Cell Illustrator™: Reference Manual© 2002-2017 Human Genome Center, Institute of Medical Science,
The University of Tokyo
All rights reserved.

TABLE OF CONTENTS:
CELL ILLUSTRATOR™: REFERENCE MANUAL .............................................. 1
1

INTRODUCTION ................................................................................................. 7

2 BIOPATHWAYS AND GENE NET MODEL................................................... 8
2.1
Differences between Gene Net and Biopathway Model ........................... 8
2.2
Documentation................................................................................................. 93

MAIN WINDOW................................................................................................. 10

4 MENU BAR ........................................................................................................ 11
4.1
File | New ........................................................................................................ 11
4.2
File | Open ...................................................................................................... 11
4.3
File | Open Recent Files ............................................................................... 12
4.4
File | Close File .............................................................................................. 13
4.5
File | Close All Files ...................................................................................... 13
4.6
File | Save ....................................................................................................... 13
4.7
File | Save As ................................................................................................. 13
4.8
File | Insert ...................................................................................................... 14
4.9
File | Export .................................................................................................... 14
4.10 File | Export All ............................................................................................... 16
4.11 File | Export to Cytoscape ............................................................................ 16
4.12 File | Look & Feel .......................................................................................... 17
4.13 File | Print Visible Area ................................................................................. 17
4.14 File | Print........................................................................................................ 17
4.15 File | Exit ......................................................................................................... 18
4.16 Edit | Undo ...................................................................................................... 18
4.17 Edit | Redo ...................................................................................................... 18
4.18 Edit | Cut ......................................................................................................... 18
4.19 Edit | Copy ...................................................................................................... 19
4.20 Edit | Paste ..................................................................................................... 19
4.21 Edit | Paste View Style ................................................................................. 19
4.22 Edit | Delete .................................................................................................... 20
4.23 Edit | Duplicate ............................................................................................... 20
4.24 Edit | Extract ................................................................................................... 20
4.25 Edit | Find........................................................................................................ 20
4.26 Edit | Select All ............................................................................................... 21
4.27 Edit | Select None.......................................................................................... 21
4.28 Edit | Select Inverse ...................................................................................... 21
4.29 Edit | Align To Grid ........................................................................................ 21
4.30 Edit | Align To ................................................................................................. 22
4.31 Edit | Move To ................................................................................................ 22
4.32 Edit | Insert Entity .......................................................................................... 23© 2002-2017 The University of Tokyo. All rights reserved.

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4.33
4.34
4.35
4.36
4.37
4.38
4.39
4.40
4.41
4.42
4.43
4.44
4.45
4.46
4.47
4.48
4.49
4.50
4.51
4.52
4.53
4.54
4.55
4.56
4.57
4.58
4.59
4.60
4.61
4.62
4.63
4.64
4.65
4.66
4.67
4.68
4.69
4.70
4.71
4.72
4.73

Edit | Insert Process ...................................................................................... 23
Edit | Insert Image ......................................................................................... 23
Edit | Insert Text ............................................................................................ 24
Edit | Insert Frame ......................................................................................... 24
Element | Show All ........................................................................................ 24
Element | Hide ............................................................................................... 24
Element | Element Type ............................................................................... 25
Element | Connector Type ........................................................................... 25
Element | Reverse Direction ........................................................................ 26
Element | Arrange ......................................................................................... 26
Element | Group ............................................................................................ 26
Element | Ungroup ........................................................................................ 27
Element | Size ................................................................................................ 27
Element | Fill Color ........................................................................................ 27
Element | Line Color ..................................................................................... 27
Element | Line Style ...................................................................................... 28
Element | Stroke ............................................................................................ 28
Element | Remove All Anchors ................................................................... 28
Element | Set Image ..................................................................................... 29
Element | Set Image Type ........................................................................... 29
Element | Edit Image .................................................................................... 29
Element | Resize Image ............................................................................... 29
Element | Edit Chemical Structure.............................................................. 30
Element | References ................................................................................... 30
Element | URL Templates ............................................................................ 31
Element | Label .............................................................................................. 31
Element | Show Name .................................................................................. 32
Element | Show Variable .............................................................................. 32
Element | Show Value .................................................................................. 32
Element | Show Firing Style ........................................................................ 32
Element | Log ................................................................................................. 33
Element | Create Chart ................................................................................. 33
Element | Update Location .......................................................................... 33
Simulation | Play ............................................................................................ 33
Simulation | Step Play .................................................................................. 34
Simulation | Pause ........................................................................................ 35
Simulation | Stop And Initialize.................................................................... 35
Simulation | Fast Play ................................................................................... 35
Simulation | Max Speed Play ...................................................................... 35
Simulation | Run Reference Simulation ..................................................... 36
Simulation | Run Parameterized Simulation ............................................. 36© 2002-2017 The University of Tokyo. All rights reserved.

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4.74 View | Mode.................................................................................................... 37
4.75 View | Zoom In ............................................................................................... 37
4.76 View | Zoom Out ............................................................................................ 37
4.77 View | Actual Size.......................................................................................... 38
4.78 View | Fit In Canvas ...................................................................................... 38
4.79 View | Duplicate Canvas .............................................................................. 38
4.80 View | Delete Canvas ................................................................................... 39
4.81 View | Show All Charts ................................................................................. 39
4.82 View | Hide All Charts ................................................................................... 39
4.83 View | Show Grid ........................................................................................... 39
4.84 View | Antialiasing ......................................................................................... 40
4.85 View | Grid Size ............................................................................................. 40
4.86 View | Background Color.............................................................................. 40
4.87 Analyze | Extract Subnet .............................................................................. 40
4.88 Analyze | Select | Downstream ................................................................... 41
4.89 Analyze | Select | Upstream ........................................................................ 41
4.90 Analyze | Select | Both ................................................................................. 41
4.91 Analyze | Keyword Search ........................................................................... 41
4.92 Analyze | Path Search .................................................................................. 42
4.93 Analyze | Entity List Search ......................................................................... 42
4.94 Analyze | Compare........................................................................................ 42
4.95 Select | Upstream .......................................................................................... 43
4.96 Select | Downstream ..................................................................................... 43
4.97 Select | Up- and Downstream .................................................................... 43
4.98 Select | Inverse .............................................................................................. 44
4.99 Select | All ....................................................................................................... 44
4.100 Select | None.............................................................................................. 44
4.101 Window | Tile Horizontal .......................................................................... 45
4.102 Window | Tile Vertical ............................................................................... 45
4.103 Window | Maximize Canvas .................................................................... 45
4.104 Window | Open Perspective .................................................................... 45
4.105 Window | Reset Perspective.................................................................... 46
4.106 Window | Show Frame ............................................................................. 46
4.107 Window | Hide All Frames........................................................................ 46
4.108 Window | Restore All Frames .................................................................. 47
4.109 Window | Preferences .............................................................................. 47
4.110 Help | Cell Illustrator Help ........................................................................ 47
4.111 Help | User Guide ...................................................................................... 47
4.112 Help | CSML Online .................................................................................. 48
4.113 Help | Cell Illustrator Web Site ................................................................ 48
4.114 Help | About Cell Illustrator ...................................................................... 48© 2002-2017 The University of Tokyo. All rights reserved.

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5 TOOLBARS ....................................................................................................... 49
5.1
Library Toolbar............................................................................................... 49
5.2
Draw Toolbar.................................................................................................. 49
5.3
File Toolbar .................................................................................................... 51
5.4
Edit Toolbar .................................................................................................... 51
5.5
Simulation Toolbar ........................................................................................ 52
5.6
Dialog Toolbar................................................................................................ 52
6 DRAWING CANVAS ........................................................................................ 54
6.1
Multiple Views ................................................................................................ 54
6.2
Canvas Popup Menus .................................................................................. 54
7 FRAMES ............................................................................................................. 57
7.1
Element Lists.................................................................................................. 57
7.2
Element Settings ........................................................................................... 61
7.3
Navigator ........................................................................................................ 71
7.4
Simulation Settings ....................................................................................... 72
7.5
Chart Settings ................................................................................................ 74
7.6
Simulation History ......................................................................................... 76
7.7
Biological Elements....................................................................................... 77
7.8
Graph Layout ................................................................................................. 79
7.9
External References ..................................................................................... 80
7.10 Comments ...................................................................................................... 81
7.11 Project Manager ............................................................................................ 81
7.12 Parts Library ................................................................................................... 82
7.13 View Settings ................................................................................................. 83
7.14 Biological Properties ..................................................................................... 85
7.15 Simulation Errors ........................................................................................... 86
7.16 Path Search Results ..................................................................................... 87
7.17 Expression Plot .............................................................................................. 87
8 DIALOG BOXES ............................................................................................... 89
8.1
Preferences .................................................................................................... 89
8.2
Compare ......................................................................................................... 89
8.3
Manage User Databases ............................. Error! Bookmark not defined.
8.4
Chart Window ................................................................................................ 91
8.5
Keyword Search ............................................................................................ 93
8.6
Path Search.................................................................................................... 95
8.7
Entity List Search .......................................................................................... 97
8.8
Reference Simulation ................................................................................... 98
8.9
SECG Passing Parameters ......................................................................... 99
8.10 Parameterized Simulation Results ............................................................. 99
8.11 About Cell Illustrator.................................................................................... 100© 2002-2017 The University of Tokyo. All rights reserved.

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9 OTHER.............................................................................................................. 101
9.1
CSO Class Tree .......................................................................................... 101
9.2
Script Editor .................................................................................................. 101
9.3
Kinetic Styles Editor .................................................................................... 109
9.4
SECG ............................................................................................................ 112© 2002-2017 The University of Tokyo. All rights reserved.

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1 Introduction
Cell Illustrator™ (CI) is a software tool that enables biologists to model,
elucidate and simulate complex biological processes and systems. It allows
researchers to model metabolic pathways, signal transduction cascades, gene
regulatory pathways as well as dynamic interactions of various biological entities
such as genomic DNA, mRNA and proteins. Cell Illustrator models are used tovisualize biopathways, interpret experimental data and test hypotheses. In addition, it
provides researchers with model diagrams of publication quality and simulation result
charts.
Using a graphical user interface environment, researchers can create andsimulate their own molecular pathway models. Some of the key features of Cell
Illustrator are: (a) Pathway construction and visualization—construct models
graphically by drag and drop Entities that represent bio-components in the biologicalpathways; (b) Pathway simulation—specify mathematical formulas for biochemical
reactions in the pathway for simulation; The simulation can be run inside theworkspace window in an interactive mode (c) Gene relationship net visualization andanalysis.
The documentation for the Cell Illustrator software includes the manuals listed
below:
Cell Illustrator User Guide: Introduction to Cell Illustrator system
Cell Illustrator Reference Manual: Detailed description of Cell Illustrator
functionsThis manual is a reference for the functional features of Cell Illustrator
Desktop version 5.0. It can be used to answer questions about specific systemcommands. For installation instructions and an introduction to modeling biologicalpathways with Cell Illustrator, please refer to the User Guide.

© 2002-2017 The University of Tokyo. All rights reserved.

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2 Biopathways and Gene Net Model
Since the version 3.0, Cell Illustrator enables the users to view and analyze
models of two types:(i)Biopathway(ii)

Gene Relationship Net

Biopathway models represent complex biological processes and systems using
Petri Net models for the simulation of time dependent processes.
A typical Gene Net cannot be simulated. Originally a gene net does notcontain any data useful for the Petri Net based simulation. However such a net can beused as the starting point for creating a simulatable biopathway model.

2.1

Differences between Gene Net and Biopathway Model
The differences between Biopathway and the Gene Net model are listed in thetable below.

Model

Biopathway Model

Gene Net Model

Includes 3 base elements:
entity, process andconnector.

Includes 2 basic elements:
entity and edge (fact edge)

Models are created by theuser within CI workspace.
Biopathway models are
smaller but more precisely
defined than the Gene Net
models.

Gene networks areautomatically generated by
special external software.
Originally gene networks arelarge models without precise
simulation data.

Biopathway models include
quantitative simulation
properties for studying the
kinetics of biologicalprocesses.

Visualization

More advanced graphics:
images for each graphelements, polygon andcurved edges forconnectors, visualization
and animation of simulation© 2002-2017 The University of Tokyo. All rights reserved.

Simple graphics: default
view styles for each gene andedge.
Visualization is faster but
includes less details. Thus it
is more suitable for large
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progress, etc.

networks.

Visualization is slower but
allows for displaying moredetails.

2.2

Editing

Many commands enablebuilding biopathway
models from the scratchand defining the simulation
properties (e.g. kinetic
styles)Extraction and Merging ofsubnetworks. Other edit
commands are used inseldom cases.

Simulation

Simulation using Petri Net
algorithm.

no Simulation capabilities

AnalysisAnalysis of simulation
results: charts

Analysis of gene networks:
Pathway and Keyword
Search, tools for extractionof subnets

Documentation
Please refer to the CI User Guide to get more information how to create andsimulate biopathway models, or to CI Gene Net User Guide to learn more about thegene net visualization and exploration capabilities.

© 2002-2017 The University of Tokyo. All rights reserved.

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3 Main Window
The Workspace is the main window of Cell Illustrator. The Menu Bar locatedat the top provides a set of commands for building and manipulating a model.
Frequently used commands can be also executed by pushing a button on one of the
Toolbars on the sides of Workspace. Menu items and toolbar buttons corresponding
to operations that cannot be performed at the moment are disabled (grayed out).
In the Workspace, multiple model files can be opened simultaneously forviewing and editing. A model file is displayed in a one or more Drawing Canvas.
The canvas window is the main view of the model and allows the model to be edited
and a simulation run to be watched. You can open several canvas windows to view
different parts of the model.
In Cell Illustrator, the user can open several Frames. The contents of theseframes reflect:- user preferences (applicable to all models),- properties of the model in the active canvas window, or- properties of a selected elements in the active canvas window.
Beside the property frames, Cell Illustrators offers frames that support
building of pathways. These frames give the user the access to many predefinedelements or pathway fragments and the ability to insert these fragments to the active
canvas.

