Section outline

• Select section General

  General

  Collapse all Expand all

  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.
• Select section Technical / software prerequisite

  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:

  https://cran.r-project.org/web/packages/SNFtool/index.html

  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")
• Select section Programme

  Programme

  Day 1 – Tuesday 15^th 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 16^th 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 17^th 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)