BME110: Computational Biology Tools

Spring 2007
Tue/Thur 10-11:45am
  Engineering 2, Rm 192

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Resource Links Problem Sets

Prof. Todd Lowe
Email: lowe @
Office: Physical Sciences Building, Rm 316
Phone: 459-1511
Office Hours:  Tues 1-2pm, Wed 1-2pm


Catalog Description:
Hands-on laboratory geared to teach basic tools used in computational biology (motif searching, primer selection, sequence comparison, multiple sequence alignment, genefinders, phylogenetics analysis, X-ray crystallography software). Web-based tools and databases are used. Open to all science students with basic biochemistry or permission of the instructor as a  prerequisite.


You must bring your own laptop to class every day.
You will need a wireless network card to get on the network in class.
You will need to install the J2SE Java Runtime Environment (JRE) if haven't already (OS X users have Java built-in already)

Teaching Assistant:
Greg Dougherty (gregd @
Hours: Monday 1-3, Wednesday, 1-2 Baskin Engineering, Rm 314

Weekly Review Sessions: 

Thursdays, 2-3pm PSB 305 (moved to PSB 319 on May 3)
Thursdays, 4-5pm, PSB 305
Mondays, 2-3pm, Baskin Engineering 314
(these locations may change if we have insufficient room in the current locations)

Required Texts
Bioinformatics for Dummies, Second Edition
Jean-Michel Claverie & Cedric Notredame
Wiley Publishing, 2006
Additional Resources
Bioinformatics and Functional Genomics
Jonathan Pevsner
John Wiley & Sons, 2003

Problem Sets: 40%
Midterm: 20%
Final Exam: 30%
In-class Exercises & Participation: 10%

Homework Turn-In & Late Policy:
Homeworks are due at the beginning of class on the day that they are due.  Homeworks turned in
after that 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 (generally 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 half-credit will be given).  Please email your homework to our TA, Greg Dougherty (
to turn it in (not the instructor).  If for some reason you cannot email your homework, please bring a printout or
CD to class and leave it at the front table.  Homeworks turned in at the middle or end of class on the due date will
have the 5% late deduction.  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:

Another example of violating academic integrity is Facilitating Academic Dishonesty:

Official University Policy on Academic Integrity for Undergraduate Students

Course Topic Outline