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4 Menu Bar
4.1

File | New
Description:- Creates a new, empty model with one view.
- The model name is “New Model number”, where the number is the number ofcurrently opened models + 1- CTRL+N is the keystroke shortcut for this command.
Constraints:- None4.2

File | Open
Description:- Opens a model from a file and displays it in the workspace. Cell Illustrator
loads data from the native CSML format as well as from other formats.
- The format of the file can be selected in the File Type combo box.
- CI tries to recognize the format of the selected file by analyzing its contents. If
the “recognized” format is different than the format selected in File Type, thewarning will be displayed prompting the user: Do you want to open the filewith a different file filter?
- CTRL+O is the keystroke shortcut for this command.
- It is not possible to open the same file twice. If the user attempts to open a filethat is already opened, then the canvas window of that file is activated anddisplayed in the foreground.

-

-

-

CSML Files – the CI “native” File Format
The native CI file format is the XML format called CSML – Cell System
Markup Language - www.csml.org
The CSML files can be written in various versions: CSML 3.0, which
normally should have .csml extension or the older CSML 1.9 files which
normally have the .gon extension. This command opens all versions of CSML
files.
Models created and simulated in CI 4.0 included Pnuts scripts only.
Simulation of these models in CI 5.0 might cause script execution errors, since
Pnuts is NOT the default scripting language of CI 5.0. In order to simulate
such models in CI 5.0, it is recommended to check the Default Script
Language in Simulation Settings frame of the model and set its value to Pnuts.
Since a CI Log (.cil extension) stores the model in the same format as in theoriginal project file, you can open a log file with Cell Illustrator as well andedit the model. However, saving the edited model into the original log file will
erase the time series and any other simulation history information. Therefore,
you should use the Save As command of Cell Illustrator if you would like torecover the model from a log file for further editing.

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--

Other File Formats: CSV – Edge Files
File | Open command also opens models from CSV file format
After importing a non-CSML file, it is recommended to save it to a CSML fileusing the File | Save as command.
Imports gene networks from a normal text file with tab or comma separated
values. The tab separated value files should have the extension *.tsv or *.txt,
while comma separated values *.csv
The text file should contain the connection table – a list of edges.
Each row in this text file represents an edge. The edge is described by several
tab (or comma) separated values as follows:<parent > <child> <property1> <property2> etc..

--

The first two columns must define name of the Parent and Child entity of eachedge. The next columns might defined the properties of the edge.
The text file might include a header row with the description of definedcolumns. The first and second row must be named Parent and Child, the next
property names can be defined by the user.
If the file does not include column headers, then the colums will be recognized
as follows:<parent> <child> <edgeScore> <relationType> <bspline>

Constraints:- None4.3

File | Open Recent Files
Description:- Displays a list of recently opened files. Click on an item in the list to open thecorresponding file.
- Up to 14 recently opened files are in the list.
- The list does not contain duplicates.
- It is not possible to open the same file twice. If the user attempts to open a filethat is already opened, then the canvas window of that file is activated anddisplayed in the foreground.
Constraints:- You can not execute this command if a simulation is running.

© 2002-2017 The University of Tokyo. All rights reserved.

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4.4

File | Close File
Description:- Closes the active model file without exiting the program.
- If a file has been modified, you are prompted to save the changes before
closing the file.
- CTRL+W is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.

4.5

File | Close All Files
Description:- Closes all model files without exiting the program.
- If a file has been modified, you are prompted to save the changes before
closing the file.
- You are always prompted for a file name if you want to close a canvas createdwith the File | New command.
- CTRL+Shift+W is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.

4.6

File | Save
Description:- Saves the active canvas in a file under the current filename.
- The model is saved in the CSML 3.0 file
- The saved file can be opened in CI workspace again using the File | Opencommand.
Constraints:- At least one canvas window must be opened in the workspace.

4.7

File | Save As
Description:- Saves the active file under a new filename selected by the user.
© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one canvas window must be opened in the workspace.

4.8

File | Insert
 Model As Group As Object
Description:- Inserts the elements from a Cell Illustrator model file into the active canvas.
- Insert Model inserts the elements of the external file as they are.
- Insert Group inserts the contents of the external file as one group.
- Insert Object inserts the contents of the external file as one hierarchical object.
- All inserted elements are in the selected state after the operation completes.
- All previously selected elements become deselected.
- The inserted item (a model, a group or an object) is placed in the center of thevisible area of the canvas.
- For multiple views of one model, the inserted elements are visible in the active
view only. In all other views, they are invisible. To make it visible, select theelements in Element List frame and check the Visible checkbox.
Constraints:- At least one canvas window must be opened in the workspace.

4.9

File | Export
4.9.1 Simulation Source Code
 Java C
 C++
 Fortran Perl PythonDescription:© 2002-2017 The University of Tokyo. All rights reserved.

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--

For the model in the active canvas, generates and exports the source code in
the selected language
The source code can be afterwards compiled and executed, resulting in a
program which performs simulation of the model
Compilation of java program requires a few additionally library classes which
are located in the directory org, package org.csml.hfpne.engine. This libraryclasses also provide a way of executing compiled engine, by starting the java
program from EngineRunner class
For all other languages except java, additional files are needed. These files
will be saved in the directory where the main engine file exists (if they aren’t
there yet)

Constraints:- At least one canvas is opened in the workspace
4.9.2 Image
Description:- Exports active canvas to JPEG or PNG file
- File name and location is selected by user in dialog window

4.9.3 SVG
Description:- The command exports the active canvas to the Scalable Vector Graphics(SVG) file.
Constraints:- At least one canvas window must be opened in the workspace.

4.9.4 HTML Report
Description:- Exports the model in the active canvas to a file in HTML format.
Constraints:- At least one canvas window must be opened in the workspace.

© 2002-2017 The University of Tokyo. All rights reserved.

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4.9.5 Simulation Log
Description:- Exports the model in the active canvas and a CSV file with log data to a Cell
Illustrator log file (CIL).
- CIL files are CSML (XML) files that consist of two sections: the main modeland the simulation log. CIL files can be opened in CI Player and the logged
simulation run can be viewed and replayed in an interactive way.
- Similar operation can be done in the Simulation History frame

Constraints:- At least one canvas window must be opened in the workspace.

4.10 File | Export All
4.10.1 PNG
Description:- Exports all views from current model or all models to a series of PNG image
file- The user chooses the destination folder in dialog window. If the selected
folder exists a warning is displayed that files in this folder can be overwritten.
- Additionally the user may choose what should be exported, selecting one of
the two options Export all views of active model (default value), or Export all
views of all opened models
4.10.2 JPEG
Description:- Exports all views from current model or all models to a series JPEG image file,- The user can choose destination folder in dialog window. If the selected folder
exists a warning is displayed that files in this folder can be overwritten.
- Additionally the user may choose what should be exported, selecting one of
the two options Export all views of active model (default value), or Export all
views of all opened models

4.11 File | Export to Cytoscape
Description:- Opens the model from the active canvas in the external Cytoscape application.
Constraints:© 2002-2017 The University of Tokyo. All rights reserved.

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-

At least one canvas window must be opened in the workspace.

4.12 File | Look & Feel
 Metal CDE/Motif Windows
 Windows Classic
Description:- With these commands, you can set the look and feel of Cell Illustrator to a
GUI selected style.
- The selected GUI style is preserved upon restart of the program

4.13 File | Print Visible Area
Description:- Prints the area that is visible in the canvas window- With this command, you can print a part of the active canvas. To do this, firstscroll and zoom the view in the active canvas and then choose this command.
- The command opens the File | Print dialog where you can select printer andspecify page setup and appearance.
Constraints:- At least one canvas window must be opened in the workspace.

4.14 File | Print
Description:- With this command, you can print the whole graph in the active canvas.
- The command opens the File | Print dialog where you can select printer andspecify page setup and appearance.
Constraints:- At least one canvas window must be opened in the workspace.

© 2002-2017 The University of Tokyo. All rights reserved.

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4.15 File | Exit
Description:- Exits the application.
- If any of the opened files has been modified after the last save operation, youwill be prompted to save the changes before closing the file.

4.16 Edit | Undo
Description:- Reverses the most recent edit action for the active model. If this model isdisplayed in multiple views, the active view will be changed to that viewwhich has been edited.
- Execute this command several times to undo results of subsequent edit
commands.
- CTRL+Z is the keystroke shortcut for this command.
Constraints:- There is an action to undo.

4.17 Edit | Redo
Description:- Reverses the action of the last Undo command for the active model. If thismodel is displayed in multiple views, the active view will be changed to thatview which has been edited.
- Effects of subsequent Undo commands are reversed by executing thecorresponding sequence of Redo commands- Shift+CTRL+Z is the keystroke shortcut for this command.
Constraints:- There is an action to redo.

4.18 Edit | Cut
Description:- Removes the selection from the active canvas and places it in the clipboard.
- CTRL+X is the keystroke shortcut for this command.

© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one element must be selected in the active canvas.

4.19 Edit | Copy
Description:- Copies the selected elements into the system clipboard- CTRL+C is the keystroke shortcut for this command.
Constraints:- At least one element must be selected in the active canvas.

4.20 Edit | Paste
Description:- Inserts the contents of the clipboard into the active canvas- CTRL+V is the keystroke shortcut for this command.
- For multiple views of one model, the inserted elements are visible in the active
view only. In all other views, they are invisible. To make it visible, select theelements in Element List frame and check the Visible checkbox.
Constraints:- At least one canvas window must be opened in the workspace.
- The clipboard must contain elements copied with the Copy or Cut operation.

4.21 Edit | Paste View Style
Description:- Copies the view style of the graph element (vertex or edge) from the clipboard
to the elements selected in the active graph- Before executing this command copy exactly one element with the desired
view style to the clipboard using Edit | Copy
- After executing this command, the Paste View Style dialog box is displayed. In
this dialog you may select the list of properties (such as size, line color, stroke,shape, image, font, etc.) to be copied from the clipboard element to theselected canvas elements.
Constraints:- At least one canvas window must be opened in the workspace.
© 2002-2017 The University of Tokyo. All rights reserved.

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-

The clipboard must contain exactly one vertex or edge copied with the Copy
or Cut operation.

4.22 Edit | Delete
Description:- Deletes the selected elements from the canvas.
- Del is the keystroke shortcut for this command.
Constraints:- At least one element must be selected in the active canvas.

4.23 Edit | Duplicate
Description:- Duplicates the currently selected elements in the canvas.
- CTRL+M is the keystroke shortcut for this command.
Constraints:- At least one element must be selected in the active canvas.
4.24 Edit | Extract
Description:- Extracts the selection to a new model and displays it in a new canvas.
- This command has the same result as the sequence of commands: Edit | Copy,
File | New and Edit | Paste.
Constraints:- At least one element must be selected in the active canvas.

4.25 Edit | Find
Description:- Opens the Edit | Find dialog where you can specify the text to search for in
the canvas- CTRL+F is the keystroke shortcut for this command.
© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one canvas window must be opened in the workspace.

4.26 Edit | Select All
Description:- Selects all visible objects in the active canvas.
- CTRL+A is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.

4.27 Edit | Select None
Description:- Deselects all elements in the active canvas- Shift+CTRL+A is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.

4.28 Edit | Select Inverse
Description:- Inverts the selection in the active canvas.
- CTRL+I is the keystroke shortcut for this command.
Constraints:- The command is disabled if the active canvas is empty.

4.29 Edit | Align To Grid
Description:- Aligns selected elements to the grid.
- See also the related commands: View | Show Grid and View | Grid Size
- CTRL+Shift+R is the keystroke shortcut for this command.
© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one element must be selected in the active canvas.

4.30 Edit | Align To
 Top Bottom Left Right
 Vertical Horizontal
Description:- Aligns all the selected elements in one line to, respectively, the top-, bottom-,left- and rightmost element in the selection.
- Align Vertical and Horizontal position the selected elements along the verticalor horizontal line respectively, in the middle of the selection area.
- Align to Top and Align to Bottom command place all selected elements in one
horizontal line. Align to Left and Align to Right command place all selected
elements in one vertical line.
Constraints:- At least two elements must be selected.

4.31 Edit | Move To Top Bottom Left Right
 Top (1px) Bottom (1px) Left (1px) Right (1px)

Description:- Moves all selected elements to the top, bottom, left or right.
- The user has the choices to translate the elements by one pixel (1px) or by one
grid element, which is the number of pixels defined in grid size
- The key strokes displayed next to the menu items are useful short-cuts tospeed up multiple move operations© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one element must be selected.

4.32 Edit | Insert Entity
 Continuous Discrete GenericDescription:- Inserts an entity into the active canvas.
- The new entity is positioned in the center of the visible area of the canvas.
Constraints:- At least one canvas is opened in the workspace.

4.33 Edit | Insert Process Continuous Discrete GenericDescription:- Insert a process into the active canvas.
- The new process is positioned in the center of the visible area of the canvas.
Constraints:- At least one canvas window must be opened in the workspace.

4.34 Edit | Insert Image
Description:- Inserts an image in a JPEG, GIF, or PNG file into the active canvas. SVG(Scalable Vector Graphics) images can also be inserted.
- In the File Open dialog you can select the file name and type (Image File or
SVG Image File) of the image to be inserted. The option Save Internallyspecifies whether the image should be saved internally - inside the model
CSML file, or externally – as a reference to an external graphics file.
- The new image is positioned in the center of the visible area of the canvas.
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Constraints:- At least one canvas window must be opened in the workspace.

4.35 Edit | Insert Text
Description:- Inserts an empty text box into the active canvas.
- Double-click the text box and enter text from the keyboard.
- The new text box is positioned in the center of the visible area of the canvas.
Constraints:- At least one canvas window must be opened in the workspace.

4.36 Edit | Insert Frame
Description:- Inserts a rectangular frame into the active canvas.
- The new frame is positioned in the center of the visible area of the canvas.
Constraints:- At least one canvas window must be opened in the workspace.

4.37 Element | Show All
Description:- Shows all elements in the active canvas.
- It will show all hidden elements by changing their Visible flag to true.
- This command is useful since hidden element cannot be selected on the canvas- The other way to make element visible is to edit their Visible property in
Element Lists frame.
Constraints:- At least one canvas window must be opened in the workspace.

