Workshop in Bioinformatics 2006

(0368-3500-23)

Instructor :  Prof. Benny Chor (benny@cs.tau.ac.il), Schreiber, room 329.
Teaching Assistants : Tamir Tuller (tamirtul@post.tau.ac.il), Schreiber, room 223.
Where : Kaplun-Physics, Room 319.
When : Wednesday 15:00-17:00, Spring 2006.

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 (tamirtul@post.tau.ac.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 Tamir's mailbox.

Tentative Timetable  (subject to changes)

 

March. 8

Lecture: Introduction to BioInformatics. Administratrivia.

March. 15

Lecture: Project’s Overview

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Suggested Workshop Topics (List Subject to Change)

 

  1. Modeling and inferring genetic networks, using DNA microarrays data.
  2. Analyzing probabilistic models for genes networks.
  3. Methods for gene finding.
  4. Large-scale detection of conserved genomic regions.
  5. Network based phylogenies.
  6. Algorithms for inferring phylogenetic networks.
  7. Relations between gene interaction and chromosomal location.