Instructor : Prof. Benny Chor (benny AT cs dot tau dot il), Schreiber 329.
Teaching Assistant: Eyal Cohen (coheneyl AT hotmail dot com).
Where: Kaplun-Physics,
Room 324
When: Monday
The workshop is open is open to all 3rd year Computer Science students, but
students of the bioinformatics track will have higher priority in registering.
The goal of this workshop is to provide experience with
small scale, supervised research projects in bioinformatics. In the past, some
of these projects have led to publication in conferences and journals. However
this is obviously not a necessary for attaining a good grade.
1.
Analysis,
design and implementation of combinatorial optimization algorithms with
bioinformatics relevance.
2.
Investigate
contemporary problems in comparative genomics, DNA chips analysis, phylogenetic analysis, and
more.
3.
Getting
acquainted with publicly available Bioinformatics databases and using them.
4.
Conducting
supervised research in computational biology.
5.
Efficient
implementation of algorithms in C, C++, Java or Matlab.
The workshop will provide
hands on experience in implementing various optimization techniques, developing
statistical tools for analyzing biological data, and using public biological
databases. Most (but not all) projects have both
research and implementation aspects. We offer projects in various current
subjects in computational biology.
Unlike other workshops, there
will be about five to six
meetings with required participation by all students. These
include (1) an introductory lecture, (2) proposed projects' descriptions, (3)
brief description, by the students, of their chosen projects, (4) mid-semester
progress reports, by the students, (5-6) final report on the projects, by
the students.
The workshop may also includes a lecture on topics in software engineering, given
by the Computer Science system staff, that are
relevant for medium to large scale software projects. Students are expected to
utilize these tools and techniques in the final projects and documentation.
An integral part of the workshop is presenting
an outline of the project, as well as the completed project, to all participants
(not just the course staff). It is mandatory to physically attend class during
these entire parts of the workshop, which are expected to take place on March
29th (outlines presentation) and during the last three meetings (final projects
presentation). Naturally, your projects should be completed by then, and
submitted no later than the last day of the semester.
Late
submissions may cause a grade penalty. Very late submissions (e.g. more than 4
months after the end of the semester) may not be accepted at all! If you
think these deadlines are too strict, you should consider a different workshop.
Projects will be performed in groups consisting of at most two students.
During the first two weeks, each group must choose two preferred
projects and send them to benny AT cs dot tau dot il
We will try to match choices with availability, but in case of collisions,
assignments will be based on the time at which the request reaches Eyal's mailbox.
March 2, 2009
|
Administratrivia.
A talk describing a former project. |
March 9, 2009
|
Overview of Proposed Projects |
March 23, 2009
|
Deadline for submitting two topics for project by each group |
March 30, 2009
|
10 minutes presentation of outlines of projects chosen
by the students |
|
|
10 minutes presentation of progress in projects, given by
the students |
|
|
20 minutes final presentation of progress in projects,
given by the students |
|
|
20 minutes final presentation of progress in projects,
given by the students |