SYSTEMS BIOLOGY - ONLINE

Prof. Patrick Meyer

Objective

The goal of this course is to give students a clear idea of what is systems biology.
Classical principles and tools will be presented in a set of five lectures (2h each).
Each lecture is followed by a practical session allowing students to learn, use and understand the tools discussed (2h each).
An additional set of hours are dedicated to interactive sessions and/or interrogations.
At the end of this course students should be able, not only to use tools and explain key concepts but also to read and understand scientific papers of the field.

Exam

The exam is typically oral (either online or face to face) where a set of theoretical questions are asked.
Written interrogations can be performed during the year (before the exam).

Tools

As a reminder: Rstudio Server - Practical Setup
Prerequisite course: Introduction to R
Prerequisite biology: Short biological reminder

Lectures

Introduction to the online course
Videos 1A on defining systems biology Videos 1B on computer architecture	Exercises 1	Solutions 1
Videos 2 on Flux Balance Analysis (FBA)	Exercises FBA [PDF]	Solutions FBA [PDF]
Videos 3A on inference Videos 3B on the igraph package	Exercises 3	Solutions 3
Videos 4 on network validation	Exercises 4	Solutions 4
Videos 5A on improving inference Videos 5B on making discoveries	Exercises 5	Solutions 5

References

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.
The modENCODE Consortium et al.
In Science (AAAS), 2010.
MINET: An open source R/Bioconductor Package for Mutual Information based Network Inference.
Patrick E. Meyer, Frederic Lafitte and Gianluca Bontempi.
In BMC Bioinformatics, Volume 9, 2008.
https://igraph.org/

Questions ?

1- Forums ecampus (for every question, answers are fast)
2- Assistant (especially for server/machine issues): bioinformatics@uliege
3- Prof. Patrick Meyer (especially for the theory or the evaluation system... but answers may take some time): Patrick.Meyer@uliege