Research Workshop in Bioinformatics, 2009


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 10:00-12:00 , Spring 2009.

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.


Goals & scope

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.

Tentative Timetable  (subject to changes)

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