BME 110 / BIOL 181: Computational Biology Tools

Spring 2011
Tue/Thur 2-3:45pm
  Engineering 2, Rm 194

 Home Class Calendar
Resource Links Problem Sets


Instructor:
Prof. Todd Lowe
Email: lowe @ soe.ucsc.edu
Office: Physical Sciences Building, Rm 316
Phone: 459-1511
Office Hours:  Mon 1-2pm, Tues 10am-11am, and by email appointment

Syllabus

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.

Requirements

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:
John Archie (jarchie@soe.ucsc.edu)
Hours: Thur 9-10:30am, Fri 2:30-4pm in PSB 313 (John's desk is at the back of the room), and by appointment (see http://www.jarchie.com/schedule/ to find open times)

Discussion Sections

Mondays, 11-12:10pm JBE Rm 373
Wednesdays, 3:30-4:40pm, Soc Sci 2, Rm 165

Required Text
Bioinformatics for Dummies, Second Edition
Claverie & Notredame

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

David W. Mount
Cold Spring Harbor Laboratory Press

Grading:
Problem Sets: 35%
Midterm: 25%
Final Exam: 30%
On-line Exercises, Participation and attendance at lab sections: 10%
(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:

Another example of violating academic integrity is Facilitating Academic Dishonesty:

Official University Policy on Academic Integrity for Undergraduate Students

Course Topic Outline