Gephi101-Ryan2012x

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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”


THEN: anyone can write code to put data into that
format or take data from that format


GEXF (Graph Exchange

XML

Format)




circa 2007, GEPHI project


Specifically intended as interchange format


<?
xml version="1.0" encoding="UTF
-
8"?>


<
gexf

xmlns
="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
>

http://gexf.net/format/

GraphML

Format


Circa 2000/2001


An XML specification for network data


<?xml version="1.0" encoding="UTF
-
8"?>

<
graphml

xmlns
=
http://graphml.graphdrawing.org/xmlns

xmlns: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
>

http://graphml.graphdrawing.org/

Pajek

.net

Format


Pajek

is a free network

analysis software tool


Circa 1990s


Simple text files


Lots of features beyond

simple adjacency,

attributes and weights

*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

Vertex
Attributes

Edge Weights

GDF


Used by GUESS (an open source Graph
Exploration System

http://graphexploration.cond.org/index.html

nodedef
> name

a

b

c

d

edgedef
> node1,node2

a,b

a,c

a,d

GML: Graph
Modelling

Language


Circa 2000s


text file
format


University Passau?

graph

[



node



[



id A



]



node



[



id B



]



node



[



id C



]



edge



[



source B



target A



]



edge



[



source C



target A



]

]

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_source

id_target
)

)

The GEPHI GUI


Intended to be flexible

GEPHI > IMPORT




Select vertex and
show its edges

Drag a vertex

Select vertices in
a square

FILE

Windows

New Project

Create a new
project.

Clustering

Runs

a clustering algorithm on the graph

Open

Open
existing
project or graph
file.

Context

Display number of nodes/edges, type of
graph and percentage of visible nodes.

Close Project

Close the project.

Data table

See and manipulate

vertex and edge data.

Properties

Project information.

Import Database

Graph import from a database connection.

Graph

“Rough

draft” of network visualization.

Import Spigot

Graph import from an external
source.

Filters

Set parameters for real
-
time

filtering of
nodes and edges.

Generate

Create a graph from a
calculated model.

Layout

Save & Save As

Save
current
project.

Partition

Node/edge grouping/coloring on attribute
or computed metric.

Export

Create a graph
or

image file in other format
.

Preview

Exit

Close the software.

Rankings

Set numerical thresholds/
cutpoints

to
assign node/edge colors, sizes, label colors
and label sizes.

Statistics

Compute node/edge

metrics (centrality,
etc.).