|Prof. Todd Lowe
Email: lowe @ soe.ucsc.edu
Office: Physical Sciences Building, Rm 316
Office Hours: Thursdays 2-4pm and by email appointment
(most afternoons Mon, Tues, and Friday are free for email
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)
John St. John (jstjohn @ soe.ucsc.edu)
Hours: Mondays & Tuesdays, Noon - 1pm, Baskin Eng Rm 358
Discussion SectionsTuesdays, 6-7:20pm and 7:30-8:50, Baskin Eng Rm 165
Bioinformatics for Dummies, Second Edition
Claverie & Notredame
Bioinformatics: Sequence and Genome Analysis
Second Edition (2004)
David W. Mount
Cold Spring Harbor Laboratory Press
Problem Sets: 35%
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 via WebCT. You may work together sharing
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).
What is cheating? In short, it is presenting someone else's work as
own. Examples would include copying another student's written or
homework assignment, or allowing your own work to be copied. Although
may discuss problems with fellow students, your collaboration must be
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
If you do collaborate (legitimately) or receive help from anyone, you
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:
on Academic Integrity for Undergraduate Students