BME205, Fall 2011, Section 01: Syllabus


David Bernick (
Office hours: PSB 312A, Wed 10:00-11:00 a.m.
TA: Evan Paull ( )

Lectures: MWF 11-12:10 PSB 305

Required Textbook


An Introduction to Bioinformatics Algorithms. Jones and Pevzner. Available at Amazon and other booksellers.

Optional and highly desirable reference text


Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Durbin, Eddy, Krough and Mitcheson. Also available at Amazon. There are a few of these texts floating around the department. It is an essential reference for anyone in Bioinformatics, and has been the required text for all previous versions of this course.

Python guides

Python in a Nutshell, Second Edition. Martelli.  Available online through the UCSC library, Amazon or as an eBook through

There are quite a few nice resources including: 

SOE computing account

Every student in the class will need a School of Engineering computer account. I will want assignments turned in by providing me with a publicly readable file (PDF for written assignments) or directory (for multi-file assignments) containing the assignment on the SoE machines. All Python programs must execute correctly on the SoE machines, without needing to install additional Python modules. I would prefer to get paper copies of assignments in addition to the electronic ones (to save me the time of printing them), but I will accept electronic-only submissions from those who are too ill to attend class.

To get an SoE computer account see


There will be four types of assignments for the class:

  • reading assignments,
  • pencil-and-paper exercises,
  • programming exercises to learn Python, and
  • bioinformatics exercises using real data.

As has been the practice for this course, there will be no exams, and we will not meet during the final exam period. 

The assignments will be distributed on the web.

The relative weights of the different types of assignment in the evaluation has not been determined yet, though ”it should be roughly proportional to how much time the different assignments take to do well. I expect that most of the assignments will be similar to ones given in previous years, with a few parts tweaked to update them, but I may replace one or more assignments with new ones.  It is likely that we will make use of some very new Illumina paired-end sequencing data from a metagenomic study of halophilic viruses.

Programming Scaffold

I have included a brief python program that follows many of the conventions I find useful (attached).  Feel free to use this as a basis for your programming assignments.  If you find changes or enhancements that you would like to offer for general use, please send them to Evan or myself for consideration.

Academic Integrity

Anyone caught cheating in the class will be reported to their college provost (see UCSC policy on academic integrity) and may fail the class. 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. If you are not certain about citation standards, please ask, as I hate having to fail students because they were improperly taught how to cite sources.

Collaboration without explicit written acknowledgment will be considered cheating. Collaboration on lab assignments with explicit written acknowledgment is encouraged - ”guidelines for the extent of reasonable collaboration will be given in class.

Accomodation Authorization

If you qualify for classroom accommodations because of a disability, please get an Accommodation Authorization from the Disability Resource Center (DRC) and submit it to me in person outside of class (e.g., office hours) within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY), or for more information on the requirements and/or process.