FCModeler User’s Manual Version 1.0 September 2002 Written by Zach Cox Julie Dickerson Adam Tomjack Copyright Julie Dickerson, Iowa State University 2002 Table of Contents 1 Introduction to FCModeler .....................................................................................................1 2 Setting Up FCModeler............................................................................................................ 1 2.1 Setting up the FCModelerConfig File............................................................................. 1 2.2 Running FCModeler....................................................................................................... 1 3 Sources of Input ...................................................................................................................... 1 3.1 Graph XML Files............................................................................................................ 1 3.1.1 XML Format ........................................................................................................... 1 3.1.2 Example of a Complete XML File.......................................................................... 5 3.1.3 Opening a Graph XML File.................................................................................... 6 3.1.4 Saving a Graph XML File....................................................................................... 7 3.1.5 Saving a JPEG Image of the Graph ........................................................................ 8 3.2 MySQL Database............................................................................................................ 8 4 Graph Layout.......................................................................................................................... 8 4.1 Simple Dot Layout.......................................................................................................... 8 4.2 Rank-Cluster Dot Layout................................................................................................ 9 4.2.1 Layout XML File .................................................................................................... 9 4.3 GEM Layout(s)............................................................................................................. 10 5 Interacting with the Graph View........................................................................................... 12 5.1 Selecting Node and Edge Figures................................................................................. 12 5.2 Node Figures................................................................................................................. 13 5.2.1 Adding................................................................................................................... 13 5.2.2 Deleting................................................................................................................. 13 5.2.3 Moving.................................................................................................................. 13 5.3 Edge Figures................................................................................................................. 13 5.3.1 Adding................................................................................................................... 14 5.3.2 Modifying ............................................................................................................. 14 5.3.3 Deleting................................................................................................................. 14 5.3.4 Moving.................................................................................................................. 14 5.4 Zooming........................................................................................................................ 15 5.5 Panning ......................................................................................................................... 15 5.6 Finding a Particular Node ............................................................................................. 15 6 Mappings............................................................................................................................... 15 6.1 Node and Edge Properties............................................................................................. 15 6.1.1 Property Viewer.................................................................................................... 16 6.2 Visual Attributes of Node and Edge Figures ................................................................ 17 6.3 Using Visual Attributes to Visualize Properties ........................................................... 17 6.4 Creating Mappings Using the Mapping Editor............................................................. 18 7 Animation ............................................................................................................................. 19 7.1 XML File Format.......................................................................................................... 19 7.2 Controls......................................................................................................................... 21 8 Graph Theoretic Operations.................................................................................................. 21 8.1.1 Subgraph Creation................................................................................................ 21 8.1.2 Strongly Connected Components ......................................................................... 22 ii 8.1.3 Cycle Search......................................................................................................... 23 8.1.4 Cycle XML Files................................................................................................... 24 8.2 Alternate Paths between Nodes .................................................................................... 25 8.3 Clustering Cycles.......................................................................................................... 25 9 FCModeler and R.................................................................................................................. 28 10 References......................................................................................................................... 28 10.1 Publications relating to FCModeler.............................................................................. 28 10.2 Open Source Code Used in FCModeler........................................................................ 28 List of Figures Figure 1. The open graph dialog box............................................................................................. 7 Figure 2. The save graph dialog box.............................................................................................. 7 Figure 3. Simple dot layout............................................................................................................ 8 Figure 4. Rank-cluster dot layout................................................................................................... 9 Figure 5: Example of a GEM layout............................................................................................. 11 Figure 6 shows the manipulation of node and edge objects in FCModeler.................................. 14 Figure 7 shows how to save graph coordinates using the save function under the File menu. .... 15 Figure 8. Property viewer showing property values of selected nodes and edges....................... 17 Figure 9. Mapping editor. ............................................................................................................ 18 Figure 10. Animation control....................................................................................................... 21 Figure 11. The subgraph creation dialog box. ............................................................................. 22 Figure 12 Example of selecting cycles and strongly connected components as subgraphs. ........ 23 Figure 13. The cycle search dialog box. ...................................................................................... 24 Figure 14. Map view showing results of the SOM algorithm. Each graph shows the model of the corresponding map unit, which is the generalized median of the cycles assigned to that map unit. ............................................................................................................................... 26 Figure 15. Full view of the bottom-left map unit, showing ten cycles clustered together........... 27 iii 1 Introduction to FCModeler FCModeler models and visualizes metabolic networks as graphs. Nodes of the graph represent specific biochemicals such as proteins, RNA, and small molecules, or stimuli, such as light, heat, or nutrients. Edges of the graph capture regulatory and metabolic relationships found in biological systems. FCModeler can dynamically display user-specified graphs and animate the results of different modeling algorithms on the graph. The fuzzy cognitive map modeling software is currently written in Matlab and interfaces with FCModeler via xml graph files. We plan to translate this software at a later date. 2 Setting Up FCModeler The FCModeler distribution is compatible with Windows 2000/XP and Linux machines. Download the file and unzip into your directory. This version is already compiled and the Java source code is included. If you make any improvements to the