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 training@sib.swiss.

    • 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:
        source("http://bioconductor.org/biocLite.R")
        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"))
        install.packages("WGCNA")
      R package: SNFtool
      1) Download either the source (Linux) or Mac OSX/Windows binaries from the CRAN directory:
      SNFtool_2.2.zip (Windows)
      SNFtool_2.2.tgz (OSX)
      SNFtool_2.2.tar.gz (Linux)
      2) Launch R and install the required package heatmap.plus

      R
      install.packages("heatmap.plus")
      # Exit R

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

      For MacOSX/Windows:
      unzip SNFtool_2.2.tgz 
      or
      unzip SNFtool_2.2.zip
      R CMD INSTALL SNFtool
      For Linux:
      tar -vxzf SNFtool_2.2.tar.gz
      R CMD INSTALL SNFtool

      4) Launch R and load the library
      library("SNFtool”)

      RStudio with Markdown
      1) Download and install RStudio from https://www.rstudio.com/
      2) Install Markdown package
      Launch RStudio
      install.packages("markdown")

      • 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)