4.38 Element | Hide© 2002-2017 The University of Tokyo. All rights reserved.

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Description:-

Hides the selected elements on the active canvas.
Hidden element cannot be selected cannot be selected on the canvas
To make the hidden elements visible, either execute the Element | Show Allor change the Visible flag in Element Lists frame

Constraints:-

At least one element must be selected in the active canvas.

4.39 Element | Element Type Continuous Discrete GenericDescription:- Sets the type of the selected entities and processes- Note that not all type combinations of connected processes, entities andconnectors are valid. Observe the connection rules specified in the User Guide.
- The element type and other properties can be viewed/edited in Element
Settings frame in more detailed way.
Constraints:- At least one entity or process must be selected.

4.40 Element | Connector Type Process Inhibitory
 Association
Description:- Sets the type of the selected connectors- Note that not all type combinations of connected processes, entities andconnectors are valid. Observe the connection rules specified in the User Guide.
- The element type and other properties can be viewed/edited in Element
Settings frame in more detailed way.
Constraints:- At least one connector must be selected.

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4.41 Element | Reverse Direction
Description:- Reverses the edge direction.
- For association and inhibitor connectors the direction is not changed
Constraints:- At least one edge must be selected.

4.42 Element | Arrange
 Bring to Front Bring Forward Send Backward
 Send to Back
Description:- With this set of commands, you can set the depth of overlapping figures in thecanvas. Depth defines the way in which overlapping figures are displayed. A
figure with a lower depth value is displayed over a figure with a higher depth
value.
- The depth value of each figure can be viewed and edited in Element Settings
frame.
- Bring Forward decreases the depth value of the selected figures by one.
- Send Backward increases the depth value of the selected figures by one.
- Bring to Front shows the selected figure at the front. This function sets depth
to value which is smaller one degree than the smallest depth value in boundsof this figure on canvas.
- Send to Back hides the selected figure behind the other figures. This function
sets depth to value which is greater one degree than the greatest depth value inbounds of this figure on canvas.
Constraints:- At least one element must be selected in the active canvas.

4.43 Element | Group
Description:- Assembles two or more selected elements into a single group element.
- A group can be moved or edited as one element.

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Constraints:- At least two elements must be selected in the active canvas.

4.44 Element | Ungroup
Description:- Disassembles a selected group into individual elements.
Constraints:- At least one group element must be selected in the active canvas

4.45 Element | Size
Description:- Sets the size of selected figures
Constraints:- At least one figure must be selected in the active canvas.

4.46 Element | Fill Color
Description:- Fills the inside of selected figures with the specified color.
Constraints:- At least one figure must be selected in the active canvas.

4.47 Element | Line Color
Description:- Sets the line color of a selected figure to a color from the list.
Constraints:- At least one figure must be selected in the active canvas.

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4.48 Element | Line Style
 Straight Curve Bezier Curve Spline

Description:- Sets the line style of the selected connectors. The user may choose between
straight and curved lines.
Constraints:- At least one connector must be selected in the active canvas.
4.49 Element | Stroke
Description:- Sets the stroke (line pattern) of selected figures to a pattern from the list ofavailable patterns.
- The user can define his own pattern using option Custom. In that case a dialog
box for define pattern will appear.
- This menu option cannot change stroke for connector end (for example arrow
stroke). To change stroke of connector end user should use element settings
frame.
Constraints:- At least one figure must be selected in the active canvas.

4.50 Element | Remove All Anchors
Description:- Transforms broken-line edges selected in the canvas into straight line byremoving all anchor points.
- If a line is broken in several places (with several anchors), all anchor points
will be removed.
Constraints:- At least one edge line must be selected.

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4.51 Element | Set Image
Description:- For one element in the canvas, the command replaces its figure with the figure
from an image file.
- This operation changes the look of an element only; It has no impact onsimulation results
Constraints:- Exactly one element must be selected in the active canvas.
4.52 Element | Set Image Type
Description:- For all selected element in the canvas, the command sets its figure type tointernal or extrenal.
- Internal images are saved inside the CSML file, while for external – the pathto an external graphics files is saved in CSML
Constraints:- At least one element must be selected in the active canvas.

4.53 Element | Edit Image
Description:- Opens the editor for the selected image.
- SVG files are edited by the GLIPS Graffiti SVG editor, which is an integral
part of CI package.
- Other files, JPEG, PNG, and GIFF are edited by the default graphics editor
that is associated with the PNG extension of your Windows or Mac OS. On
Linux platform the default graphics editor is gimp.
- Standard CI images, e.g. process, entity or connector images cannot be edited.
Only images inserted into the canvas from user files can be edited. To insert
an image use the commands: Element | Set Image.
Constraints:- Exactly one editable image must be selected. Editable images are images
saved in external or internal image files: JPEG, PNG, GIF or SVG files.
4.54 Element | Resize Image Fit to Current Width© 2002-2017 The University of Tokyo. All rights reserved.

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 Fit to Current Height Original Size
Description:- Resizes each selected image to its original size/ratio using 3 methods:
o Keep current width and adjust heighto Keep current height and adjust widtho Change width and height to its original value- Every bitmap image (JPEG, PNG, and GIFF) or SVG image has its original
size: width and height. The width/height relation defines the image ratio.
Displaying images in original size assures the best quality. Also good quality
can be achieved when keeping the original ratio. Resizing the image without
keeping the ratio is possible however it may lower the image quality.
- This command allows to improve the image quality by reverting to its original
ratio or size

Constraints:- At least one image must be selected.

4.55 Element | Edit Chemical Structure
Description:- Opens the Chemical Structure Editor for the selected entity.
- In the Cell System Ontology (CSO), the biological property Chemical
Structure is meaningful for the CSO Class SmallMolecule only. If the edited
vertex has a different CSO Class, you will be asked whether he wants tochange the CSO Class to SmallMolecule.
- You may replace the current entity image by the SVG image of thecreated/edited chemical structure. For this select the Replace SVG Image
checkbox, when closing the Chemical Structure Editor,

Constraints:- Exactly one entity must be selected.

4.56 Element | References
Description:- Displays the list of external references in a popup menu. Choose an item fromthe pop up menu to open the URL in a Web Browser window.

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External References menu item opens the External References frame where
you can view and manage the list of references associated with the selected
element.
References define links from the selected element to external resources
specified as URLs. Reference may define a link from the selected element to a
to database element, such as an entry in a database or a term in a controlled
vocabulary.
URL References can be associated to all elements: entities, processes,
connectors.

Constraints:- Exactly one element is selected in the active canvas.

4.57 Element | URL Templates
Description:- Displays the list of URL templates available for this element.
- Choose a link from the list to open the URL in a Web Browser window.
- The URL templates are associated to all elements: entities, processes,
connectors. You can view/edit the list of predefined URL templates in theHyperlink Templates section in the Preferences dialog
Constraints:- Exactly one element is selected in the active canvas.
4.58 Element | Label Fill Color Line Color Stroke FontDescription:- The Fill Color command sets the text background color for all labels of theselected elements.
- The Line Color command sets the label border color.
- The Stroke command sets the label border pattern.
- The Font command sets the label font style.
Constraints:- At least one item must be selected in the active canvas.

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4.59 Element | Show Name
 On
 Off

Description:- Shows or hides, respectively, names of all selected elements.
Constraints:- At least one element must be selected in the active canvas.

4.60 Element | Show Variable
 On
 Off
Description:- Shows or hides, respectively, the variable name for all selected elements
Constraints:- At least one element must be selected in the active canvas.

4.61 Element | Show Value
 On
 Off
Description:- Shows or hides the value labels of selected elements
Constraints:- At least one element must be selected in the active canvas.
4.62 Element | Show Firing Style
 On
 Off
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-Shows or hides the firing style of the selected elements. The firing style is theproperty of process elements.

Constraints:- At least one element must be selected in the active canvas.

4.63 Element | Log
 On
 Off
Description:- Switches on/off the log property of the selected elements.

Constraints:- At least one element must be selected in the canvas.
4.64 Element | Create Chart
Description:- Creates a new chart for the entities, processes and connectors that are selectedin the canvas window.
- The list of charts can be viewed and controlled in the Chart Settings frame
Constraints:- At least one element must be selected in the canvas.

4.65 Element | Update Location
Description:- For selected elements, sets their Cell Component property to the value of
underlying/overlapping cell component.
Constraints:- At least one element must be selected in the canvas.

4.66 Simulation | Play
Description:© 2002-2017 The University of Tokyo. All rights reserved.

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If the model in the active canvas is in the “initialized” or “paused” state, thecommand starts the simulation.
The accuracy and length of simulation are controlled by the Sampling interval
and the Simulation time which are properties of the model. You can set theseand all other parameters in the Simulation Settings frame.
For a new canvas, the Sampling Interval, Simulation Time and all othersimulation settings are initialized on the base of user preference settings. See
Preferences dialog for more details.
The speed of simulation corresponds to the Speed setting in the
Simulation Settings frame. By default it is 1, which is 1 Petri Net time per 1
second. Increasing the Speed parameter speed up the simulation execution
proportionally. However, it is limited by the hardware on which the program
runs.
Process firing and changes of entity values are shown in the canvas during thesimulation. The Canvas Update Interval defines how often the canvas is
updated.
The status of a simulation run is displayed on the progress bar at the top of theactive canvas.
If there are any charts defined for the model, they are opened when thecommand is executed. The charts are periodically updated as the simulation
runs. The update time is defined by the Chart Update Interval.
The simulation stops when: (1) the user has executed theSimulation | Stop And Initialize command, or (2) the user has executed theSimulation | Pause command, or (3) the simulation time has reached thevalue specified (in pt units) by the Simulation time setting in the Simulation
Settings frame.

Constraints:- At least one canvas is opened in the workspace- The model in the active canvas is not in the “simulation end” state

4.67 Simulation | Step Play
Description:- The command executes one simulation step for the model in the active canvas.
- One step corresponds to 1 Sampling Interval in Petri net time units. The
Sampling interval is a property of the active model and it is displayed in the
Simulation Settings frame.
- For a new canvas, the Sampling interval is initialized on the base of the user
preference settings. See Preferences dialog for more details.
- The Speed setting and the Simulation time is ignored for this command.
- The simulation status is displayed at the top of the CI canvas.
Constraints:- At least one canvas is opened in the workspace© 2002-2017 The University of Tokyo. All rights reserved.

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4.68 Simulation | Pause
Description:- Pauses a running simulation.
- The simulation can be resumed with the Simulation | Play and other playcommands: Step Play, Fast Play, Max Speed Play.
Constraints:- The command is disabled if no simulation is running.

4.69 Simulation | Stop And Initialize
Description:- If there is a running simulation, it is stopped and initialized- Variables associated with entities are reset to their initial values.
Constraints:- The command is enabled if a simulation for the model in the active canvas has
been paused or completed.

4.70 Simulation | Fast Play
Description:- Starts the simulation in fast mode for the model in the active canvas. The
command behaves like Simulation | Play but the simulation execution is 10
times faster.
- The simulation speed is limited by the hardware on which the program runs.
- The charts are updated rarely in comparison to Play mode.
- The canvas updates normally – in the same way as in Play mode.
- Before starting a fast simulation run, it is recommended convert all Pnuts
scripts to in Java or simplemath, because the evaluation of scripts written in
Pnuts is much slower than of scripts written in Java or simplemath.
- If the active model includes Pnuts scripts, a simulation warning dialog box
will be displayed with the list of all detected Pnuts scripts. Using this dialog
box you may convert all Pnuts scripts to Java or simplemath.

4.71 Simulation | Max Speed Play
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Starts the simulation in the fastest mode. The command behaves like
Simulation | Fast Play but the simulation is executed as fast as possible
The speed of the simulation is the highest possible speed given by the
hardware limits. The canvas is not updated during simulation and charts are
updated very rarely.
Before starting a fast simulation run, it is recommended convert all Pnuts
scripts to in Java or simplemath, because the evaluation of scripts written in
Pnuts is much slower than of scripts written in Java or simplemath.
If the active model includes Pnuts scripts, a simulation warning dialog box
will be displayed with the list of all detected Pnuts scripts. Using this dialog
box you may convert all Pnuts scripts to Java or simplemath.

4.72 Simulation | Run Reference Simulation
Description:- Starts a reference simulation. During this simulation the entity values are set
from the external file.
- At the start of the simulation, the Reference Simulation dialog box isdisplayed. In this dialog the user specifies the CSV data file with time series ofvalues (format similar to Cell Illustrator CSV simulation log) and otheroptions.

Constraints:- The file must be chosen and it must be a proper CSV file
4.73 Simulation | Run Parameterized Simulation
Description:- Starts a series of SECG simulations in the bulk mode
- Allows specifying some entities as parameters (their start value will change in
different simulations)- For each parameter a value range is specified (the smallest/starting and thebiggest possible value of the entity is selected, as well as description how thevalues should differ from each other). The parameters are set in the
SECG Passing Parameters dialog- Runs simulation for each combination of parameter values- Long simulations can be canceled- The view of the simulation results is controllable by theParameterized Simulation Results
Constraints:- At least one parameter must be selected© 2002-2017 The University of Tokyo. All rights reserved.

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4.74 View | Mode None View
 Edit Simulation
 All
 CustomDescription:- This command sets the global mode of displaying labels. Changing the View
Mode causes that specific information is not displayed on the canvas and that
selected labels are always hidden.
- To see the details of global label view settings, open the View Settings frame.
- The Custom view mode can be defined by the user in the View Settings frame.
- This command is a short-cut that allows for changing the view setting forseveral label types at once.
- Depending on the selected View Mode, selected labels of entities, processes,
connectors or fact edges are always hidden, e.g after View | Mode | Nonecommand all labels will be hidden. In the other view modes only the lessimportant labels are hidden, e.g. after View | Mode | View all simulationrelated labels will be hidden. After View | Mode | All, all labels are shown.
- The View Mode setting is global. It applies to all canvases in the workspace.
Constraints:- None4.75 View | Zoom In
Description:- The command brings a virtual camera closer to the model in the active canvas- If necessary, the command will enlarge the canvas by increasing its width
and/or height.
- View | Actual Size, reverts the canvas to its original scale and size.
Constraints:- At least one canvas window must be opened in the workspace.

