Note: a good journal club presentation not only presents the paper itself, but looks forward and back a bit: what papers did it cite? who has cited it? has the work been replaced by newer methods?

Lecture times:

MWF 2-3:10 PSB 305Baskin 169

Instructors:

Kevin Karplus (karplus@soe.ucsc.edu)

Phone: +1-831-459-4250

Office: PSB 318

Office hours: Mondays 4–5

Dietlind Gerloff (gerloff@soe.ucsc.edu)

Phone: +1-831-459-4833

Office: PSB 320

Office hours: TBA

We will each have one open office hour each week, plus a regularly scheduled meeting with each student enrolled in 220L for 20-30 minutes a week (mainly to discuss the project, but homework, research, and other topics are also expected).

There are pictures of the students in the class in the Rogues' Gallery, to help you find out who might be able to help with homework or class projects. (Also to help Kevin remember the names of the students in the class.)

Although both professors expect to attend almost all classes, we have tentatively split the repsonsibility for the class content by weeks (we may do some trading to handle shorter or longer topics):

Monday	Wednesday	Friday
---	Apr 4, Kevin	Apr 6, Kevin
Apr 9, Dietlind	Apr 11, Dietlind	Apr 13, Dietlind
Apr 16, Kevin	Apr 18, Kevin	Apr 20, Guest: Martin Paluszewski
Apr 23, Dietlind	Apr 25, Dietlind	Apr 27, Dietlind
Apr 30, Dietlind	May 2, Dietlind	May 4, Dietlind
May 7, Kevin	May 9, Kevin	May 11, Kevin
May 14, Kevin	May 16, Kevin	May 18, Kevin
May 21, Dietlind	May 23, Dietlind	May 25, Dietlind
---	May 30, students	Jun 1, students
Jun 4, students	Jun 6, students	Jun 8, students

We are also keeping a more detailed schedule, with the topics and pointers to material to read.

Textbooks:

There are no textbooks for BME 220 this quarter, as we will be working primarily from original literature. You may wish to have a protein-structure text such as Introduction to Protein Structure by Branden and Tooze or Protein Structure and Function by Petsko and Ringe. (Kevin likes Branden and Tooze better, but Petsko and Ringe were used for Chem 200B and for BME 220 when Carol Rohl taught it.)

If you are unfamiliar with PDB files and how protein structure is determined, we highly recommend reading Gale Rhodes's Crystallography Made Crystal Clear.

Class format:

The class will be a mixture of lectures and journal-club presentations, with somewhat more lecturing than in the past. Evaluation will be based on participation in class discussions, on journal-club presentations, and on the term project done in BME 220L. We will have a poster session during exam week in place of a final exam. That poster session will be Tuesday 12 June 4-7 p.m. All students are expected to present a poster.

Prerequisites:

The only official prerequisite for grad students in this course is either BME 205 (bioinformatics) or CHEM 200B (protein structure), though it is best to have both. Students lacking BME 205 may need to choose a project that uses existing tools, rather than one that requires extensive programming. Students lacking CHEM 200B should have at least some knowledge of protein chemistry (at the level of BIOC 100A, for example).

For undergraduates, the prerequisites are BME 205, BIOC 100A, and CMPS 101.

Evaluation:

Roughly 40% of the evaluation will be based on the class project, 20% on in-class presentation of a journal article, 30% on homework, and 10% on general participation in class discussions (including reading most of the presented journal articles). These percentages may need to be adjusted somewhat for students doing mini-projects or for students who do multiple journal-club presentations.

Computers:

Students will be using the computers set up for bioinformatics grad students in PSB. Students can get keys for the doors at the SoE facilities office (Baskin 217) MTWTF 1–3. The office will have a list of students in the class. School of Engineering accounts are obtained by filling out the , getting my signature on it, and turning it in to the Techstaff office. (Bioinformatics grad students already have keys and accounts.)

WWW resources for biosequence analysis

URLs for web sites containing biosequence analysis tools, but not well annotated. This is Kevin's personal list of interesting sites, but it needs some updating, reorganizing, and annotating.

International Society for Computational Biology

ISCB is the primary professional organization for bioinformatics, sponsoring (or co-sponsoring) several conferences and having PLoS Computational Biology as its official journal. Membership pays off in reduced conference fees and journal subscriptions. Disclaimer: both Kevin and Dietlind are on the Board of Directors for ISCB.

SoE home

Kevin Karplus's home page

Dietlind Gerloff's home page

BS, MS, and PhD programs

Karplus's lab page

UCSC Bioinformatics research

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