Research Workshop in Bioinformatics, Fall, 2009

(0368-3500-07)

Instructor :  Dr. Eran Halperin (heran AT post dot tau dot ac dot il), Schreiber 310.
Teaching Assistant: Yael Baran (yaelbara AT post dot tau dot ac dot il)
Where: Kaplun-Physics, Room 319
When: Thursday 11:00-13:00 , Fall 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 and particularly in computational genetics. The research projects suggested are exploring the state of the art in science and genetics today, and they may potentially lead to publication in conferences and journals. However this is obviously not a necessary for attaining a good grade.

• Probabilistic modeling of human population genetics data.
• Analysis, design and implementation of algorithms that stem from such models.
• Investigate contemporary problems in computational biology as a whole, and particularly in computational genetics.
• Getting acquainted with practical heuristics, algorithms. and machine learning techniques that are widely used in computational biology and outside of the field.
• Conducting supervised research in computational biology
• Efficient implementation of algorithms in C, C++, Java, R, 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. Most of the projects we will offer are related to computational human genetics; that is, we will search for ways of improving the scientific understanding of human diseases, as well as human evolutionary history..

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.

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 November 19th (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. Some flexibility on the submission date of the projects will be given under some circumstances, for example, if the project that was taken was too large to finish on time (this has to be coordinated a few weeks before the submission date with us (Halperin and Baran).

Note that very late submissions may not be accepted, so do try to hand the submission before the end of the semester.

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 heran AT post dot tau dot ac 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 Eran's mailbox.

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Tentative Timetable  (subject to changes)

October 22, 2009	Administratrivia. A talk describing the subject of computational human genetics.
October 29, 2009	Still introduction + Overview of Proposed Projects
November 12th, 2009	Deadline for submitting two topics for project by each group
November 19th, 2009	10-20 minutes presentation of outlines of projects chosen by the students
December 17th, 2009	10-20 minutes presentation of progress in projects, given by the students
January 21st, 2010	20 minutes final presentation of progress in projects, given by the students

 

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Slides 

Intro to Computational Genetics