/ase/ASEUCSC2.pdf It seems that UCOP can't keep their URLs the same from one year to the next, so a local copy was made. Also, this contract expired and negotiation of the new contract broke down---that is what the TA strike was about on 3 Oct 2003.

SoE home

Kevin Karplus's home page

BS, MS, and PhD programs

BME 205 home page

Karplus's lab page

UCSC Bioinformatics research

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