Topic outline

  • General

    Introduction to Biological Network Analysis

    Lausanne, 15-17 November 2016

    Location: Génopode Building, room 2020

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact

  • Technical / software prerequisite

    Participants must bring a laptop and install the following:

    • 64-bit Java 8
    • the latest version of the R, R Studio and Cytoscape software installed.
    • the R package WGCNA and some Bioconductor packages that are used by WGCNA using these commands:
      biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore"))
      install.packages(c("gtable", "munsell", "plyr", "RColorBrewer", "stringr","digest"))
      install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))
    R package: SNFtool
    1) Download either the source (Linux) or Mac OSX/Windows binaries from the CRAN directory: (Windows)
    SNFtool_2.2.tgz (OSX)
    SNFtool_2.2.tar.gz (Linux)
    2) Launch R and install the required package

    # Exit R

    3) Unzip/unpack the archive and move SNFtool folder to a new directory

    For MacOSX/Windows:
    unzip SNFtool_2.2.tgz 
    For Linux:
    tar -vxzf SNFtool_2.2.tar.gz

    4) Launch R and load the library

    RStudio with Markdown
    1) Download and install RStudio from
    2) Install Markdown package
    Launch RStudio

  • Programme

    Day 1 – Tuesday 15th November 2016

    08:30-09:00              Welcome coffee

    Morning - Short Symposium on Network analysis (9h-12h)

    09:00-09:30              Introduction (SIB)
    09:30-10:30              Introduction to the Analysis and Visualization of Biological Networks (Scooter Morris)
    10:30-11:00              Break
    11:00-12:00              Linking network connectivity information to biologically relevant knowledge (Francisco Azuaje)
    12:00-13:00              Systems Biology & Networks in Diabetes (Mark Ibberson)

    Afternoon – Practical on network visualization and analysis in Cytoscape

    14:00-17:00              Network Visualization and analysis with Cytoscape (Scooter Morris)
    19:00                         Social dinner - Les Brasseurs, Rue Centrale 4, Lausanne


    Day 2 – Wednesday 16th November 2016

    Morning – Weighted gene correlation network analysis (WGCNA)

    09:00-10:30              WGCNA theory 1 (SIB)
    10:30-11:00              Break
    11:00-13:00              WGCNA practical 1 (SIB)

    Afternoon – Weighted gene correlation network analysis (WGCNA)

    14:00-15:30              WGCNA theory 2 (SIB)
    15:30-16:00              Break
    16:00-17:30              WGCNA practical 2 (SIB)


    Day 3 – Thursday 17th November 2016

    Morning – Similarity Network Fusion (SNF) - A short course (theory and practicals)

    09:00-10:30              SNF introduction and overview (SIB)
    10:30-11:00              Break
    11:00-13:00              SNF tutorial parts 1 & 2 (SIB)

    Afternoon – Similarity Network Fusion (SNF) - A short course (practicals)

    14:00-15:30              SNF tutorial part 3 (SIB)
    15:30-16:00              Break
    16:00-17:30              SNF tutorial parts 4 & 5 (SIB)