4.76 View | Zoom Out
Description:- The command brings a virtual camera farther from the model in the active
canvas window.
- View | Actual Size reverts the canvas to its original scale© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one canvas window must be opened in the workspace.
4.77 View | Actual Size
Description:- The command moves the virtual camera so that the canvas is displayed with
its actual size.
- If necessary, the command will shrink the canvas by decreasing its width
and/or height.
Constraints:- At least one canvas window must be opened in the workspace.

4.78 View | Fit In Canvas
Description:- If one or more elements are selected, the command scrolls and zooms thegraph in the window to display the selected elements in the canvas.
- Otherwise, the virtual camera is moved to fit the display of all elements in theactive window.
- If necessary, the command will enlarge the canvas by increasing its width
and/or height.
- View | Actual Size reverts the canvas to its original scale and size
Constraints:- At least one canvas window must be opened in the workspace.

4.79 View | Duplicate Canvas
Description:- Creates a new Canvas Window for the active model.
- Initially the new canvas is identical to the original one. However changes ofview attributes (element visibility, colors, sizes, location, images, etc.) will
apply to the selected canvas only, so that the duplicated canvas will differ
from the original one.
- You can open several canvas windows to view different parts of the model or
to view the same model in a different way.
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At least one canvas window must be opened in the workspace.

4.80 View | Delete Canvas
Description:- Deletes the active Canvas Window for the active model.
- This operation is opposite of View | Duplicate Canvas
Constraints:- At least two canvas window must exist for the active model.

4.81 View | Show All Charts
Description:- Opens all charts defined for the active canvas
Constraints:- At least one canvas window must be opened in the workspace.

4.82 View | Hide All Charts
Description:- Closes all charts defined for the active canvas
Constraints:- At least one canvas window must be opened in the workspace.

4.83 View | Show Grid
Description:- Toggles the grid display on and off for the active canvas window.
- If grid is on, entities are aligned to the grid automatically, when they are
inserted or moved.
- If the grid is off, the entities are moved and inserted freely without gridalignment- Changing the grid size (View | Grid Size) may disturb the alignment. In sucha situation, the elements can be aligned using this command
Edit | Align To Grid
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Constraints:- At least one canvas window must be opened in the workspace.

4.84 View | Antialiasing
Description:- Toggles antialiasing on and off for the active canvas windows.
- With the antialiasing in the on state, model diagrams look better but it takes
more time to draw them.
Constraints:- At least one canvas window must be opened in the workspace.

4.85 View | Grid Size
Description:- Sets the grid size for the active canvas windows
Constraints:- At least one canvas window must be opened in the workspace.
4.86 View | Background Color
Description:- Sets the background color for the active canvas window
Constraints:- At least one canvas window must be opened in the workspace.

4.87 Analyze | Extract Subnet
Description:- Creates a new canvas with the selected elements from the active canvas.
- Selected edges are added to the new canvas if target and source vertex are
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At least one element must be selected.

4.88 Analyze | Select | Downstream
Description:- Extends the current selection in the canvas by children of the selected entities
Constraints:- At least one element must be selected in the active canvas.

4.89 Analyze | Select | Upstream
Description:- Extends the current selection in the canvas by parents of the currently selected
entities
Constraints:- At least one element must be selected in the active canvas.

4.90 Analyze | Select | Both
Description:- Extends the current selection in the canvas by selecting children and parents
the currently selected genes
Constraints:- At least one entity must be selected in the active canvas.

4.91 Analyze | Keyword Search
Description:- Opens the Keyword Search dialog where you can specify the text to search
for in the canvas- CTRL+F is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.
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4.92 Analyze | Path Search
Description:- Opens the Path Search dialog, where you can search for closest neighbors of
the selected entity or perform start-to-end path search
Constraints:- At least one canvas window must be opened in the workspace.
4.93 Analyze | Entity List Search
Description:- Opens the Entity List Search dialog where you can search for a given list ofentities.
Constraints:- At least one canvas window must be opened in the workspace.
4.94 Analyze | Compare
Description:- Compares (merges) two or more networks from the workspace.
- This operation compares selected networks and finds the common part of the
networks (intersection), the differences between the networks and the sum of
the networks (union).
- The active graph (Main Graph) is treated in a unique way during network
merge: The graph elements in the intersection network and also common
graph elements in the union network inherit their properties fromcorresponding elements from the Main Graph.
- The comparison results are displayed as new models arranged side by side in
the tabbed pane:• Union of Main Graph and Other networks• Intersection of Main Graph and Other networks• Differences between Main Graph and Other networks• Differences between the union of Other Networks and Main Graph- This command opens the Compare dialog box, in which the user specifies thecomparison options.

Constraints:- Two or more models must be opened in the workspace.

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4.95 Select | Upstream
 Vertex and Edge
 Vertex Only
 Edge Only
Description:- Extends the current selection in the canvas by parents of the selected elements- The sub-menu item - Vertex and Edge, Vertex Only, Edge Only – defines thetype of the newly selected elements
Constraints:- At least one element must be selected in the active canvas.

4.96 Select | Downstream
 Vertex and Edge
 Vertex Only
 Edge Only
Description:- Extends the current selection in the canvas by children of the currently
selected elements- The sub-menu item - Vertex and Edge, Vertex Only, Edge Only – defines thetype of the newly selected elements
Constraints:- At least one element must be selected in the active canvas.

4.97 Select | Up- and Downstream
 Vertex and Edge
 Vertex Only
 Edge Only
Description:- Extends the current selection in the canvas by selecting children and parents ofthe currently selected elements- The sub-menu item - Vertex and Edge, Vertex Only, Edge Only – defines thetype of the newly selected elements© 2002-2017 The University of Tokyo. All rights reserved.

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Constraints:- At least one entity must be selected in the active canvas.
4.98 Select | Inverse
 Entities
 Processes
 Entities and Processes
 Connectors
 Fact Edges
 Any Type
Description:- Inverts the current selection in the canvas for the selected type of elements:
Entities, Processes, Entities and Processes, Connectors, Fact Edges, Any TypeConstraints:- At least one element must be selected in the active canvas.

4.99 Select | All Entities
 Processes
 Entities and Processes
 Connectors
 Fact Edges
 Any Type
Description:- Selects all elements of the given type - Entities, Processes, Entities andProcesses, Connectors, Fact Edges, Any Type - in the active canvas

4.100 Select | None
 Entities
 Processes
 Entities and Processes
 Connectors
 Fact Edges
 Any Type
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-Deselects all elements of the specified type - Entities, Processes, Entities andProcesses, Connectors, Fact Edges, Any Type - in the active canvas

4.101 Window | Tile Horizontal
Description:- Tiles the canvas windows horizontally.
Constraints:- At least two models must be opened in the workspace.

4.102 Window | Tile Vertical
Description:- Tiles the canvas windows vertically.
Constraints:- At least two models must be opened in the workspace.

4.103 Window | Maximize Canvas
Description:- Maximizes the canvas windows of the active model.
- It removes the split created by the Window | Tile commands.
Constraints:- At least two models must be opened in the workspace.

4.104 Window | Open Perspective
 All
 Edit View
 Simulation
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This command sets the global perspective of Cell Illustrator. Changing theperspective causes that specific frames are displayed in the selected layout,
while other, less useful, frames are hidden.
By default, each perspective displays only those frames which are related to its
name, e.g. in the perspective Simulation or View, only the frames related tosimulation or view properties are displayed, in the Edit perspective, all frames
important for editing are displayed, while for perspective All, all frames are
displayed
The default (initial) layout of each perspective can be changed by common
window operation on the frames (show, hide, translate, etc.). The frame layout
is saved upon exiting the application and restored at startup.
To revert to the initial (default) layout, execute Window | Reset Perspective

Constraints:- None4.105 Window | Reset Perspective

Description:- Resets the layout of the currently selected perspective by reverting to theinitial (default) location, size, layout and visibility of all frames.
Constraints:- None4.106 Window | Show Frame
Description:- Display and activate the selected frame.
- This command drops down the list of all frames available in Cell Illustrator.
Constraints:- None4.107 Window | Hide All Frames
Description:- Hide all frames and display the canvas window in maximal size.
Constraints:- None© 2002-2017 The University of Tokyo. All rights reserved.

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4.108 Window | Restore All Frames
Description:- Restore the frames which were hidden, e.g. by Window | Hide All Framescommand or other user actions.
Constraints:- None4.109 Window | Preferences
Description:- Opens the Preferences dialog box, in which the user can view/edit the global
settings.
Constraints:- None4.110 Help | Cell Illustrator Help
Description:- Opens the HTML help system for Cell Illustrator.
Constraints:-

Internet connection is required

4.111 Help | User Guide
Description:- Downloads and opens the Cell Illustrator User Guide.
Constraints:- The User Guide is a PDF document. Adobe Acrobat Reader or anothersoftware capable of reading PDF documents needs to be installed andconfigured on your machine.
- Cell Illustrator uses your default internet browser to open document so you
have to be connected to the internet to download the User Guide.
Constraints:- Internet connection is required© 2002-2017 The University of Tokyo. All rights reserved.

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4.112 Help | CSML Online
Description:- Opens the www.csml.org web site in the default browser.
- CSML (Cell System Modeling Language) is the XML file format that is usedin Cell Illustrator to store and exchange models.
Constraints:- The Internet connection must be available.

4.113 Help | Cell Illustrator Web Site
Description:- Opens the CI web site in the default browser.
Constraints:- The Internet connection must be available.

4.114 Help | About Cell Illustrator
Description:- Displays the dialog About Cell Illustrator with the version and license
information© 2002-2017 The University of Tokyo. All rights reserved.

Page 48 of 112

5 Toolbars
5.1

Library Toolbar
This toolbar is located at the top of the main window and contains a set of
buttons that connect to the libraries of biological elements, fragments and models tofacilitate model building.
Icon

Button Name
Part Library
Biological Elements
Project Manager

5.2

Description
Opens the Parts Library
frame
Opens Biological Elements
frame
Opens Project Manager
frame

Draw Toolbar
This toolbar is located at the top of the main window and contains a set of
buttons for the most frequent edit operations.
Icon

Button Name
Selection Mode
Create Continuous
EntityCreate Continuous
Process
Create Discrete Entity
Create Discrete
Process
Create Generic Entity
Create Generic
Process
Create Process
Connector
Create Inhibitory
Connector

Description
In this mode, you can select elements on thecanvas with the arrow cursor.
Push this button and click on the active canvas
to insert a continuous entity. Each subsequentclick adds a new entity.
Push this button and click on the active canvas
to insert a continuous process. Eachsubsequent click adds a new process.
Push this button and click on the active canvas
to insert a discrete entity.
Push this button and click on the active canvas
to insert a discrete process.
Push this button and click on the active canvas
to insert a generic entity.
Push this button and click on the active canvas
to insert a generic process.
Push this button and draw a line between twoelements on the active canvas to insert a
process connector.
Push this button and draw a line between twoelements on the active canvas to insert an
inhibitory connector© 2002-2017 The University of Tokyo. All rights reserved.

Page 49 of 112

Create Association
Connector

Push this button and draw a line between twoelements on the active canvas to insert anassociation connector

Create Fact Edge

Push this button and draw a line between two
entities on the active canvas to insert a factedge.

Create Frame

Push this button and drag the mouse cursor on
the active canvas to insert a frame

Create Note

Push this button and drag the mouse cursor on
the active canvas to insert a text note.

Insert Image

See Edit | Insert Image

View Style
Paintbrush

Select the element whose view style you wantto copy and push this button. With the View
Style Paintbrush tool active, select elementson the canvas to apply the copied viewproperties. This operation is similar to the
Edit | Paste View Style

Zoom In
Zoom Out

Push this button and click on the active canvas
to zoom in.
Push this button and click on the active canvas
to zoom out.

Reset Zoom

See View | Actual Size

Fit in Canvas

See View | Fit In Canvas

Toggle theAntialiasing Status
Toggle the Grid
Visible Status

See View | Antialiasing
See View | Show GridGroup

See Element | Group

UngroupSee Element | Ungroup

Set View Mode

With this button, you can set global viewmode. See View | Mode

Set Color

Changes fill color of selected elements. If
connector is selected arrow fill color change© 2002-2017 The University of Tokyo. All rights reserved.

Page 50 of 112

5.3

Line Color

Changes line color of selected elements. If
connector is selected arrow line color doesn’tchangeSelect Color Tool

With this button, you can select the Fill Color,
Line Color or the Text Color as the current
setting for the Set Color command

Set Line Stroke

Sets line stroke of selected elements. If
connector is selected arrow line stroke doesn’tchangeFile Toolbar

This toolbar is located at the left side of the main window, above theUndo/Redo and Simulation toolbars. It consists of a set of buttons for file
management operations.

Icon

ToggleButtonNo

NameFull Description

Create New Canvas

See File | New

NoOpen Canvas File

See File | OpenNo

Close FileNo

Close All Files

No

Save Active Canvas
Save Canvas To Selected
File

See File | Close File
See
File | Close All Files
See File | Save

No

5.4

See File | Save As

Edit Toolbar
This toolbar is located at the left side of the main window, below the FileToolbar and above the Simulation Toolbar. It contains buttons for Undo/Redo andAlign commands.
Icon

Name
Undo

Description
See Edit | Undo

Redo

See Edit | Redo

© 2002-2017 The University of Tokyo. All rights reserved.

