Applications en bioinformatique et modélisation

INFO-F-435

 
  1. Description in the ULB program

  2. Objectives

  3. Summary

  4. Staff

  5. Schedule

  6. Evaluation

  7. Rules

  8. Reference works

Prof. T. Lenaerts

2009-2015

Summary

Staff

Tom Lenaerts,

Bureau 2O8.117,

tel 02 650 60 04,

email: tlenaert@ulb.ac.be


Elisa Cilia

Bureau 2O0.121

email : ecilia@ulb.ac.be

Course objectives

The goal of this course is to build a bioinformatics or modeling application in which the students can test their newly acquired skills obtained in the different courses on bioinformatics and modeling.   At the same time they will get acquainted with a particular subject in computational biology

This year the students will perform a reimplementation of of the algorithm discussed in Borghans, J. A. M., Beltman, J. B., & De Boer, R. J. (2004). MHC polymorphism under host-pathogen coevolution. Immunogenetics, 55(11), 732–739. doi:10.1007/s00251-003-0630-5


The PDF : Immunogenetics 2004 Borghans.pdf


As discussed in this article MHC molecules, which play an important role in the immune response of vertebrates, are among the most polymorphic genes within this class of animals.


The explanation for this polymorphism is based on the idea that it provides an increased protection for the host against pathogens.  The causes for having these polymorphisms were either;

  1. 1.selection favoring a heterozygous hosts

  2. 2.selection favoring rare alleles through host-pathogen coevolution


In the article they examine which of these causes has a higher impact on the polymorphisms observed in the population of MHC molecules.


A model, not so different from a standard genetic algorithm was created to make the analysis.


The aim of this project is to reproduce to make your own implementation and reproduce the results discussed in the article

Schedule

Students will work individually on this project. 




The deadline for the SECOND SESSION is Friday August, 21 2015 at 12h. 

Suggested exam date is Thursday August, 27 2015 at 12h. 

Evaluation

Students will create a website (login and password will be provided) which contains

  1. 1.An explanation for the problem;

  2. 2.A schematic explanation of the algorithm

  3. 3.A zip file containing the python3 code, with input files and a readme file describing how to run your code

  4. 4.Put on the wiki the figures showing that you can reproduce the results discussed in the paper and explain your results..

  5. 5.Use images where suitable to explain things


Accessing the wiki.pdf


The student will be evaluated on his or her capacity to complete the project and present the results.  Hence the quality of the implementation, the ease of use and the visualization and the documentation are important aspects to determine the final grade.

Rules

The project is an individual effort.  Hence all forms of plagiarism or copying or all participation in such acts will be punished.


An oral defense will take place within the exam period .  The date will be decided upon agreement with Prof. T. Lenaerts and Dr. E. Cilia.


The code will be tested on a machine with an equivalent configuration (C++/java compiler version, libraries, etc) as the public machines installed in room NO4.008.  All programs that  do not compile on these machines are considered wrong.

References

Additional references on MHC can be found online