INFO2053-1 : Introduction to Programming under Linux

Study Programmes 2015-2016

INFO2053-1

Introduction to Programming under Linux - Part B

Duration :

10h Th, 30h Mon. WS

Number of credits :

Master in biochemistry and molecular and cell biology (120 ECTS)		4
Master in biochemistry and molecular and cell biology (120 ECTS)		4

Lecturer :

Denis Baurain

Language(s) of instruction :

French language

Organisation and examination :

Teaching in the second semester

Units courses prerequisite and corequisite :

Prerequisite or corequisite units are presented within each program

Course contents :

1. Linux

UNIX environment (Bio-Linux)
text files and file formats
CLI features (jokers, variables, loops, history...)
bash shell

2. Perl

Perl basics and Modern Perl
Perl Object-Oriented Programming using Moose
Perl for Bioinformatics (Bioperl, Ensembl Perl API)

3. other Open Source technologies

LaTeX (XeTeX) and co
WWW programming (HTML/CSS and PHP)

Learning outcomes of the course :

This course is the first of three courses -- "Introduction to linux programming" [INFO0097-2], "Introduction to databases for biology" [INFO0099-2], "Introduction to algorithms in bioinformatics" [INFO0094-3] -- taught by the same teacher in the context of the specialized approach in bioinformatics of M2-BBMC. The course "Introduction to biological data analysis" [INFO0115-2] by Prof. Patrick Meyer shares the same goals. At the end of this series of courses, students will be able to use the computer as a scientific instrument. More specifically, they will have been trained towards the following objectives: 1. Experimental design

how to choose appropriate controls
how to think in a statistical framework

2. Conducting experiments

how to run large series of analyzes
how to harness the power of grid computing

3. Interpretation of results

how to automate the analysis of output files
how to generate informative but nice looking graphs
how to draw statistically sound conclusions

4. Documentation and archiving

how to document experimental protocols
how to reorganize a series of past analyzes
how to manage multiple versions of the data sets, of the required programs and of the generated results

Prerequisite knowledge and skills :

This course is part of a specialized approach in bioinformatics. Even if it requires no special knowledge in computer science, it is nevertheless based on the Genomics [GENE0003-1] and Bioinformatics [BIOL0008-1] courses of the M1-BBMC.

Planned learning activities and teaching methods :

brief theoretical lectures
challenges to solve
computer practicals
self-learning (textbooks and online tutorials)

Mode of delivery (face-to-face ; distance-learning) :

This course is partly face-to-face but as a problem-oriented course, it will require that students work also outside of the classroom.