| Instructor: |
| Prof. Todd Lowe Email: lowe @ soe.ucsc.edu Office: Physical Sciences Building, Rm 316 Phone: 459-1511 Office Hours: Wednesdays, 4-6pm and by email appointment (most afternoons M-Th are free) |
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:
Andy Nguyen (atnguyen@ soe.ucsc.edu)
Hours: 12:30-1:30 on Tuesdays and Wednesdays, Sinsheimer Labs 144
David Bernick (dbernick@ soe.ucsc.edu)
Hours: by email appointment
Discussion Sections
Mondays, 5-6:30pm, Physical Scienes Building, Rm 305Required 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: 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).
Turn in homework via WebCT. 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).
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:
Official
University Policy on Academic Integrity for Undergraduate Students