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S03 - Computational biology + project

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2021-2022 Computational Biology planning

Biology Master, ENS
Year : 1 (M1)
Semester : 1 (S1)

Course code :

BIO-M1-S03-S1

Course name :

Computational biology

Coordinators :

Pierre Vincens
Morgane Thomas-Chollier

ECTS :

3 ECTS (Computational Biology) for the DENS or 6 ECTS (Computational Biology with project)

Project with limited number of places. To enroll, it is mandatory to directly contact the coordinators before September.

Keywords :

Bioinformatics, genomics, proteome, gene, protein structure, images, models

1) Computational Biology

ECTS : 3 only for the DENS

This course takes place on Thursday mornings throughout the first semester, not facing any other Imalis course in parallel. It is thus accessible to all students (see below for pre-requisites).

Prerequisites for the course :

Basic Python programming and Unix command-line is mandatory for this course. Students without this background can enroll for the course “BIO-M2-E01-S1 Training in mathematics and computer science” that takes place before the beginning of the semester. Students who would not enroll to this training will be asked to demonstrate their programming skills.

Course objectives and description :

The aim of this course is to introduce students to bioinformatics, by consolidating their knowledge in fundamental principles, as well as opening to current research topics in computational biology.

The course includes programming (Python) applied to biology, and courses with practicals in computational biology. The program evolves each year, and covers topics among : nucleic and proteic sequence analysis (determining functional and structural properties based on primary sequences, search for common characteristics among a collection of sequences, …), management of genomic information (annotation), approaches to predict tridimensional structure of proteins (“threading”, analogy,…), interactions between molecules, images analyses, modeling.

Assessment / evaluation : :

The evaluation consists in a written report of an informatics project (in Python).

Course material (hand-outs, online presentation available, …) :
Suggested readings in relationship with the module content (textbook chapters, reviews, articles) :


2) Computational Biology project

ECTS : 6 for the Master

The project will be started as early as possible in the semester, by aking contacts with the researchers, understanding the project and preparing it. In addition, time will be allocated to progress on the project during the whole weeks of 5th and 12th December.

Prerequisites for the project :

The project has a limited number of places. Students with a basic level of programming at M1 entry may have more difficulties because the project necessitate to be already at ease with programming (bash or Pyhton or R). Priority will be given to students with a good level in programming.

Course objectives and description :

Researchers in IBENS will provide projects to be conducted with them, by groups of 2. The pedagogic team will also ensure guidance. The aim is to perform a short scientific project in computational biology, the subjects are very large (genomics, imaging, neurocomputing...)

Assessment / evaluation : :

The evaluation consists in a written report and oral presenation in January.