Page 51 of 112

Align Top
Align Bottom
Align Left
Align Right
See Edit | Align To

Align Vertical
Align Horizontal
Space Evenly VerticalSpace Evenly Horizontal

5.5

Simulation Toolbar
This toolbar is located on the left side of the main window below the FileToolbar and Undo/Redo Toolbar. It contains buttons for starting and stopping
simulation.
Icon

Name
Play Simulation
Step Play simulation
Pause Simulation
Stop Simulation andInitialize
Fast Play Simulation
Max Speed Play
Simulation
Play with Animation
Save Simulation Log

5.6

Description
See Simulation | Play Simulation |Play
See Simulation | Step Play
Simulation | Step PlaySee Simulation | Pause Simulation |Pause
See Simulation | Stop And Initialize
Simulation | Stop and Initialize
See Simulation | Fast Play
Simulation | Fast PlaySee Simulation | Max Speed Play
Simulation | Max Speed PlaySee Simulation | Play withAnimationSee Simulation Settings

Dialog Toolbar
This toolbar is located on the right side of the main window and contains
buttons that open or recall property frames.
Icon

Name
Element Lists Frame.

Description
See Element Lists frame

Element Settings Frame

See Element Settings frame© 2002-2017 The University of Tokyo. All rights reserved.

Page 52 of 112

Biological Properties
Frame
External References
Frame

See Biological Properties frame
See External References frame

Navigator Frame

See Navigator frame

View Settings Frame

See View Settings frame

Chart Settings Frame

See Chart Settings frame

Simulation Settings
Frame

See Simulation Settings frame

Simulation Errors Frame

See Simulation Errors frame

Simulation History
Frame

See Simulation History frame

Graph Layout

See Graph Layout frame© 2002-2017 The University of Tokyo. All rights reserved.

Page 53 of 112

6 Drawing Canvas

The canvas window is the place where you build a model. In addition tocommands available in the Menu Bar and the toolbars, you can right click (CTRL
click on a Macintosh) on the canvas or on a selected element in the canvas to access a
popup menu customized to your selection.
Right click on an edge element adds/removes break-point for the edge line.
Use CTRL+click to open the popup menus for edges.
During simulation, the canvas window is updated with entity value changes. In
some simulation modes, processes that fire are marked with color and animatedtokens move between entities.
You can customize the background color and other properties of your canvas
windows by editing the Canvas section of the application global settings in the
Preferences dialog. Simulation visualization options are defined in the Animation
Options section.

6.1

Multiple Views
In Cell Illustrator one model can be displayed on multiple canvases, which arelocated side by side in a tabbed pane. Different views can be used to show the modelin a different way or to view different parts of the model. To create a new view for theactive model the command View | Duplicate Canvas should be used.
When working with multiple views, the user edit-operations can apply to:-

the active view only, when the operation applies to view-specific attributes, or-

all views of the active model, when the operation applies to model-specificattributes.

View-specific attributes are graphical properties, such as element visibility,
selection, size, location, image, color, line style, font, while model-specific attributes
are element name, simulation properties, biological properties, element connectivity.
Inserted elements are added to all views of the model; however they are
visible in the active canvas only, while in the other canvases they are initially hidden.
To make elements visible, execute Element | Show All command or change the
Visible flag in Element Lists frame

6.2

Canvas Popup Menus© 2002-2017 The University of Tokyo. All rights reserved.

Page 54 of 112

Selection
None (Canvas)

Single Element

Popup Menu Item
Find

Referenced Command
Edit | Find-----------Undo
Redo-----------Select All-----------Paste-----------Insert Entity
Insert Process
Insert Image-----------Insert-----------Background Color-----------Duplicate Canvas
Delete Canvas
Cut
Copy
DeleteDuplicate-----------Ungroup-----------Arrange
Set Image
Edit ImageResize Image-----------------------Edit | Undo
Edit | Redo-----------Edit | Select All-----------Edit | Paste-----------Edit | Insert Entity
Edit | Insert Process
Edit | Insert Image-----------File | Insert-----------View | Background Color-----------View | Duplicate Canvas
View | Delete Canvas
Edit | Cut
Edit | Copy
Edit | Delete
Edit | Duplicate-----------Element | Ungroup-----------Element | Arrange
Element | Set Image
Element | Edit Image
Element | Resize Image------------

Edit Chemical Structure Element | Edit Chemical
Structure----------------------Size
Element | Size
Fill Color
Element | Fill ColorLine Color
Element | Line Color
StrokeElement | Stroke----------------------SelectAnalyze | Select | Downstream
Analyze | Select | Upstream
Analyze | Select | Both----------------------Create Chart
Element | Create Chart----------------------References
Element | References© 2002-2017 The University of Tokyo. All rights reserved.

Page 55 of 112

Multiple

URL Templates
Cut
Copy
DeleteDuplicate-----------Group
Ungroup-----------Align To
Arrange
Set Image
Edit ImageResize Image-----------Size
Fill ColorLine Color
Stroke-----------Select-----------Create Chart------------© 2002-2017 The University of Tokyo. All rights reserved.

Element | URL Templates
Edit | Cut
Edit | Copy
Edit | Delete
Edit | Duplicate-----------Element | Group
Element | Ungroup-----------Edit | Align To
Element | Arrange
Element | Set Image
Element | Edit Image
Element | Resize Image-----------Element | Size
Element | Fill Color
Element | Line Color
Element | Stroke-----------Analyze | Select | Downstream
Analyze | Select | Upstream
Analyze | Select | Both-----------Element | Create Chart------------

Page 56 of 112

7 Frames

7.1

Element Lists
For the model in the active canvas, this frame displays the elements together
with their major properties in a table

The Element Lists frame consists of the tabbed tables Entity, Process,Connector, Fact Edge, Fact Vertex and Group.
The following operations can be done for each of the table:-

Select an element on the canvas by clicking on a row-

Sort rows according to the specified column by clicking on the column header,-

Filter rows by specified column by clicking on combo box on header of thecolumn,-

Edit a given property by double clicking a cell-

Customize the visible column by right click on column header and choosing
one of the menu items:o Hide column
o Show All Hidden Columnso Select Visible Columnso Restore Default Columns

7.1.1 Entity Table
Each row in the table corresponds to an entity in the active canvas. The
following properties are listed in the table:© 2002-2017 The University of Tokyo. All rights reserved.

Page 57 of 112

o
o
o
o
o
o
o
o
o
o
o

o
o
o
o
o
o
o
o
o

Element Id – unique identifier (not editable)
Name – entity name
CSO Class – Cell System Ontology Class
Type – the value type of entity, Integer represent a discrete entity,
Double – a continuous entity, String and Boolean – a generic entity,
Unknown is a universal value.
Variable – name of variable associated with the entity
Initial Value – initial value or script for simulation
Eval Once – tells whether the Initial Value script is evaluated only
once at the simulation start up, or many times at each simulation step
Max Value – maximum value of the entity during simulation
Min Value – minimum value of the entity during simulation
Log – if the box is checked the entity is included in a simulation log.
The logged values can be viewed and analyzed in Simulation History
Frame or exported to a CSV file.
Global – by default for normal entities this flag is false. If the Flag istrue, the entity is global. Global entities are used to represent cellbiological compartments, containers for normal entities, such as cellcomponents. The global entities cannot be connected to any processusing connectors.
Visible – toggles element visibility on the canvas.
Show Name – toggles visibility of name label on the canvas.
Show Variable – toggles visibility of variable label on the canvas.
Show Value – toggles visibility of value label on the canvas.
Show Biological Property – toggles visibility of biological property
label on the canvas.
Depth – changes how deep will be the entity painted.
Location – biological location of the entity.
GO, PubMed - display database IDs defined in external references(read-only)
TRANSFAC, TRANSPATH – display Transpath database ID definedin external references (read-only)

7.1.2 Process Table
Each row in the table corresponds to a process in the active canvas. The following
process properties are listed in the table:o Element Id – unique identifier (not editable)o Name – process name.
o CSO Class – Cell System Ontology Class, e.g.: biological process
o Type – discrete, continuous or generic.
o Calc Style – The meaning of the Calc Style depends on the process
type. The Speed property is for a continuous process, for a discrete
process – the Add property and for generic process – the Update.
o Firing Style – determines the firing style of the process. For “And”
style, the process fires if all input connectors fulfill the firing condition.
The “Or” firing style can be used if the process has two or more input© 2002-2017 The University of Tokyo. All rights reserved.

Page 58 of 112

o
o
o
o
o
o
o
o
o
o
o
o
o
o
o
o
o
o

connectors of type Inhibitor or Association. For the “Or” firing style atleast one Inhibitor or Association connector must fulfill the firingcondition in order to the process to be enabled. Additionally \, all input
Process connectors must be enabled.
Kinetic Style –Kinetic Script – a value of script that defines how to calculate th valuechange in each simulation step.
Delay Script – defines delay parameter.
Activity – if the Activity is set to false a process does not fire. The
Activity can be defined by mathematical formula.
Priority – priority of the process used during simulation. Process withhigher priority fires before a process with lower priority.
Log – if the box is checked the process state is included in simulationlog. You can see simulation log in Simulation History frame or export
it to a CVS file.
Activity Log –Visible – toggles visibility of the element.
Show Name – toggles visibility of name label on the canvas.
Show Speed – toggles visibility of speed label on the canvas
Show Delay – toggles visibility of delay label on the canvas.
Show Firing Style – toggles visibility of firing style label on the canvas.
Show Biological Property – toggles visibility of biological property
label on the canvas.
Depth – changes how deep will be the entity painted.
Location – biological location of the process.
Biological Process – defines which process in real cell is represented
by this element.
GO, PubMed - display database IDs defined in external references(read-only)
TRANSFAC, TRANSPATH – display Transpath database ID definedin external references (read-only)

7.1.3 Connector Table
Each row in the table corresponds to a connector in the active canvas. The following
connector properties are listed in the table:o Element Id – unique identifier (not editable)o Name – connector name.
o CSO Class – Cell System Ontology Class.
o Type – process, inhibitory or association.
o From – the input element (entity or process) of the connector.
o To - the output element (entity or process) of the connector.
o Kinetic Script – a value of script that defines how to calculate the valuechange in each simulation step.
o Firing Style – the firing style of the connector.
o Firing Script – the script or value that defines the firing condition.

© 2002-2017 The University of Tokyo. All rights reserved.

Page 59 of 112

o Log - if the box is checked the connector state is included in simulationlog. You can see simulation log in Simulation History frame or export
it to a CVS file.
o Visible – toggles element visibility.
o Show Name – toggles visibility of name label on the canvas.
o Show Firing Operation – toggles visibility of firing operation label on
the canvas.
o Show Firing Style – toggles visibility of firing style label on the canvas.
o Depth – changes how deep will be the entity painted.
o Line Style – changes style of connector line. You can choose between:
 Straight,
 Curve Bezier, Curve Spline.
7.1.4 Fact Edge
Each row in the table corresponds to a Fact Edge in the active canvas. The following
properties are listed in the table:o Element Id – unique identifier (not editable)o Name –fact edge name.
o Parent – parent entity (source of the edge)o Child – child entity (target of the edge)o Type – directed or undirected relation.
o Relation Type – one of the predefined types of relation in gene nets.
o Comments – doesn’t need explanation o Visible – toggles visibility of selected elemento Show Name – toggles visibility of name label on the canvas.
o Show Biological Property – toggles visibility of biological propertyo Depth – changes how deep will be the entity painted.
o GO, PubMed - display database IDs defined in external references(read-only)
o TRANSFAC, TRANSPATH – display Transpath database ID definedin external references (read-only)
7.1.5 Fact Vertex
Each row in the table corresponds to a Fact Vertex in the active canvas. The following
properties are listed in the table:o Element Id – not editable identifier.
o Text – if vertex is a text field you can change text here.
o CSO Class – Cell System Ontology Class.
o Visible – toggles visibility of selected element.
o Depth – changes how deep will be the entity painted.
7.1.6 Group
Each row in the table corresponds to a connector in the active canvas. The following
connector properties are listed in the table:o Element Id – not editable identifier.
o Name – connector name.
© 2002-2017 The University of Tokyo. All rights reserved.

Page 60 of 112

o Visible – toggles visibility of selected element.
o Entity/Process/Connector/Fact Edge/Fact Vertex/Group Count – thenumber of elements of given type that are in the groupo Depth – changes how deep will be the entity painted

7.2

Element Settings-

The Element Settings frame allows viewing and setting of properties of a
selected element:
If exactly one element is selected, the frame displays its properties. If morethan one element is selected, the frame displays the Multiple Selection frame.
Otherwise the frame shows global properties of the model in the active canvas.

Selection
Single Selection: Exactly
one element is selected

Multiple Selection: morethan one element isselected

Empty Selection

-

Frame
Element Settings frame.
Depending on the type of
selected element it
displays the property sheet
for: Entity, Process,Connector, Fact Vertex,
Fact Edge, Group.
Multiple Selection frame:
displays common viewand biological properties
for the selected elements

Description
The Single Selection
frames give the user theability to view and edit theproperty values for theselected element

The Multiple Selection
frames give the user theability to view and edit theproperty values for several
selected elements at once

Model and Canvas
Property Sheet

Change of selection or switching between canvas frames results in an updateof the frame.
Changing a setting in the frame has an immediate effect in the model.
For models with multiple views, the view properties of the element in theactive canvas are displayed or edited, e.g. the change of color will be shown in
the active view only, while other views will remain unchanged.

© 2002-2017 The University of Tokyo. All rights reserved.

Page 61 of 112

Most of the properties are self-explanatory and are already described in
Element List frame. Therefore only the non-trivial properties will be described in thischapter including:-Simulation Settings-

Biological Properties-

Custom Biological Properties-

Model and Canvas Properties-

Multiple Selection Frame© 2002-2017 The University of Tokyo. All rights reserved.

Page 62 of 112

7.2.1 Simulation Section

The Element Settings frame allows the setting of mathematical formulas as
element properties to define dependencies between elements during the simulation.
The mathematical formulas can be set for specific entity, process or connector
properties with the help of the Script Editor.

