Cell Illustrator™: Reference Manual

 

 

 

 

 

 

 

 

 

 

 

 

© 2002-2006 GNI Ltd. and Human Genome Center, Institute of Medical Science, The University of Tokyo

All rights reserved.

           


Table of contents:

1      Introduction.. 4

2      Biopathway Modeling Mode.. 6

2.1       Switching to the Biopathway Modeling Mode. 6

2.2       Differences between Gene Network and Biopathway Modeling Modes. 7

2.3       Documentation for Gene Network Mode. 8

3      Workspace - Main Window of CI 9

3.1       Menu Bar Commands. 10

3.2       CI Toolbars. 52

4      Drawing Canvas.. 57

4.1       Canvas Popup Menus. 57

5      Element Lists.. 60

6      Element Settings.. 64

6.1       Model and Canvas Property Sheet. 65

6.2       Entity Property Sheets. 65

6.3       Process Property Sheets. 67

6.4       Connector Property Sheets. 74

6.5       Object Property Sheets. 76

7      Navigator.. 77

8      Simulation Settings.. 78

9      Chart Settings.. 80

10        Chart Window... 82

11        Preferences.. 85

12        View Settings.. 86

13        Finder.. 87

14        Biological Elements.. 89

15        Simulation History.. 91

16        Graph Layout.. 93

16.1    Graph Layout Algorithms. 94

17        Edit Units.. 96

18        Submitted Simulations.. 98

19        Setup Servers.. 99

20        Print Model.. 100

21        Print Area Setup.. 101

22        Print Area Selection.. 102

23        External References.. 103

24        Add/Edit References.. 104

25        Edit Parts Dialogs.. 105

26        KEGG-BioPACS.. 109

27        Save Dialog.. 110

28        Script Editor.. 112

29        Pathway Search.. 114

29.1    Search From Combo Box. 114

29.2    Search To Combo Box. 115

30        Pathway Search Results.. 117

31        Gene Mining.. 118

32        About Cell Illustrator.. 121