BME110, Spring 2012, Section 01: Syllabus

BME 110 / BIOL 181: Computational Biology Tools

This is a hands-on laboratory, lecture, & problem solving course geared to teach basic tools used in computational biology.  Some topics covered include motif searching, sequence searches, multiple sequence alignment, genefinders, using genome annotation, phylogenetics, human SNP analysis, and viewing molecular structures from X-ray crystallography data. Web-based tools and databases are primarily used, but a few Java-based apps are also used. Open to all bioinformatics, bioengineering, or science students with basic biochemistry (or permission of the instructor).


You must bring your own laptop to class every day, and to discussion sections.
You will need wireless access in class.
You will need to install the J2SE Java Runtime Environment (JRE) if you haven't already (OS X users have Java built-in already)

Instructor Office Hours:

Mon 1-2pm, Wed 11-Noon

Teaching Assistants:

Brandon Rice (
Paola V. Castro (

TA Office Hours: 

Paola:   Monday: 9:30am-10:30 Basking Lounge; Thursday: Noon-1pm PSB-213

Brandon: Tues and Thurs at 4pm-5pm, PSB 213

Discussion Sections (Required)

  1. Tuesdays 6-7:15pm PSB 305
  2. Tuesdays 7:30-8:45pm PSB 305
  3. Thursdays 6-7:15pm PSB 305

Required Text
Bioinformatics for Dummies, Second Edition
Claverie & Notredame

(Kindle edition available)

Optional Texts
Bioinformatics: Sequence and Genome Analysis
Second Edition (2004)

David W. Mount
Cold Spring Harbor Laboratory Press

Genomes, Browsers, & Databases (2008) by Peter Schattner
(Kindle edition available)

There will also be numerous readings taken from scientific literature, on-line tutorials, and current news articles dealing with the rapidly changing social impact of genome information on our society.


Problem Sets: 25%

Midterm: 25%

Final Exam: 30%

On-line Exercises, participation and attendance at lab sections: 20%

(One discussion section absence may be allowed if cleared with me ahead of time.
For each unexcused lab absence, you will lose 1% of your Participation grade)

Homework Turn-In & Late Policy:

Homeworks turned in after the deadline will have 5% deducted if turned in within 24 hours,
and an additional 10% for every additional day late until homeworks are returned or answers are
given in class or on-line (usually one week after homeworks are turned in).  Please type homeworks
in simple text or Word format files, including the tool, web site address, database, or other resource
you used to solve the problem (if no documentation is given, only partial credit will be given). 

Turn in homework electronically using the eCommons dropbox. 

You may work together sharing ideas and teaching each other how to solve problems on study section sequences (i.e, Sequence-A, Sequence-B, etc.), but you must do the analyses for homework sequences (i.e. Sequence-1, Sequence-2, etc.) on your own, described in your own words.  You may not share/trade/lend/borrow written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers with others (see below).

Academic Honesty and Academic Integrity:

In recent years, there has been an increased number of cheating incidents in many UC campuses, and unfortunately, UCSC is no exception. The School of Engineering has a zero tolerance policy for any incident of academic dishonesty. If cheating occurs, there may be consequences within the context of the course, and in addition, every case of academic dishonesty is referred to the students' college Provost, who then sets the disciplinary process in motion. Cheating in any part of the course may lead to failing the course and suspension or dismissal from the university.

What is cheating? In short, it is presenting someone else's work as your own. Examples would include copying another student's written or electronic homework assignment, or allowing your own work to be copied. Although you may discuss problems with fellow students, your collaboration must be at the level of ideas only. Legitimate collaboration ends when you "lend", "borrow", or "trade" written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers. If you do collaborate (legitimately) or receive help from anyone, you must credit them by placing their name(s) at the top of your paper. 

What is Academic Integrity? This question is better answered with how we violate academic integrity. One prime example is fabrication. Fabrication:

  • In any academic exercise, submitting falsified data including bibliographic resources and experimental data, or altering graded coursework/exams and resubmitting to the instructor for a higher score.

Another example of violating academic integrity is Facilitating Academic Dishonesty:

  • One form of this is answering questions on someone else's exam or doing someone else's homework for them.
  • Another form is helping another student take a test (allowing them to cheat from you).

Official University Policy on Academic Integrity for Undergraduate Students