7.2.1.1 Entity
Property NameType
Variable

Initial Value

Eval Once

Max Value
Min Value
Log

Description
The Double type is associated with continuous entities,
Integer with discrete entities, the other value types:
Boolean and String with generic entities.
Name of variable associated with the entity
The value of the entity at the simulation startup. The
property can be a fixed value or a script. If it is a script, it
can be evaluated only at simulation startup (normal case),or at each simulation step (special case) - see Evaluate
Script Once. The right, drop-down button allows for thedefinition of the mathematical formula within the
Script Editor.
This property is ignored if the Initial Value is a fixedvalue. Otherwise, if the Initial Value is a script, there are
2 possibilities:
 If the property is on, the Value property is
initialized with value set by the script at the
beginning of simulation.
 If the property is off, the Value property is set byevaluating the script at each simulation step
The maximum value that can be assigned to the variableassociated with the entity. It can be 1, infinite or any
other value entered by the user. This entry is enabled
only for scalar value types: Integer, Long or Double.
Tells, whether to log the entity values during simulation
Tells, whether this entity is global. Global entities cannot
be connected with connectors.

Global

7.2.1.2 Process
Property Name

© 2002-2017 The University of Tokyo. All rights reserved.

Description

Page 63 of 112

Calc Style

Determines how the variables in the connected entities
are modified when the process fires. The following
operations (calculation styles) can be specified: Speed – the process defines the speed ofproduction or consumption of the entities. Speed
determines the continuous process type.
 Add – the process calculates the concrete values
that should be added (subtracted) to the entities.
Add determines the Discrete process type.
 Update – the process calculates a concrete valuethat will replace the entity value. Update
determines the Generic process type.
Note: The Update and Add calculation styles are time
independent. Thus it is recommended that they beused in conjunction with a Delay value. This willassure that the process fires at a constant time interval
and makes the simulation results independent of thesampling interval.

Firing Style

Determines how the enabled/disabled state of the process
is calculated. The following styles can be selected fromthe drop-down list: And – All connected input connectors must fulfill
their conditions to enable the process.
 Or – At least one Inhibitor or Association input
connector must fulfill its condition to enable theprocess. Additionally, all Process input
connectors must fulfill their conditions.

© 2002-2017 The University of Tokyo. All rights reserved.

Page 64 of 112

The following values can be selected from the drop downlist:
 Custom Connector Custom
 Connector Rate
 Mass Stochastic Mass
 Michaelis Mentens
 MM
 Stochastic Log Normal Mass
Kinetic Style

Kinetic Script

Delay Script

Activity

Priority

Each kinetic style requires different parameters. These
parameters can be specified below Kinetic Script
property:- coefficient1, coefficient2,- variance,- rate,- connector stoichiometry,- speed/add/update- connector speed/add/update.
Only the parameter fields that are meaningful for theselected kinetic style are displayed.
This is not editable property which is generated
automatically using kinetic style property and parameterswhich are displayed below (as a sub tree) this property.
For discrete and generic processes, if the delay time
T >0, then the process fires just after the delay time T if
it is still active. Otherwise, it can lose its chance to fire. If
the delay time T=0, the process fires immediately when it
is possible. For continuous processes, there is no delay;
The process fires immediately when the enabling
conditions become true and its Activity property is set totrue.
If the property is set to false, the process does not fire.
The button allows for the definition of the mathematicalformula within the Script Editor.
Sets the priority of the process during simulation. If two
processes P1 and P2 with equal priority fire at the time t,
the order of firing P1 and P2 is random. But if thepriority of P1 is larger than P2, then P1 always fires
before P2.

Log
Activity Log

7.2.1.3 Connector© 2002-2017 The University of Tokyo. All rights reserved.

Page 65 of 112

Property Name

Description

Kinetic Script
Firing Style

Specifies the way, and how to calculate the firing activityof the connector. The Firing Style can take one of thefollowing values:- Threshold- Rule- No Check

Firing Script

Depending on the Firing Style, this script can define
either the Firing Threshold or the Firing Rule.
Firing Threshold
The Threshold should be used for input connectors todiscrete or continuous entities. The Threshold is a realvalue or a script that returns real value. The Threshold isused to control the connected discrete or continuous
process; If the current value of source entity is larger
than the threshold specified by the connector, theconnector is enabled. If all input connectors of a process
are enabled and the Activity property of the process istrue, the process is enabled.
Firing Rule
The Firing Rule is used to control the enabled/disabledstate of a linked generic process; If the Firing Rule is set
to true, the connector is enabled. As with discrete andcontinuous processes, a generic process is enabled if allof its input connectors are enabled and the Activity
property of the process is set to true. The Firing Rule
option can be a Boolean value or a script that returns a
Boolean value.

Log

Tells, whether to log the process values during
simulation

7.2.1.4 Calculation Style
This section gives more details on the calculation style concept. The tablebelow describes the impact of a firing process on the connected entities for different
process types and calculation styles.

Calc Style

Process behavior© 2002-2017 The University of Tokyo. All rights reserved.

Page 66 of 112

SpeedWhen the process fires, the value of each input/output entity isdecreased/increased by change value (delta). The formula for thechange value (delta) depends on the kinetic style – see the tablebelow.
For the kinetic style Custom the absolute value of delta is thesame for all input/output entities. For all other kinetic styles, thevalue of delta depends on connector specific parameters(e.g. Connector Stoichiometry or Connector Custom. Thus, thedelta value may be different for different input/output entities.

Add

When the process fires, the value of each input/output entity isdecreased/increased by change value (delta). The formula for thechange value (delta) depends on the kinetic style – see the tablebelow.
For the kinetic style Custom the absolute value of delta is thesame for all input/output entities. For all other kinetic styles, thevalue of delta depends on connector specific parameters(e.g. Connector Stoichiometry or Connector Add. Thus, the delta
value may be different for different input/output entities.

UpdateWhen the process fires, the value of each input/output entity is set
to the update value. The script for the update value is specified in
the connector update field. The update value may be different fordifferent input/output entities.

7.2.1.5 Kinetic Styles
This chapter gives more details on the kinetic style concept. The table below
specifies the mathematical formula that is used to calculate the entity value change(delta) for all the various kinetic styles. Also, the parameters used for each kinetic
style are listed in the table.

Kinetic style

Process type

Customcontinuous(speed calc
style)

delta = speed * sampling interval

discrete(add calc
style)

delta = addparameter:
speed / add

Formula for the change value delta© 2002-2017 The University of Tokyo. All rights reserved.

Page 67 of 112

connector
customparameters:
speed / add /update for
eachconnector

Massparameters:
coefficient1,
coefficient2,
stoichiometryfor eachconnector

continuous(speed calc
style)

delta = connector_speed *sampling_interval

discrete(add calc
style)

delta = connector_add

continuous(speed calc
style)

delta = m_product * coefficient1 *coefficient2^[number_of_input_entities] * stoichiometry *sampling_interval
where m_product is the product of all input entity
values. For the input entity variables (m1, m2, ..., mn)
m_product = m1 * m2 * ... * mn

discrete(add calc
style)

delta = m_product * coefficient1 *coefficient2^[number_of_input_entities] * stoichiometry
where m_product is the product of all input entity
values. For the input entity variables (m1, m2, ..., mn)
m_product = m1 * m2 * ... * mn

stochastic
mass
parameters:
coefficient1,
coefficient2,
standard
deviation andstoichiometryfor eachconnector

continuous(speed calc
style)

delta is randomly generated using the Gaussian
distribution with the calculated delta_mean andspecified standard deviation.
delta_mean is calculated using the formula for themass kinetic style:delta_mean = delta_mass(coefficient1, coefficient2,
stoichiometry)© 2002-2017 The University of Tokyo. All rights reserved.

Page 68 of 112

discrete(add calc
style)

delta is randomly generated using the Gaussian
distribution with the calculated delta_mean andspecified standard deviationdelta_mean is calculated using the formula for themass kinetic style:delta_mean = delta_mass(coefficient1, coefficient2,
stoichiometry)

connector
rate

continuous(speed calc
style)

delta = rate * stoichiometry *sampling_interval

parameters:
rate andstoichiometryfor eachconnector
discrete(add calc
style)

delta = rate * stoichiometry

7.2.2 Biological Properties
The biological properties are divided in predefined (or well-known) biologicalproperties and user-defined or custom ones. Both, custom and well known properties,
can be also displayed in Biological Properties frame.
The well-known properties depend on element type and CSO Class, e.g. aprocess will have different properties than an entity. An entity with CSO Class
Protein will have many properties, while a non-biological entity (CSO Class) will
have no biological properties. Therefore the number of rows displayed in the
Biological Properties section changes with the change of element type or CSO Class.
Several Biological Properties can be set with values from a predefined CSO
dictionary. In such a case the CSO Hierarchy tree control will be displayed.

© 2002-2017 The University of Tokyo. All rights reserved.

Page 69 of 112

7.2.3 Custom Biological Properties
The Custom Biological Properties allow the user to add his own properties. To
add a new property:-

Double click the “…” in the New Property row-

Enter the name of the new property, e.g. A

This will display the new property A as a new row in the Custom Biological
Properties. Now you can:-Double click the “…” in the A row to set a new value for that property

7.2.4 Multiple Selection SheetThis pane displays common properties of multiple objects selected in theactive canvas. In this pane you may change a given property for all the selected
objects at once in the following way:-

Select the elements to be modified on the canvas. You might select allelements.

-

Go to the Element Setting frame and find the desired property in the property
tree.

-

Double click the cell and set the new value

Please note that the properties tree is normally in collapsed state and allproperties are hidden. This is done to speed up the software, since the calculation ofproperties for multiple elements might be time consuming.
A concrete value is displayed in the property cell only if all selected cells havethe same value of the property. Otherwise the cell is empty.

The Multiple Selection pane consists of 3 sections (categories) with suchproperties as:-

Shape section: Figure Type, Depth, Size, Fill Color, Line Color, Stroke-

Biological Properties and Custom Biological Properties sections as
described above© 2002-2017 The University of Tokyo. All rights reserved.

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7.2.5 Model and Canvas Property SheetThis pane displays a number of properties describing the model in the active
canvas and the canvas window itself. These properties cannot be edited

7.2.5.1 File Section
Property Name
Name
Modified
LoadedDescription
Full path to the file
Date of the last file modification
Date when the file was opened from filesystem

7.2.5.2 Model Section
Property Name
EditedTotal Count
Entity Count
Process Count
Connector Count
Fact Vertex Count
Fact Edge Count
Group Count

Description
Date when the model was last time edited
Count of all elements in the modelCount of all entities in the modelCount of all processes in the modelCount of all connectors in the modelCount of all fact vertexes in the modelCount of all fact edges in the modelCount of all groups in the model

7.2.5.3 Canvas Section
Property Name
View Size
Actual Size
Antialias Status
Grid Status

Property Name
Organism
Cell Type
Tissue7.3

Description
The size of the visible area
The actual size of the active model
Toggles antialiasing on and off for the active canvas window
Toggles the grid display on and off for the active canvas

7.2.5.4 Biological Section
Description
Defines the CSO property for the model
Defines the CSO property for the model
Defines the CSO property for the model

Navigator© 2002-2017 The University of Tokyo. All rights reserved.

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For a large model, the Navigator frame provides a convenient way to locateand display in the canvas window a desired part of the model. The Navigator displaysa small view of the entire model, with a red rectangle marking the portion of themodel currently shown in the active canvas. You can drag this rectangle around inorder to navigate the model in the canvas window.

7.4

Simulation Settings© 2002-2017 The University of Tokyo. All rights reserved.

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The Simulation Settings frame allows the setting of parameters that control thesimulation execution for the model in the active canvas:
Sampling Interval is the basic simulation input parameter that controls thesimulation accuracy and performance. The smaller the Sampling Interval, thehigher the accuracy.
Simulation Time tells how long the simulation should last. The ratio
Simulation Time/Sampling Interval defines the number of steps to be executedin the simulation.
Chart Update Interval defines how often the Chart Window should be
updated. This parameter has no impact on simulation results.
Canvas Update Interval defines how often the canvas should be updated. Thisparameter is ignored if the simulation is executed in the fastest mode.
All the times are specified in Petri net time units (pt).
For a new model, all the settings are initialized on the base of user preferences– see the Simulation Extra Options in Preferences dialog box. The current
settings are preserved in the model file.
For the Play and Fast Play menu commands, the Speed option specifies how
many times the simulation speed should increase over the speed in the regularPlay mode. In reality, the maximum speed is limited by the hardware on which
Cell Illustrator runs. Simulations started with the Play command with For
Speed value 1, 1pt should be executed in 1 second. Fast Play mode is always
10 times faster than Play mode – for Speed value 1, 10pt should be executed in
1 second. For simulations started with the Fastest Play command, Speed has
no effect and the simulation is run with highest possible speed.
Continuous Weak Firing enables/disables the weak firing option forcontinuous processes. By default, if this option off, a process cannot fire if
there are not enough tokens in a connected input entity, i.e. if the calculateddelta value is greater than the available entity value . Such behavior is inagreement with the Petri Net model, but is sometimes difficult to understandfor normal biological reactions. If this option is on and weak firing is enabled,
the process can fire even if the connected entity value is smaller than the delta
calculated for the current step. In such a case the weak firing scale iscalculated using the formula:o scale = availableDeltaValue / calculatedDeltaValue--

After this the delta value for all input and output entities connected to the“weak firing” process are multiplied by the scale. The scale value is less than
1.
Discrete Weak Firing. Enables/disables the weak firing option for discrete
processes. By default this options is off.
Firing Accuracy. The minimum change value for which a process fires. If thecalculated delta value is less than the firing accuracy, the delta value isthreated as zero and the process does not fire. This option is useful for the caseof entity value converging to a given value in an asymptotic way.
Use SECG determines whether to use the standard simulation engine or thesimulation engine code generator (SECG). Both engines base on the same
simulation model - Hybrid Petri-net with extensions. However the SECG

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executes the simulation in a different way: first Java source code is generated
for the model to be simulated; then it is executed as a usual Java program. The
SECG engine is recommended for the following two cases:o Simulation of large models; SECG will run large models much fasterthan the standard engine.
o Customization/integration of simulation model; The command Export |Simulation Source Code enables you to generate source code that canbe customized by a programmer and/or reused in another software.
Update After Step – defines whether the entity value should be updated after
the step or after each process firing. In the later case the order of process firingin the same step will affect the simulation results.
Default Script Language - defines the default script language for the model.
Save Log File – If this option is true the values of selected elements will be
loggedLog Update Time defines how often the internal simulation log should be
updated. The simulation log can be enabled by Save Log File option in thisframe. This parameter has no impact on simulation results. The Log Update
Time is ignored if the simulation is played in step mode.
Logged Elements – defines which elements should be logged. It offers thefollowing choices:o All Entities – Log all entity values, but do not log other elements(connectors and processes)o All without Firing – Log entity values and process/connector speed forall elements but do not log process stateo All with Firing – Log everything: entity values, process/connector
speed and process state for all elementso Chart – Log these elements which are displayed on charts – see Chart
Settings frame. By default, no one element is added to he chart. In sucha case, nothing will be logged during simulation and a CIL file will not
be created during the simulation.
o Log – Log these elements, which have the log option set to true. This
option is displayed in Element Lists frame. By default, the Log optionof all entities, processes and connectors is off. In such a case, nothing
will be logged during simulation and a CIL file will not be createdduring the simulation.
o Chart and Log – Log all these elements, which are displayed on chartor have the Log option set.
You need to set simulation parameters prior to starting simulation.

