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Gephi 101

Gephi 101. Dan Ryan Mills College Spring 2012. What is XML?. Circa 1997/9 E x tensible M arkup L anguage  a  markup language for encoding/transmitting/storing data both  human-readable and machine-readable.  A “schema” says “this kind of data has this format”

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Gephi 101

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  1. Gephi 101 Dan Ryan Mills College Spring 2012

  2. What is XML? • Circa 1997/9 • Extensible Markup Language  • a markup language • for encoding/transmitting/storing data • both human-readable and machine-readable.  • A “schema” says “this kind of data has this format” • THEN: anyone can write code to put data into that format or take data from that format

  3. GEXF (Graph Exchange XML Format) http://gexf.net/format/ • circa 2007, GEPHI project • Specifically intended as interchange format <?xml version="1.0" encoding="UTF-8"?> <gexfxmlns="http://www.gexf.net/1.2draft" version="1.2"> <meta lastmodifieddate="2009-03-20"> <creator>Gexf.net</creator> <description>A hello world! file</description> </meta> <graph mode="static" defaultedgetype="directed"> <nodes> <node id="0" label="Hello" /> <node id="1" label="Word" /> </nodes> <edges> <edge id="0" source="0" target="1" /> </edges> </graph> </gexf>

  4. GraphML Format http://graphml.graphdrawing.org/ • Circa 2000/2001 • An XML specification for network data <?xml version="1.0" encoding="UTF-8"?> <graphmlxmlns=http://graphml.graphdrawing.org/xmlnsxmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"> <graph id="G" edgedefault="undirected"> <node id="n0"/> <node id="n1"/> <node id="n2"/> <node id="n3"/> <node id="n4"/> <edge source="n0" target="n2"/> <edge source="n1" target="n2"/> <edge source="n2" target="n3"/> <edge source="n3" target="n4"/> </graph> </graphml>

  5. Pajek.net Format Vertex Attributes *Vertices 6 1 "1" 0.3034 0.7561 2 "2" 0.4565 0.6039 3 "3" 0.4887 0.8188 4 "4" 0.5687 0.4184 5 "5" 0.3574 0.4180 6 "6" 0.7347 0.2678 *Arcs *Edges 1 2 1 1 3 1 2 3 1 2 4 1 2 5 1 4 5 1 4 6 1 • Pajek is a free networkanalysis software tool • Circa 1990s • Simple text files • Lots of features beyond simple adjacency, attributes and weights Edge Weights

  6. GDF • Used by GUESS (an open source Graph Exploration System nodedef> name a b c d edgedef> node1,node2 a,b a,c a,d http://graphexploration.cond.org/index.html

  7. GML: Graph Modelling Language graph[  node  [   id A  ]  node  [   id B  ]  node  [   id C  ]   edge  [   source B   target A  ]  edge  [   source C   target A  ]] • Circa 2000s • text file format • University Passau?

  8. TLP • C. 2007 • “Tulip is an information visualization framework dedicated to the analysis and visualization of relational data.” • (tlp "2.0“ • (nodes id_node1 id_node2 ...) • (edge id id_sourceid_target) • )

  9. The GEPHI GUI • Intended to be flexible

  10. GEPHI > IMPORT

  11. Select vertex and show its edges Select vertices in a square Drag a vertex

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