Download Cell Illustrator User Guide

TABLE OF CONTENTS:
1 INTRODUCTION............................................................................................4
2 GETTING STARTED......................................................................................5
2.1 Cell Illustrator Online and Desktop Versions...............................................5
2.2 Run Cell Illustrator Online (CIO)..................................................................5
2.3 Install and Run Cell Illustrator (desktop version).........................................6
2.4 Licensing Information...................................................................................8
2.5 Command Line Simulation Engine..............................................................9
2.6 CI Memory Customization......................................................................... 10
3 CELL ILLUSTRATOR ELEMENTS............................................................. 11
3.1 Concept Overview......................................................................................11
3.2 Entities.......................................................................................................12
3.3 Connectors.................................................................................................13
3.4 Processes..................................................................................................14
3.5 Element Combinations ..............................................................................15
3.6 Discrete Elements Example 1....................................................................17
3.7 Discrete Elements Example 2: Connector Speed..................................... 18
3.8 Continuous Elements Example 1.............................................................. 19
3.9 Continuous Elements Example 2.............................................................. 21
4 BIOLOGICAL PROCESS MODELING WITH CELL ILLUSTRATOR.........24
4.1 Degradation...............................................................................................24
4.2 Translocation.............................................................................................26
4.3 Transcription..............................................................................................27
4.4 Complex.....................................................................................................29
4.5 Tetramerization..........................................................................................32
4.6 Stochastic Tetramerization........................................................................33
4.7 Custom Tetramerization............................................................................ 34
4.8 Separation..................................................................................................35
4.9 Inhibition.....................................................................................................37
4.10 Catalysis..................................................................................................39
5 CELL ILLUSTRATOR USER INTERFACE AND MODEL CREATION...... 43
5.1 Add Elements.............................................................................................43
5.2 Modify a Model ..........................................................................................44
5.3 Change Element Properties ....................................................................45
5.4 Element Settings Dialog and Element Lists Dialog................................... 47
5.5 Biological Elements and Pathway Fragments...........................................54
5.6 Script Editor and Pnuts Scripts..................................................................58
5.7 Preferences Dialog....................................................................................62
5.8 Graph Layout Dialog..................................................................................63
© 2002-2008 GNI Ltd. and Human Genome Center, Institute of
Medical Science, The University of Tokyo. All rights reserved.
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