7.5

Chart Settings
The Chart Settings frame allows the visualizing of the simulation results withconcentration or amount versus time graphs. You can:- create a new chart,- edit/customize an existing chart, and- remove an existing chart.
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The Chart Tree displays all defined charts and their properties on two levels.
The main level of the tree is the list of charts labeled by the chart names. The leavesof the tree are model elements that are included in the parent chart. A chart candisplay time series of the following simulation values:-

entity value-

process speed-

connector speed
One and the same element can be included in one or more charts.

The checkboxes allow for changing visibility of all charts, a single chart or asingle data series. To hide all charts uncheck the tree root node – Charts.
You can add/define/remove charts or change its properties using context
sensitive popup menu, which depends on selection item and includes the following
commands:

Create New Chart – creates new chart from entities and processes selectedon active canvas. If nothing is selected chart will be empty

Remove All charts – removes all charts defined in active document.



Add Selection from Canvas – adds selected elements to the selected chart,
if selection will be empty nothing happen.If more than one chart isselected, the entities are added only to the first one.



Remove Selected – removes selected elements



Rename – changes name of the chart

Set Item Color – sets color of line on the chart. After add or create chart allitems have random selected color. The User can also change color by
double clicking Chart ItemShow on Canvas – selects related entities or process on the canvas© 2002-2017 The University of Tokyo. All rights reserved.

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Centerize All ChartsCenterize on Canvas – brings chart to the center of canvas

The entity, process and connectors names cannot be edited in the Charts Tree.
The Charts Tree supports multiple selections including all possible combinations ofchart and entity nodes - several charts and entities can be selected at once.

7.6

Simulation History

In this frame, you can view and manage the simulation log files related to themodel displayed in the active canvas. The simulation log file is either a comma
separated value file (CSV) or a CSML file with log items (CIL) located in thesimulation output folder of the model.
The simulation log file is created automatically after each simulation start if
the Save Log File option was enabled in the Simulation Settings frame. Beside theCSV log file, the original CSML file that was used as input for this simulation log isstored in the log output folder .
The Simulation History frame consists of the main table that contains a list of
the log files and a context menu with the following commands: Rerun, Open Log,
Open Backup CSML File, Open Directory, Export CIL/CSV File.
Each row in the Simulation History table represents one log file (CSV or CIL)
and contains the following properties displayed in columns:-

Name – the filename-

Creation Date - date and time of the simulation-

Type – CSV or CIL© 2002-2017 The University of Tokyo. All rights reserved.

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The CI logs are presented in the alphabetical order of their file names. The list
supports multiple selections: zero, one or more items can be selected in the list to
mark the scope of Rerun command.
The button Rerun opens the selected logs (one or more) in the main window of
CI Player application. The main window of CI Player application becomes the active
application and the selected simulation log is ready for a replay.
The command Open opens the selected log file in the default CSV fileviewer/editor.
The command Open Directory opens the simulation output directory that
contains all the log files.
The command Export CIL File allows you to create and save a special CI log
file (CIL) which can be viewed and analyzed in Cell Illustrator Player. A CI log is an
XML file that consists of two parts: the input model and a time series of values for thelogged properties. Since CIL stores the model in the same format as in the original
project file, you can open a log file with Cell Illustrator and edit the model. However,saving the edited model into the original log file will erase the time series and anyother simulation history information. Therefore, you should use the Save As
command of Cell Illustrator if you would like to recover the model from a log file forfurther editing.

7.7

Biological Elements-

While you can use the menu options and toolbar buttons to add elements,
biological pathways can be created faster and more intuitively by dragging anddropping appropriate elements from the Biological Elements frame.

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You can use this frame to:-find a picture that represents a given biological entity, process or cellcomponent-

add a new element to the canvas
replace the image of an existing elements

To find a picture that represents a given biological entity, process or cell component:- Go to the desired tab: Entity, Process or Cell Component.
- Enter one or more characters into the filter box- The possible choices that contain the entered characters are displayed in thedrop down list. Also the list of pictures is filtered, so that only the possible
choices are displayed, while all other pictures are hidden- Select the desired element from the drop down list. The corresponding picture
is displayed.
To insert a biological element, proceed as follows:© 2002-2017 The University of Tokyo. All rights reserved.

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--

Select a picture in the Element, Process or Cell Component tab. The picture
description and size will be displayed in a fly-over help string when you
position the mouse cursor over the picture.
Select the Element/Process Type
Select the Element Size by defining the picture scale.
Click on the chosen picture, drag it to the active canvas and drop it there by
releasing the mouse button.

Pictures from the Entity or Process tabs are inserted as elements of thespecified type: Continuous, Discrete or Generic. Pictures from the Cell Component
tab are inserted as images and they do not have any impact on the simulation results.
To replace the image of an existing element, proceed as follows:- Select a picture in the Element or Process tab. The picture description and size
will be displayed in a fly-over help string when you position the mouse cursor
over the picture.
- Click on the chosen picture, drag it to the active canvas and drop it over the
existing entity or process by releasing the mouse button.
Please note that pictures from the Entity can be used to replace entity elements
only, while pictures from Process tab can replace process elements only. The replace
function is not available for pictures from the Cell Component tab.

7.8Graph Layout

Using this frame, you can “beautify” the graph layout of the model in theactive canvas. This option can be especially useful when importing models from otherformats (e.g. Edge files)© 2002-2017 The University of Tokyo. All rights reserved.

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7.9

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Each of the algorithm buttons BLK, CB, SCCB, Eades, Random Grid,
Adjustment, Sugiyama, CCL, Tree, Radial Tree, Compact Tree, Circle, etc.
start the layout algorithm for the graph that is displayed on the active canvas-

The Enlarge and Shrink buttons allow for linear scaling of the graph in thehorizontal, vertical or both directions.

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Layout Selected Elements Only allows to limit the layout to the canvas
selection.

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Fit Into Original Rectangle allows to keep the graph size unchanged after the
layout operation.

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Advanced Option button – opens the Graph Layout Options dialog .

External References
In this frame you can view/manage references of the selected elements in the active
canvas. You can edit single table cell by double clicking on it or open the context
menu by right clicking on it.

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External References is a frame that displays the list of references associatedwith the currently selected elements.
The references are shown in two tabbed tables: Publications and Database
References.
The reference table displays the reference details in four columns: Database,
Reference Name, Comment and URL. You can edit any of those reference
details by double clicking on the desired table cell.
If more than one element is selected, the references are grouped by their parent
element (entity, process, connector, etc..)
For database and publication references, the name and URL is generated
automatically when the reference is defined. In some cases you might want tochange the default name or URL, e.g. by adding a special, non-default
parameter to the URL. Therefore editing of cells in the table is useful for therefinement of automatically generated URL and name attributes.
Depending on the reference type, the comment property can be used forvarious purposes. E.g. for it can be the term that is defined by a vocabularyreference, or it can be a description of the relationship between the element
and the reference.

7.10 Comments
In this frame you can view/manage comments of the selected element in the active
canvas. You can edit single table cell by double clicking on it or open the context
menu by right clicking on it.
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Comments is a frame that displays the list of comments associated with thecurrently selected element.
The table displays the comments details in two columns: Type and Comment.
You can edit any of those reference details by double clicking on the desired
table cell.

7.11 Project Manager
CI Project Manager is a user interface to pathway models stored onwww.csml.org web site.

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To find a pathway in project tree:- Enter the search string, one or more characters, into the edit box- Press the Next/Previous button to select the next/previous item that matches
the search string.
To open a biological element, proceed as follows:- Select the desired element(s) in the project tree
- Click on the chosen tree item, drag it to the active canvas and drop it there by
releasing the mouse button. This will create a new canvas and drop theselected model there.
- Alternatively, double-click the selected tree-item.

7.12 Parts LibraryWith Part Library, you can organize a repository of frequently used model
parts in a tree. Then, you can assemble more complex models out of lower-level“parts” stored in the repository. Cell Illustrator comes with several pre-registered parts
to demonstrate this function. Models in the repository are organized into a tree ofcomponents. Each model is stored as a separate file in the user’s home folder; thecomponent tree is stored in the parts.xml file.

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-Within the Edit Parts frame, you can:Insert a model part into the active canvas by clicking on its nameOpen a model from the library in a new window.
Add a new part to the repository using Add Model as Part or Add Selection as
Part commands
Manage and organize the parts in the repository by clicking the Create Folder,
Remove, Rename menu item.

All the above commands are available in the popup menu that is displayed after
clicking a tree element with the right mouse button.
To insert/open a part to the active canvas:- Select the desired part to be inserted in the tree
- Right-click on selected item and choose Insert/Open in the popup menu
- Alternatively, click on the chosen tree item, drag it to the active canvas anddrop it there by releasing the mouse button.

7.13 View Settings© 2002-2017 The University of Tokyo. All rights reserved.

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This frame allows you to set global visualization settings for the Cell
Illustrator. The view settings are stored as user preferences and apply also the nexttime you start the application. A change in the settings results in an immediate updateof all canvas windows.


View Mode
This option allows you to change the visibility of several label types by
one click. In the list of available choices, the user can select:All – all label types visible

Edit, Simulation, View – display label types which areimportant for the selected scopeNone –all label types are hidden

Custom – user defined label visibility

Depth Threshold - Display
This option allows you to set depth threshold of active canvas. Every
item on canvas has Depth parameter. Global Depth Threshold Display
setting sets depth that elements can be displayed to. E.g. if entity has
depth of 60, and global Depth Threshold -Display is set to 50, entity
can’t be displayed. To be visible, item must have Depth smaller thanactual Depth Threshold value© 2002-2017 The University of Tokyo. All rights reserved.

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

Depth Threshold - Selection
This option allows you to set depth threshold of active canvas. Every
item on canvas has Depth parameter. Global Depth Threshold setting
sets depth that elements can be selected to. E.g. if entity has depth of60, and global Depth Threshold is set to 50, entity can’t be selected(but is still visible on canvas). To be active, item must have Depthsmaller than actual Depth Threshold value.

Show Label Type
This flag tells whether the selected label type can be displayed. If theflag is off, then the selected label type is always hidden.



Choose Biological Property
In this entry the user can select the biological property that should be
displayed on the canvas.

Save As Custom
This command saves the current label visibility settings to Custom
view mode.

7.14 Biological Properties
For the model in the active canvas, this frame displays elements together with
their biological properties in a tabular view.

The Biological Properties frame consists of the tabbed tables Entity, Process,Connector, Fact Edge, Fact Vertex and Group.
The following operations can be done for each of the table:-

Select an element on the canvas by clicking on a row-

Sort rows according to the specified column by clicking on the column header,-

Filter rows by specified column by clicking on combo box on header of thecolumn,-

Edit a given property by double clicking a cell

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Customize the visible column by right click on column header and choosing
one of the menu items:o Hide column
o Show All Hidden Columnso Select Visible Columnso Restore Default Columns

7.15 Simulation Errors
This frame is displays the errors that occurred during script execution in themost recent simulation.

The frame consists of two panes: the left panes with the list of all errors andthe right pane with the details of the selected error.
Each row in the left pane represents one script execution error. Each error isdescribed by the element name, the error location - number of line and position in thescript and the short error message. Selecting a row in the left pane, selects thecorresponding element on the canvas and displays the error details in the right pane.
Many script execution errors will occur due of invalid script language
selection. A valid script in Java language might be invalid if the script is executed inanother language, e.g. simple-math, Pnuts, or JS. Therefore, if you get many errors,
please make sure that the default script language for the model and the individual
script language for the selected elements are correct.

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7.16 Path Search Results
This frame displays the list of paths that have been discovered during the Path
Search.

Each path is displayed in one row and described by the following properties:
column 1: path length – the number of connectors in the pathcolumn 2: the first entity in the path – the entity specified in the Search
From fieldcolumn 3: connector direction – the direction of the connector between
the first entity (column 2) and the connected process (column 4)
column 4: the first process in the pathcolumn 5: connector direction – the direction of the connector between
the first process (column 4) and the second entity (column 6)
column 6: the second entity in the pathetc.
Click a row in the table to select the corresponding path on the canvas.
CTRL+click (Apple+click on Mac) and SHIFT+click allow for the addition or
removal of multiple items to the selection.

7.17 Expression Plot
The expression plot displays more detailed information about the results of the microarray experiments, which have been executed to obtain a gene network.
Note: To create and view the standard expression plot an additional expression file isrequired. This file contains additional experimental data that is not included in CSML
model file. Each entity must have defined the probeID biological property to matchthe value in expression file. To view the partial residual plot, bspline data stored inedge comments (in CSML file) is required.

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The Expression Plot frame is displayed for the selected pair of entities or for theselected edge. The selected entities are displayed on the X and Y axis.
Note: The expression plot will be displayed only if the canvas selection contains
exactly two entities or exactly one edge. Otherwise the expression plot cannot be
displayed.

To view the expression plot:-

Make sure that the expression file is available. For this, open the Preferences
dialog box and check that the Expression File location is correctly defined in
the Expression Plot section-

Select exactly two entities or exactly one edge on the canvas.

-

Choose Analyze | Expression Plot from the menu or the Expression Plot iconfrom the right side toolbar-

Press the Freeze button to keep the selected expression plot-

Select a pair of entities (or another edge) to view its expression plot.

