Workshop in Bioinformatics 2005


Instructor :  Prof. Benny Chor (, Schreiber, room 223.
Teaching Assistants : Tamir Tuller (, Schreiber, room M20 (basement).
Where : Schreiber, Room 309.
When : Mondays 11:00-13:00, Spring 2004.

The workshop is open is open to 3rd year Computer Science students, but students of the bioinformatics track will have higher priority in registering.


Goals & scope

  1. Analysis, design and implementation of combinatorial optimization algorithms with bioinformatics relevance.
  2. Some 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, including analysis of gene expression data and DNA microarrays, analysis of gene structure, understanding genomic pathways, construction of phylogenetic trees and networks, etc.

The workshop also includes three lectures on various topics in software engineering, given by the Computer Science system staff. These will include subjects relevant to  medium to large scale software project. Students are expected to utilize these tools and techniques in the final projects and documentation. Attending these three lectures is mandatory.

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.

Projects will be performed in groups consisting of at most two students (if the number of students is odd, one triplet may be allowed).

In the first two weeks, each group must choose two preferred projects and send them to Tamir (
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 Tamir's mailbox.

Tentative Timetable  (subject to changes)


Feb. 21

Lecture: Introduction to BioInformatics. Administratrivia.

Feb. 28

Lecture:  Projects' Overview

March 7

Lecture on parallel processing and Condor by Edward Aronovich from the CS system staff (slides).
Project selection completed.

March 14

No Meeting

March 21

No Meeting

March 28

Meeting cancelled due to teachers/students strike

April 4

Outlines of all planned projects presented by students in class   (10 minutes per group)


Lecture on selected software engineering topics by CS system staff


Presentation of completed projects in class   (20 minutes per group)


Last date for projects submission, including detailed presentation of the projects to the course staff.



Suggested Workshop Topics (List Subject to Change)


  1. Modeling and inferring genetic networks, using DNA microarrays data
  2. Methods for gene finding
  3. Large scale detection of conserved genomic regions
  4. Network based phylogenies
  5. Exploring global properties of the likelihood function in phylogenetic reconstruction
  6. Relations between gene interaction and chromosomal location
  7. Tools for identifying associations between cancer related genes, based on gene expression datasets
  8. Finding regulatory motifs in the promotor region, using MeX.


Assigned Projects


Tamir Tuller