CSCE 496/896 (Fall 2002) Project Ideas
From the syllabus:
In this course you will do a substantial project. This project can be:
(1) a very extensive literature search and summary on a particular
topic, (2) a good implementation and evaluation of a known result in
computational biology, or (3) a small (but nontrivial) amount of original
research related to bioinformatics. You may work on these
projects individually or in groups. Later this semester I will set a deadline
for submission of 1-3 paragraph proposals on your projects. You must do this
in order to get full credit for your project, and you must get my approval on
it before starting work on your project.
You will summarize your project results in a written report and an oral
presentation. If your project involves an implementation, then you may
be asked to also give a brief demonstration. The written report must
use a professional writing style similar to that found in an ACM or IEEE
journal, including abstract, introduction, summary of related work, your
contribution, references, and an appendix (if necessary). The oral
will be to the entire class at the end of the semester: during dead
week (December 9-13), and if necessary, during the week prior to dead
week (December 2-6). You will submit your written report to
me no later than
December 13 (the last day of dead week) December 15 at
accordance with UNL dead week policies, you have now been informed in
writing of the nature and scope of this project prior to the eighth week
Suggestions for projects can be found below, but
you may propose your own topic as well. You must receive my
approval on your topic before proceeding with your work! To be a
valid topic, it must go beyond the scope of the course. So your
project could be on a topic we did not cover in class at all, or could
more deeply explore a topic we covered in class.
Rules on projects, a.k.a. what to turn in for your final project writeup
Tips on Presenting Technical Material
List of this semester's projects
Oral presentation schedule
Sources of project ideas:
- If your thesis research or a project you are doing
for another course is appropriate for this course's project, I may allow you to
use it for this course. But you still need to submit a proposal.
- I have some projects that are related to some ongoing research by one of my
students. We are trying to identify new thioredoxin fold (Trx) proteins by
various methods. Typically such a search is handled easily by profile hidden
Markov models built on the primary structure (original amino acid sequence)
of related proteins (what we will discuss in class). However, primary
structure is not well-conserved across the Trx superfamily. Thus my student is
exploring other methods (based on structural properties of the proteins) to
identify new Trx proteins. Good related course projects include: (1) further
exploring HMMs on primary structure but using new prior distributions than what
is used by default in HMMER; (2) improving work by Haifeng Ji in his
used profile HMMs built on secondary structure) by developing new prior
distributions or model structures; (3) extending Haifeng Ji's and Peggy Wen's
work by running extensive database searches with their current results.
- Prof. Jitender Deogun
has some project ideas, including working on a new algorithm for
RNA folding, working on a new algorithm for multiple alignments, and
implementing a new algorithm that works on of suffix trees.
Contact him for more information.
- You may check our list of other
bioinformatics courses to see what projects were done there. If you
choose a project from one of these courses and need to contact the instructor
of that course for more information, please contact me first and I'll contact
the instructor on your behalf.
- Look at the "Further Reading" sections at the end of each chapter of
and Setubal (all three
books are described in the syllabus).
- Review papers from recent conference proceedings and journals.
(see my bioinformatics
hotlist for some links).
- See this list from the Fall 2000 bioinformatics course.
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