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Class Calendar (+ lecture
slides) |
Resource Links | Problem Sets |
| Instructor: |
| Prof. Dietlind Gerloff Email: gerloff @ soe.ucsc.edu Office: Physical Sciences Building, Rm 320 Phone: 459-4833 Office Hours: Mon 2-3pm, or by appointment |
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
(please let us know at the first class meeting on Tuesday if you don't
have a laptop and cannot borrow a laptop from a friend for the quarter,
we may be able to help you).
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) - we will help ensure that you get help with fulfilling these
requirements if necessary.
Teaching Assistant:
Grant Thiltgen (thiltgen @ soe.ucsc.edu)
Group Tutor (on as need basis):
Thomas Jüttemann (juettemann @ soe.ucsc.edu)
TA Hours: Wednesday 10-12 (Grant) + Friday 1-2 (Thomas), in Physical
Sciences PSB 313, or by arrangement
Additional Section:
Thursday 6-7:45pm (usually done by 7:30pm)
in SocSci 1-135 (Mac Lab) + another room if we are too crowded
Attending this section will be mandatory (unless you have prior experience) and will ensure that you can do much of your homework with knowledgeable people in the room who can answer your questions right then and there.
Note that the first additional section will be held on Jan 8 (first
week)
| Required Text |
| Bioinformatics
for Dummies, Second Edition Jean-Michel Claverie & Cedric Notredame Wiley Publishing, 2006 |
| (Advanced students may also consider the book listed below or talk to us about more technically challenging books in the field they are most interested in - instead of the B4D book listed above, or in addition. Note that specialist books usually cost more, and that this is not required of you for passing the course:) |
|
Bioinformatics:
Sequence and Genome Analysis Second Edition (2004) David W. Mount Cold Spring Harbor Laboratory Press |
Additional Resources |
| A great variety of good entry-level books exist that could be helpful to consult for course content that is not covered in the required course text. We will mention some along the way in the lectures and you may have your own preferences. However you will find that the majority of valuable resources providing more in-depth discussion of a specific topic are found on the WWW these days (see for example our Resource Links). |
Grading:
Problem Sets: 40% (four homework assignments during the quarter)
Midterm: 20% (Thu February 12)
Final Exam: 30% (Wed March 18, 4-7pm)
In-class Exercises & Participation: 10%
Homework Turn-In & Late Policy:
Homeworks are due at the
specified time (on course days this is at the beginning of class).
Homeworks turned in late 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). You cannot get credit at all if you submit your
homework later than that - therefore you have to contact us prior
to the due date/time if you have a serious circumstance!
Submit homeworks in simple text or Word format files, and your answers will include two parts for each question, (a) the answer you arrived at and (b) a brief description of how you arrived at this conclusion (including the tool, web site address, database, or other resource you used). We will explain during class how your answers are to be structured. If no documentation is given, only half-credit will be given.
Submission of your homework will be electronically via WebCT. Do not email it to the instructor, it is likely to get lost! If for some reason you cannot submit your homework, please bring a printout or CD to class or hand it personally to the instructor or TA. The same deductions apply if this were to be after the due date/time.
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.). However you must do the analyses for homework
sequences (i.e. Sequence-1, Sequence-2, etc.) on
your own, and the solution must be 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