attachment:ba_model.py of ScriptingPlugins

Attachment 'ba_model.py'

   1 from cytoscape import Cytoscape
   2 
   3 import cytoscape.layout.CyLayouts as CyLayouts
   4 import java.lang.Integer as Integer
   5 import random
   6 
   7 ORIGINAL_NODES = 2
   8 MAX_LOOP = 1000 - ORIGINAL_NODES
   9 EACH_TRIAL = 2
  10 
  11 # Create network
  12 graph = Cytoscape.createNetwork("Barabasi-Albert generated by Python Script");
  13 
  14 #Create seed graph
  15 node1 = Cytoscape.getCyNode("Seed 1", True)
  16 node2 = Cytoscape.getCyNode("Seed 2", True)
  17 nodes = [node1, node2]
  18 
  19 graph.addNode(node1)
  20 graph.addNode(node2)
  21 edge = Cytoscape.getCyEdge(node1, node2, "interaction", "-", True);
  22 graph.addEdge(edge);
  23 
  24 degree = 0.0
  25 prob = 0.0
  26 i = 0
  27 
  28 # Grow the seed graph
  29 print "\n\n============Barabasi-Albert Random Graph Generator ============"
  30 print "\nGenerating network (1000 nodes).  Please wait..."
  31 
  32 while (i<MAX_LOOP) :
  33     newNode = Cytoscape.getCyNode(Integer.toString(i), True)
  34     graph.addNode(newNode)
  35     
  36     j = 0
  37     while (j<EACH_TRIAL):   
  38         created = False
  39         while (created == False):
  40             idx = random.random() * len(nodes)
  41             selectedNode = nodes[int(idx)]
  42             degree = graph.getDegree(selectedNode)
  43             prob = (degree + 1.0) / (graph.getNodeCount() + graph.getEdgeCount() - 1.0)
  44             if prob >= random.random() and newNode.getIdentifier != selectedNode.getIdentifier:
  45                 created = True;
  46         
  47         edge = Cytoscape.getCyEdge(newNode, selectedNode, "interaction", "-", True)
  48         graph.addEdge(edge)
  49         nodes.append(newNode)
  50         j = j+1        
  51     
  52     i = i+1
  53 
  54 # Layout nodes
  55 
  56 print "Network generated.  Start layout..."
  57 
  58 CyLayouts.getLayout("force-directed").doLayout();
  59 Cytoscape.getCurrentNetworkView().redrawGraph(False, True);
  60 
  61 print "\n\nDone!"
  62 

Attached Files

• [get | view] (2011-10-20 20:44:43, 1.7 KB) [[attachment:ba_model.py]]
• [get | view] (2011-10-20 20:44:43, 1.4 KB) [[attachment:ba_model_generator.rb]]
• [get | view] (2011-10-20 20:44:43, 0.6 KB) [[attachment:complete_graph.js]]
• [get | view] (2011-10-20 20:44:43, 0.9 KB) [[attachment:dialog.js]]
• [get | view] (2011-10-20 20:44:43, 64.3 KB) [[attachment:groovyEngine1.png]]
• [get | view] (2011-10-20 20:44:43, 0.2 KB) [[attachment:hello_cytoscape.js]]
• [get | view] (2011-10-20 20:44:43, 0.2 KB) [[attachment:hello_cytoscape.rb]]
• [get | view] (2011-10-20 20:44:43, 5.7 KB) [[attachment:javascriptSample1.png]]
• [get | view] (2011-10-20 20:44:43, 291.8 KB) [[attachment:javascriptSample2.png]]
• [get | view] (2011-10-20 20:44:43, 70.6 KB) [[attachment:javascriptSample3.png]]
• [get | view] (2011-10-20 20:44:43, 59.0 KB) [[attachment:javascriptSample4.png]]
• [get | view] (2011-10-20 20:44:43, 1.7 KB) [[attachment:kegg_sample1.rb]]
• [get | view] (2011-10-20 20:44:43, 0.4 KB) [[attachment:load_multiple_networks.rb]]
• [get | view] (2011-10-20 20:44:43, 0.6 KB) [[attachment:matrix.rb]]
• [get | view] (2011-10-20 20:44:43, 5.4 KB) [[attachment:matrix1.png]]
• [get | view] (2011-10-20 20:44:43, 49.2 KB) [[attachment:pythonEngine1.png]]
• [get | view] (2011-10-20 20:44:43, 286.7 KB) [[attachment:pythonEngine2.png]]
• [get | view] (2011-10-20 20:44:43, 116.9 KB) [[attachment:rubyConsole1.png]]
• [get | view] (2011-10-20 20:44:43, 64.2 KB) [[attachment:rubyConsole2.png]]
• [get | view] (2011-10-20 20:44:43, 19.6 KB) [[attachment:rubyEngine.png]]
• [get | view] (2011-10-20 20:44:43, 12.1 KB) [[attachment:rubySample1.png]]
• [get | view] (2011-10-20 20:44:43, 136.9 KB) [[attachment:rubySample2.png]]
• [get | view] (2011-10-20 20:44:43, 194.9 KB) [[attachment:rubySample3.png]]
• [get | view] (2011-10-20 20:44:43, 284.7 KB) [[attachment:rubySample4.png]]
• [get | view] (2011-10-20 20:44:43, 1.8 KB) [[attachment:sample_human_network.sif]]
• [get | view] (2011-10-20 20:44:43, 45.6 KB) [[attachment:scripting1.png]]
• [get | view] (2011-10-20 20:44:43, 343.9 KB) [[attachment:scripting2.png]]
• [get | view] (2011-10-20 20:44:43, 1.1 KB) [[attachment:social_graph.js]]
• [get | view] (2011-10-20 20:44:43, 2.7 KB) [[attachment:social_graph_new.js]]
• [get | view] (2011-10-20 20:44:43, 120.9 KB) [[attachment:twitterSample1.png]]
• [get | view] (2011-10-20 20:44:43, 324.2 KB) [[attachment:twitterSample2.png]]

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