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

Who, When, and Where:

lecture and discussion section (REQUIRED): PSB 305 Thurs 4–5:45 p.m.

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, teaching, speaking loudly, ...

All new grad students should also plan on taking BME 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 8 of the 10 class sessions (and all 10 would be preferable).
• You must turn in all four assignments, and do passing work on at least three.

Homework assignment: LaTeX assignment Due 8 Oct 2015. Reproduce the example in latex-assign.pdf using LaTeX.

Homework assignment: fellowship application Due Fri 16 Oct 2015 (joint with BME 205).

Homework assignment: LaTeX/BibTeX assignment Due 19 Nov 2015.

Homework assignment: Web page assignment Due Wed 9 Dec 2015 noon (exam slot for course)

Texts

Required:

• LaTeX User's Guide and Reference Manual Leslie Lamport. This is a generally useful reference and I recommend keeping a copy handy for working on your thesis proposal and thesis. You can now find almost all the material from the book on-line, so it may no longer be necessary to have a physical copy.
• Art of Problem Solving LaTeX tutorial
• One student recommended this reference: http://en.wikibooks.org/wiki/LaTeX
• TA handbook: A practical reference for Graduate Student Teachers Division of Graduate Studies, UCSC, 2003
• Teach Like a Champion: 49 Techniques that Put Students on the Path to College Doug Lemov
  This book is aimed at elementary-school teachers (and, to a lesser extent, high-school teachers), but has a lot of practical advice on running a classroom that can be applied at any level. We'll probably have each person in the class present one or two of techniques to the rest of the class, as practice teaching. There is now a second edition Teach Like a Champion 2.0: 62 Techniques that put Students on the Path to College. Either edition is usable for this course, as we will only cover a few of the techniques.

• 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.

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.

Classroom accommodations for disabilities

A former Dean for Undergraduate Education (William Ladusaw) recommended 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)."

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 6 different floors in 4 buildings, a physical bulletin board of students wouldn't help much), so I encourage students to allow their names and pictures to be posted.

The pictures below have links to larger images.

Alana Weinstein

Audrey Lyman

Darrin Shultz

Jacob Pfeil

Jordan Eizenga

Tentative schedule of topics

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

24 Sept 2015

Notes for content in week1.html Syllabus, texts, FERPA, PSB tour, seminars, mailing lists, ...

1 Oct 2015

Notes for content in week2.html LaTeX, Speaking loudly

8 Oct 2015

Notes for content in week3.html Publication, copyright, choosing journals, poster design. Being a TA.

15 Oct 2015

Notes for content in week4.htmlTech staff presentation, graphical presentation of data.

22 Oct 2015

Notes for content in week5.html Lab Safety and Ergonomics

29 Oct 2015

Notes for content in week6.html Presentations and BibTeX

5 Nov 2015

Notes for content in week7.html Women in computational fields

12 Nov 2015

Topic to be determined

19 Nov 2014

student presentations of techniques from Doug Lemov's Teach Like a Champion: 49 Techniques that Put Students on the Path to College

3 Dec 2014

Feedback on student presentations of techniques from Doug Lemov's Teach Like a Champion: 49 Techniques that Put Students on the Path to College

Wed 9 Dec 2014, noon–3 p.m.

Final exam slot, not used. (noon final deadline for all homework)

Topics that haven't been scheduled, but probably should be

Writing proposals (thesis proposals, funding applications, ...) (Covered in BME 205.)

Funding sources.

Useful resources

• Guidelines for mentoring grad students
• http://genome.ucsc.edu/ UCSC Genome Browser - gateway to over 27 complete genome sequences
• A 5 Step plan for better journal writing.
• Ethan Miller's 2002 presentation on security

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• UCSC list of journals for which we have electronic subscriptions

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• If you need to use the campus-wide computing facilities: Instructional Computing Homepage
  
• The on-line ITS Help Desk

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• The Baskin Center Policy about Cheating (postscript).
• UCSC Policy on Academic Integrity.
• UCSC Policy on Research Integrity.
• Learning Technologies Services provides some support for teaching, mainly in the form of infrastructure support for audiovisual presentations, computer labs, and distance education.
• A guideline for creating class web pages in SOE.
• Advice for dealing with difficult situations/students:
  • Red Folder
  • Disruptive Students
  • Distressed Students
  You should consult the instructor of your course if you encounter these types of problems as a TA.
• http://ucnet.universityofcalifornia.edu/labor/bargaining-units/bx/contract.html Current TA Contract
• Academic Personnel Manual Section 410 (particularly 410-20) lists the university rules for TA employment.
• http://www.ucop.edu/academic-personnel-programs/compensation/2015-16-academic-salary-scales.html has the full set of salary scales for academic titles (including student employment titles).
• 2013–14 Grad student research salary scales Remember that academic term appointments are only at 49.99%, so cut the posted salaries in half. Bioinformatics uses step VIII.
• 2015–16 Teaching assistant salary scales Remember that academic term appointments are only at 49.99%, so cut the posted salaries in half.

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SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

BME 200 home page

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
318 Physical Sciences Building