Introduction to Genome Bioinformatics, PLPTH
890
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We will be online with a computer and projector, accompanying theoretical material with practical demonstrations. Lecture notes and assignments will be placed on K-State Online, usually in advance of the lecture (but sometimes not until the last minute!).
The readings are given as preparation, not followup, for the corresponding
class meeting. Of course many students think it's the lecturer's job to
introduce the material cold, and so that's what he does. However the lecturer
also adores questions from lively students who don't wait for him to feed
them. There's a lot of bioinformatics we can't get to in this class (information
theory, SNPs, LD, ANNs, SVMs. POEs, DAGs, MCMCs, BNs...). Still, I'll try
to take you as far as you want to go (or at least pack you a lunch to carry
with you).
In following the schedule,
recognize that the readings for a given session often contain very similar
information, presented in different ways. Please read at least one of them.
If you want more information or a different presentation, you can find it
with Google (no kidding).
We have been granted the use of the Agronomy Department's student computer lab for our lab session this semester. We have it for only the weekly 3-hour lab period, so unless you're a student in Agronomy you'll need to use your department or personal computer resources to do computer work outside of lab.
You will receive an account on CN's Unix machine and instruction in logging
in remotely and transferring data across the network. This computer, and
(by arrangement with CN) one or more Linux/Windows workstations in CN's lab,
may be used to run various bioinformatics software applications and develop
and test Perl scripts. You may also find your account on the KSU host to
be useful (though it has never been necessary for the course).
Some students like to bring a Zip disk or memory stick to lab, but it isn't necessary.
Though you can't store any files on your lab computer, you can store everything
on the course machine by copying it across the network.
Output from problem sets (and all other written submissions) will be in HTML, submitted via K-State Online by the end of the Thursday following the date of assignment. Please don't use Microsoft Word to compose and save your files as HTML. They will be large and full of tags that Composer doesn't recognize. This is annoying to me since I view and comment them with Composer. Please use either Composer or some other HTML editor that is compatible with Composer.
You'll present research-project
results on your own WWW pages, the most natural medium for publishing bioinformatics
results. You'll find -- if you don't already know -- that making and publishing
HTML documents is no harder than using any other text- and image-processing
medium. You'll also find that I expect decent organization
and writing from you.
Do your own
work. While in general you're free to use WWW and printed sources for supplementary
information, you must, when reporting results, acknowledge the source. Whether
or not you do so, you may expect to receive little or no credit for presenting
work done by others in place of work that was to be done by you. The only
exception is work done with the direct help of the instructors.
In
lab we follow a set of written instructions. Students are free to help one
another, but each should work the exercises on his or her own computer.
Students give a 10-minute presentation of research-project results. This can be in any effective medium, but imaginative use of presentation tools (and online action) is encouraged. The purposes of this presentation are to demonstrate proficiency in bioinformatics tools and methods, to describe research, and to work on communication skills.
Ph.D. student Roby Joehanes will be available for help, mostly with computing issues..
Final grades will be based on assessment of work on problem sets, the term project, the midterm exam, and your comportment as a scholar (see cell-phone policy above). In borderline cases, your attendance and the interest and intellectual contribution you've brought to class will be taken into account.
Office hours for drop-in student help are from 3 to 5 PM on MTWF, Throckmorton 4022B. I'm usually available at other times too, but you can make sure by contacting me by e-mail or telephone to arrange a meeting, or catching me at the end of lecture. When teaching, I consider it the most important work I do. You'll get prompt attention.
Group tutorial sessions are arranged when students feel they would be useful.