* Slides:
  * [[attachment:EMBLCytoscapeWorkshop-Part1-Sep2010.pptx]] - !PowerPoint format

  * [[attachment:EMBLHeidelbergCytoscapeCourse.pdf]] - PDF format

  * [[attachment:EMBLCytoscapeWorkshop-Part2-Dev-Sep2010.ppt]] - !PowerPoint format

 * Introductory Cytoscape tutorial: http://opentutorials.rbvi.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape
  * To follow during the first lab

 * Collaborative course notes: https://docs.google.com/document/edit?id=117SJMdDmaih39iBLCrFIvwvPuDS5z6_tztnVYJZb3rM&hl=en&authkey=CJKno5oC
  * Have anything to share with others in the course? Feel free to add it to this document.

 * Background reading:
  * [[http://www.ncbi.nlm.nih.gov/pubmed/19816451|How to visually interpret biological data using networks]]
  * [[http://www.ncbi.nlm.nih.gov/pubmed/17947979|Integration of biological networks and gene expression data using Cytoscape.]]
  * [[http://www.ncbi.nlm.nih.gov/pubmed/14597658|Cytoscape: a software environment for integrated models of biomolecular interaction networks.]]


 * Multiple Testing Correction tutorial
  * [[http://www.silicongenetics.com/Support/GeneSpring/GSnotes/analysis_guides/mtc.pdf]]

 * Some interesting networks made with cytoscape
  * [[attachment:yeast-map_large.jpg|Genetic landscape of the cell]], BooneLab, (Sciencepaper: http://www.ncbi.nlm.nih.gov/pubmed/20093466)

 * Additional datafiles
  * [[attachment:NOTCH3-knockout-timeseries.xgmml|Gene knockout timeseries]]
  * [[attachment:TimeseriesPluginSrc.rar|Sample src for TimeSeriesPlugin (note, to have it working needs a database, serves as sample code only)]]

 * Cytoscape source code
  * http://chianti.ucsd.edu/svn/