Algorithms in Computational Biology

INFO-F-438 (master bioinfo&mod)

 
  1. Goals

  2. Course content

  3. Staff

  4. Schedule

  5. Assignments

  6. Course book (mandatory)

  7. Slides

  8. exam projects

  9. exam groups (see end)

Course content

Staff

Sébastien Colette (Algo, ULB), telephone ???,

email:Sebastien.Collette@ulb.ac.be


Tom Lenaerts (MLG, ULB and AI-lab, VUB), telephone 02 650 60 04,

email: tlenaert@ulb.ac.be


Prof. J.Cardinal and Prof. T. Lenaerts

2015-2017

Goals

The goal of this course to provide basic expertise in algorithm development to students with no background in computer science and to provide computer science students with an overview of the algorithms typically used in Computational Biology.


In addition, this knowledge will allow students to better understand the algorithmic  literature in bioinformatics and computational biology.

The course follows completely the book “An introduction to Bioinformatics Algorithms’ by Neil C. Jones and Pavel A. Pevzner.  More information related to this book can be found on :  bioalgorithms.info   An electronic version of the book is provided here.


During the year students will have to complete 3 assignments related to 3 topics discussed in the course. See at the end of this page for the announcements and the deadlines.  Students will be graded individually for these assignments.    


For the exam, students will need to select an article related to the area of bioinformatics and computational biology, with a focus on articles that discuss an algorithmic solution to a biological problem.  The exam consists of making a presentation discussing the article.   These projects will be made in groups of 2 students.


The score of the course will be 50% on the assignments and 50% on the exam.

Schedule

Sessions :

  1. Tuesdays between 12:00 and 14:00, (starting February 6, 2017) at the ULB La Plaine campus, room P.OF.2080.

List of sessions (provisional)

Course book (mandatory)

Assignments

The first assignment covers the Multi-digest problem : assignment1.pdf(deadline March 7, 2017)


The second assignment covers interval graphs and exon chaining: assignment2.pdf(deadline, March 28. 2017)


The third assignment focussing on an efficient implementation of string matching: assignment3.pdf(deadline May 16th, 2017)

Slides

The slides linked to this course can be found on :  bioalgorithms.info

Exam projects

Like in previous years the exam will consist of a presentation on an article presented and published in the WABI workshops.  The proceedings for the last two years of this workshop can be found via the following links


WABI 2015

WABI 2016


You should be able to download an article or even the entire proceedings when you’re at the ULB or via EZ-proxy to the ULB.


To prepare for the exam:

  1. 1)create a group of 2 students

  2. 2)select an article from the 2015 or 2016 proceedings

  3. 3)send this information together with the PDF of the article before 2/05/2017 to tlenaert@ulb.ac.be with [BIOINFO-EXAM] in the subject of your email.

  4. 4)prepare a 20 minute presentation discussing the motivation, problem and the algorithmic solution.  Try to also discuss the relevance and be critical on the claims made by the authors of the paper.

  5. 5)Send this presentation no later than 5/06/2017 to tlenaert@ulb.ac.be with [BIOINFO-EXAM] in the subject of your email.


The exam is organized on June 6, 2017 between 9:30-13:00.  Groups will be assigned to slots of 30 minutes. Room 1C6111 (Meeting room IB2)


Each student group will have 20 minutes (max 16 slides) to present their article and there will be 10 minutes for questions.


Evaluation criteria:

  1. 1.Quality of the presentation (slides, explanation, examples, clarity, language, ...)

  2. 2.Link to the course (wherever possible draw relationships with the knowledge you acquired during the course, ...)

  3. 3.Understanding of the paper (maths, formulas, functionality, proofs, biological and medical relevance, ...)

  4. 4.Originality (extensions by looking up additional papers, critical analysis of the paper, going beyond the paper content, consider improvements, ...)

Exam groups