BME110/BIOL181: Computational Biology Tools

Fall 2009
Tue/Thur 4-5:45pm
  Engineering Building 2, Rm 192 (enter from the courtyard)
Home Class Calendar+Topics
 (filled as the quarter progresses)
 Resource Links Problem Sets
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Instructor:
Prof. Dietlind Gerloff
Email: gerloff @ soe.ucsc.edu
Office: Physical Sciences Building, Rm 320
Phone: 459-4833
Office Hours:  Fri 12:45-1:45pm but see below for extra hours, or by appointment

News

Thank you for taking the class and all your participation. We wish you a very Happy Holiday when it comes.
Dietlind Gerloff + Grant Thiltgen

Learning Services provide some FREE GROUP TUTOR SESSIONS for this class (see email message from Oct 27). Jimmy Perrott took this class with us last year and did great. Online Sign-up page: https://eop-apps.ucsc.edu/OTSS/

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 (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)
Office Hours: Monday 1:00-3:00 pm PSB 313

Group Tutor (on as need basis):

Thomas Jüttemann (juettemann @ soe.ucsc.edu)

TA Hours: tba (in Physical Sciences PSB 313)

Additional Section:

As you will have seen when enrolling, there will be a mandatory additional course section each week. This will consist of hands-on work with the tools that were discussed in class, typically on the home work assignments and/or other exercises. We are considering to move the time for this section away from the formally scheduled time (to enable everyone to attend and have access to a more suitable room for it).

The preferred option (by far) according to the poll was...
B: Th 6-7:30pm

If you can absolutely not make this time, please get in touch asap, we may have to advise that you consider taking the class in the Spring. Thank you!

 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 in the second week of teaching (Sep 28- Oct 2)

Required Text

Note: We have not asked the book shop to carry additional copies of these texts because class size is difficult to predict. We recommend that you purchase your books either new or used via Amazon or student-exchange resources like Uloop. Order early, delivery may take a few days! If you have any problems, please let us know, we'll be happy to help.
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 November 5)
Final Exam: 30% (Tue December 8, 7:30-10:30pm)
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).

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