Download FCModeler User`s Manual

Table of Contents
1
2
3
4
5
6
7
Introduction to FCModeler ..................................................................................................... 5
FCModeler Installation ........................................................................................................... 5
2.1
Customizing the Configuration....................................................................................... 5
2.2
Running FCModeler ....................................................................................................... 5
Sources of Input ...................................................................................................................... 6
3.1
Zipped Graph Archives................................................................................................... 6
3.1.1
contents.xml ............................................................................................................ 6
3.1.2
topology.xml ........................................................................................................... 6
3.1.3
index.xml ................................................................................................................ 6
3.1.4
extended.xml........................................................................................................... 6
3.1.5
pathways.xml .......................................................................................................... 6
3.2
Individual Files ............................................................................................................... 7
3.2.1
Mappings................................................................................................................. 7
3.2.2
Coordinates ............................................................................................................. 7
3.2.3
Animation ............................................................................................................... 7
3.3
Reading and Writing Graphs in FCModeler................................................................... 7
3.3.1
Reading a Zipped Graph Archive ........................................................................... 7
3.3.2
Saving a Graph XML File....................................................................................... 8
3.3.3
Saving an Image of the Graph ................................................................................ 8
Graph Layout .......................................................................................................................... 9
4.1
Simple Dot Layout.......................................................................................................... 9
4.2
Rank-Cluster Dot Layout................................................................................................ 9
4.2.1
Layout XML File .................................................................................................. 10
4.3
GEM Layouts................................................................................................................ 11
4.3.1
GEM...................................................................................................................... 11
4.3.2
AGEM................................................................................................................... 12
4.3.3
FastGEM ............................................................................................................... 13
Interacting with the Graph View........................................................................................... 13
5.1
Selecting Nodes and Edges........................................................................................... 13
5.2
Node Operations ........................................................................................................... 13
5.2.1
Modifying Node Information................................................................................ 13
5.2.2
Adding New Nodes............................................................................................... 14
5.2.3
Deleting Existing Nodes ....................................................................................... 15
5.3
Edge Operations............................................................................................................ 15
5.3.1
Modifying Edge Information ................................................................................ 16
5.3.2
Adding New Edges ............................................................................................... 17
5.3.3
Deleting Existing Edges........................................................................................ 17
5.4
Moving Nodes and Edges ............................................................................................. 17
5.5
Zooming........................................................................................................................ 18
5.6
Finding a Particular Node ............................................................................................. 18
Using the Identify Node Dialog ................................................................................... 19
Node and Edge Properties..................................................................................................... 20
7.1
Viewing Properties with the Property Viewer..................................................... 20
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