Research and Teaching in Bioinformatics

Being a Bioinformatics Grad Student

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 (
Office hours: PSB 318, times not determined yet.

lecture and discussion section (REQUIRED): PSB 305 Thurs 4-5:45

On-line discussion forum: BME 200 forum

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 9 class sessions (and all 9 would be preferable).
  • You must turn in all four assignments, and do passing work on at least three.




  • How to solve it G. Polya
    I found this book to be very useful in explaining to someone who just doesn't get it how to go about solving math problems. The advice also applies well to explaining the process of debugging computer programming.
  • I was going to recommend What the best college teachers do by Ken Bain, based on some recommendations by teachers whose blogs I read.
    This book attempts to capture what distinguishes great college teachers from merely adequate ones.  Unfortunately, it is not very well written and is more likely to put you to sleep than to enlighten you. I also found some claims in it to be rather unsupported by evidence, probably reflecting Bain's beliefs rather than the practices of "best college teachers".  I also found some ideas about the proper goals of college courses incompatible with educating engineers—in particular, a disdain for getting correct results on tests and homework.

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.

Note: the above boilerplate is probably unecessary in BME 200, as I've never had even a whiff of a cheating incident in this course.  It is essential for many classes, though, so that students have been appropriately warned.  It is no longer acceptable to assume that all students have the same cultural assumptions about what is permitted academic behavior.

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: FERPA prohibits the dissemination of academic records without permission, and UCSC has taken the particularly paranoid view that any mention of a student could be considered an academic record.  So pictures and names can't be posted here without student permission. Other faculty and grad students use these pictures to help get to know who the new students are (with our tiny department spread over  5 buildings, a physical bulletin board of students wouldn't help much), so I encourage students to allow their names and pictures to be posted.

After some discussion in class, it was decided not to have pictures posted on the class web page, but to have a separate grad students' web page, where students will be able to opt-in to have their name, picture, and/or web page listed.

Homework assignment: LaTeX assignment Due 11 Oct 2012 (see assignment on 4 Oct web page)

Homework assignment: fellowship application Due Fri 19 Oct 2012. [Note: updated 12 Oct 2012]

Homework assignment: LaTeX/BibTeX assignment Due Wed 21 Nov 2012. [updated 8 Nov 2012]

Homework assignment: Web page assignment Due 6 Dec 2012 [updated 24 Nov 2012]

Tentative schedule of topics

Note: The schedule should be updated throughout the quarter to reflect what really happens.

27 Sept 2012 welcome, group advising, FERPA, list of mailing lists and blogs.

4 Oct 2012  TAships and union, Fellowship and LaTeX assignments

11 Oct 2012 Rita Walker??, Jorge Garcia, speaking loudly

18 Oct 2012 writing and teaching

25 Oct 2012 Lab Safety and Ergonomics

1 Nov 2012 LaTeX review and BibTeX

8 Nov 2012 Student presentations

15 Nov 2012 more student presentations

29 Nov 2012 feedback on videotaped presentations, poster design, web design

6 Dec 2012 Instructor evaluation. feedback on videotaped presentations.

Tues 11 Dec 2012 8am–11am Final exam slot (probably 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
318 Physical Sciences Building

Instructors and Assistants