• DEMA: an algorithm to model and layout biomolecular networks with quantitative properties

  • DEMA (Distance-bounded Energy-field Minimization Algorithm) is a plugin of Cytoscape for data visualization. By generating a layout according to the network information, data analyst can use the layout to perceive the data relations.
  • Installing

  • Install Cytoscape of version ≥ 3.4.0.
    Put the DEMA plugin file in the folder CytoscapeConfiguration\3\apps\installed.
  • Usage

  • Open Cytoscape, import the files, and launch the DEMA plugin. The necessary file is the protein-protein interaction (PPI) network file. By importing the PPI network file, DEAM will show a basic layout. Read the tutorial for details on various available options.
  • Test Models

  • Base model Layout
  • input file:
  • Base model PPI link
  • Advance model Layout with grouping
  • input file
  • Advance model PPI link
    Advance node link
  • Optional file
  • Advance node set color file link