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8 Dialog Boxes

8.1

Preferences

With the Preferences dialog, you can set the global properties of Cell
Illustrator. The settings are stored as user preferences and apply also the next time you
start the application. A change in the Preferences dialog is effective immediately andapplies to new elements, canvas windows and simulations runs that are executed after
the change unless the setting is one for the whole application, such as the grid size. In
such a case, the setting applies to all (already existing and new) canvas windows. The
Restore Defaults button restores the default (factory) settings for the selected branchof the option tree.

8.2

Compare-In the Compare dialog the user specifies the details of the compare task

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Clicking the OK button compares (merges) two or more networks from theworkspace. This operation compares selected networks and finds the common
part of the networks (intersection), the differences between the networks andthe sum of the networks (union).
The active graph (Main Graph) is treated in a unique way during network
merge: the common processes, entities and edges in the intersection network
and also in the union network inherit their properties from corresponding
processes, entities and edges from the Main Graph.
The other networks are selected in the Compare Graph list.

The following different graph can be generated as Compare result:• Union of Main Graph and Other networks• Intersection of Main Graph and Other networks• Difference between Main Graph and Other networks• Reverse Difference, which is the difference between the union of
Other Networks and Main Graph
If Color Edges option is selected, all edges in Main Graph are marked by one
color denoted by the difference1 color (default is red) and all edges in Network
2 are marked by another color denoted by the difference2 color (default is© 2002-2017 The University of Tokyo. All rights reserved.

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green). The same colors are used for the corresponding edges in the resulting
networks. The edges that are common in Network1 and Network2 are coloredby the intersection color (default value is magenta).
The default values for the predefined colors difference1, difference2 andintersection can be defined in the Preferences dialog box, section Compare
The edge colors resulting from the merging operation are persistent, i.e., you
can save the output networks and view the edge colors after you open thesefiles.
The Gene Net Mode option should be selected for the correct comparison offact edges. If this option is not selected the fact edges will be treated as fact
vertexes.
If the option Force Edges is on, the edges in the output graph areautomatically completed by adding the source and target graph vertexes, even
if the vertexes were removed by the merge operation. If this option is off
incomplete graph edges will not be added to the output graph. This Force
Edges option is important when calculating the difference of the Main Graphand other networks. Please note that if this option is on the difference
operation gives higher priority to edges, rather than to their source and target
vertexes. The difference excludes the common (intersecting) edges from theoriginal Main Graph first. Then, all source and target vertexes are added forthese edges that are left. This means that a common (intersecting) entity orprocess might be in the difference network, if Force Edges is on.

Identity Definitions:- Equality between two graph vertexes (entity or process): two elements areequal if values of the property selected in Comparison Property (e.g. Name,
ID, etc.) is equal.
- Equality between two edges: two edges are equal if their corresponding source
and target are equal according to the above definition of the relation ofequality between the objects.

Constraints:- Two or more models must be opened in the workspace.

8.3

Chart Window
A Chart Window presents how element values change over time in the courseof simulation and the time dependence of one or more element variables in a chart.

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After simulation is started the Chart Windows appear. Each Chart Window
contains the list of the plots defined in the Chart Settings frame. The Chart Window
enables you to:- Display plots with time series of entities, processes, connector values,- Choose which of the plots are displayed or hidden,- Customize chart and plot properties (set colors, fonts etc.),- Zoom in, zoom out and auto range axes,- Save Chart Window as PNG files,- Print chart,- Rasterize (freeze) a specified chart for later analysis or comparison,- Copy the time series to system clipboard in a tab-separated text format. You
can paste the chart data to another application, e.g., Microsoft Word or Excel
The Chart Window consists of the Chart Panel with the time series plots, theElement List Panel, and the popup menu.
8.3.1 Chart Panel
The chart panel presents how element values change over time in the courseof simulation and the time dependence of one or more entity variables in a chart.
Chart Panel update interval depends on the mode of simulation:o in the Step mode: for each step the Chart Window is updated,o in the Play mode: update by each Chart Update Interval, default is one
update per 1 Petri net time,o in the Fast Play or Max Speed mode chart updates are done rarely:
each time the time series increases by 10% or 50% respectively incomparison to the last updated time and at the end of simulation.
You can see the value of the data point once you move the mouse cursor overit. You can zoom into a chart area by dragging the mouse over this area from upper
left to the bottom right corner. To reset the original size drag the mouse in the
opposite direction from the bottom right to the upper left corner.

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8.3.2 Element List Panel
The element panel contains the list of elements displayed in the chart. It consist of
3 columns: Name, Show, Color. In this panel you can:- Show or hide the plot associated with a given element by clicking on the Show
cell of a given element.
- Customize colors of data series in the chart by clicking on the Color cell of agiven element.
8.3.3 Popup menu
Right-click on the chart control opens a popup menu where you can customize
the chart display:-

Properties - set chart visualization properties.

-

Save As – save the chart in PNG file.

-

Print – print image on printer-Zoom In/ Zoom Out – specify the range for x and y axis. Only the data points
that fit that range will be displayed-

Auto Range – Automatically adjusts the range of X and Y axis-

Rasterize - creates a window that is a snapshot of the chart. The snapshot is
not updated during simulation. If you close it, the rasterized chart is destroyed.
In contrast, if the original chart is closed, it just becomes hidden and reappears
at the simulation start.
Copy To Clipboard - Copy the time series to system clipboard in a tabseparated text format. You can paste the chart data to another application, e.g.,
Microsoft Word or Excel-

8.4

Keyword Search
Using this dialog, you can locate elements (entities, processes and connectors)
containing the specified text in one of their properties. The keyword search is
performed by execution of the following steps:-

Enter a search string into the Search For edit box,-

Select search options using the checkboxes-

Select the properties to be searched for, in the Search In panel.

-

Press the Find button.

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-Left click an item in the Search Result list to select the elements

The Keyword Search is a modeless dialog. After finding an element, the user
can switch back to the canvas window and edit the element without closing the
Keyword Search window.
- Regular expressions can be used to find groups of similar elements.
- The following object types can be found: entity, connector, process.
- You can search in the following element properties: element name, element
comment, entity variable name, variable names in scripts, gene extension,
gene id- Elements found in the search process are displayed in the Search Results list
box at the bottom of the dialog. Also, the number of found objects is displayed
above the list box.
- Clicking an item in the Search Results list box selects the corresponding
element in the workspace. CTRL+click (Apple+click on Mac) and
SHIFT+click allow for selecting/deselecting multiple items.
- To select an object, the canvas that has been searched must be active. If theactive canvas is changed after the search, the Search Results list is cleared.
- The Close button dismisses the dialog window.

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8.5

Path Search
Using this dialog, you can find sub-networks around the specified entity orentity-to-entity paths. The path search is done in the following steps:
Select an entity in the Search From combo box.
Select a target entity in the Search To combo box. This step is optional.
Leave the Search To field empty, if you want to find a sub-network
around the specified entity.
Specify the Number of Edges to be searched for.
Specify the search Direction.
Specify the auxiliary options Passing Vertexes
Press the Execute button. This will display the Path Search Results
frame

The Path Search dialog consists of the following controls
8.5.1 Search From Combo Box
In this combo box you can select the starting entity for each search. This
combo box contains list with all entities in the active canvas.
Each entity is represented as a pair Entity Name and Entity Variable Name inthe entity list. The additional variable name is useful to handle ambiguous situations.
In some cases, two entities may have the same Entity Name, but they will possess
different Variable Names.
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8.5.2 Search To Combo Box
In this combo box you can select the target entity for each search. This combo
box contains the list with all the entities in the active canvas.
If this field is empty, the target entity can be any entity in the canvas and thesearch results will include all paths beginning in the Search From.
If this field is not empty the search results will include only those paths thatstart in the Search From entity and end in the Search To entity.
Use this field, if you want to find a path between two entities (entity-to-entity
paths) only. Otherwise, if you want to find a subnetwork around the starting entity
leave this field empty.

8.5.3 Number of Edges
In this field you specify the number of edges to be searched for. To search forthe nearest neighbors only, specify 1. To search for the nearest neighbors plus theirnearest neighbors specify 2. The larger the number of connectors the more search
results will be found.
8.5.4 Direction Combo Box
In this combo box you specify the search direction. You may choose one of
the following 3 possibilities:
Forward - to search for output (target) entities/processes only.
Reverse - to search for input (source) entities/processes only.
Both to search for any connected entities/processes.
8.5.5 Passing Element
A Passing Element is an entity or process that must be included in the Search
Results paths. You may define up to 4 Passing Elements, by specifying their names inthe edit boxes.
8.5.6 Execute Button
This starts the search with the specified options. The discovered paths are
displayed in the Path Search Results frame.

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8.6

Entity List Search

Using this dialog, you can locate a subnet by specifying a list of entity names.

The search is done in the following steps:-

Open the Entity List Search dialog box.

Note: The Search For edit box is initialized by the names of the currently selected
entities. This is useful if you want to search for a subnet that consists of the selected
entities and their connections within a given distance of edges.
-

Enter (paste) the list of names into the Search For edit box

Note: After copying nodes of one canvas, you may paste the list of their names into
any text editor, including the Search For edit box.
-

Select where to search by choosing the options in the Search In box-

Specify the Entity Distance in edges. For the default value 0 no edges will beselected. If the specified edge distance is larger than 0 then all paths (entityedge-entity-edge-entity-...) connecting found entities within the given numberof edges will be selected. The larger the Entity Distance value the moreelements will be selected)-

Press the Select button. The Entity/probe names might be separated by any
standard separator, such as space, tab, coma, semicolon, new line. The entity
name list to be searched for can be copied from an external database or
spreadsheet or from another canvas.

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-

The found sub-network is highlighted on the canvas with the selection color(green is the default). After inspecting the search results on the canvas, you
may change the search criteria (e.g. the Entity Distance) and resume the searchby clicking the Select button.
The Close button dismisses the dialog window.

8.7

Reference Simulation
This dialog is opened by invoking Simulation | Run Reference Simulation.
Reference Simulation gives the user the ability to:-insert reference data contained in CSV file into the simulation
run.

-visually compare simulation results versus reference data.

To setup a reference simulation:-

Load the data file. The file should be a tab-separated values filewith time series data stored in columns. The first row must havethe column headers (names). The first column must be the timecolumn, while the next columns should be identified by unique
names.

-

Map the column names from data file to entity names of thesimulated model. The buttons Automap and Clear are helpful for
this-

Choose the way how the reference data should be displayed oncharts in the Interpolator combo-box (optional step)© 2002-2017 The University of Tokyo. All rights reserved.

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8.8

-

Choose the method and moment of setting values from the list ofavailable choices: Only At Simulation Start, When Presenting
Data, At Each Step.

-

Press the Run button. If the Reference Simulation setup wascorrect, the simulation will be started in the CI workspace.

-

Use the standard buttons Step Play, Play, Pause, Fast Play, etc.
to continue the simulation in the usual way; the results of thesimulation are displayed on charts and/or saved to log file.

SECG Passing Parameters
This dialog allows selecting the entities which should be treated as parametersin the passing parameters simulation. You can specify the parameter range andinterval in a table with available entities.
For example, in the bellow window, the e1 and the e5 entities where selected
to be parameters. The simulation will be run for each combination of the parameters.
In this case entity e1 will have following values 10.0, 12.5, 15.0, 17.5, 20.0, and theentity e5 following 0, 1, 2, 3, 4, 5.

The parameter settings can be saved and load to a text file using the Load andSave buttons. The simulation is executed by pressing Run button. The last button withname Cancel All, cancels (stops) all SECG Passing Parameter simulations,.

8.9

Parameterized Simulation Results
This dialog box is displayed after the SECG parameter simulation has finished.
It enables you to select what should be viewed and how.

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The Chart Type combo box allows specifying what kind of chart should be
used - a 2D chart or a 3D grid or line chart.
In the 3D chart, the simulation results shows the dependency of selected entity
values time series on one and only one parameter value, while other parameters are
fixed (constant). Which parameter dependency is to be reflected on the charts isselected by choosing the entity in the Variable Entity combo box. The actual values ofthe other parameters are selected by choosing the entity in the list and selecting it
value using the Constant Value slider.

8.10 About Cell Illustrator
About Cell Illustrator is a modal dialog that contains tabs: Version, License
Information, Licensed Modules, License, and Third Party Components.
- Version contains the version number and the copyright information.
- License contains the End User License Agreement text.
- License Information sheet displays the license details, including license type,
expiration date, etc.
- License Modules sheet displays the list of modules that are accessible to theuser..
- Third Party Components sheet displays information about software
components used in Cell Illustrator.

© 2002-2017 The University of Tokyo. All rights reserved.

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9 Other
9.1

CSO Class Tree
The Cell System Ontology (CSO) is a dictionary that contains terms for the
specific biological properties, such as biological class and location of the entity,
process or connector. For each biological property there is a limited number ofchoices defined in the CSO Class Tree. The CSO Class Editor facilitatesbrowsing/searching through the hierarchy of the terms and finding/selecting theproper one.
With this editor you can:-Select one element from the CSO hierarchy list of available choices-

Browse through the CSO dictionary-

Find a term in the CSO dictionary, the edit box shows after you press any key

To find a proper CSO term:- Enter one or more characters into the edit box. You can use special characterssuch as:o * - replaces many characterso ? – replaces single character- The possible choices that start with the entered characters are displayed in thetree, you can navigate between them using up and down arrow on yourkeyboard

9.2

Script Editor
An advanced user of Cell Illustrator may need to write a custom function to
specify changes of a property value. With the Script Editor, you can write a scripts todefine:- Threshold, Speed, Updater, and Firing Rule property of a connector,- Activity, Speed and Delay of processes as well as- Initial Value of entities.

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At the top left in the dialog is the Script Language drop-down list.
At the top right, there are 3 buttons: Check, OK and Cancel. You can check
whether the syntax of your script is correct by pressing the Check button. Error
messages will be displayed as tool tip text over the point in the right side of the script
pad. The OK button saves the changes and closes the window. The Cancel button
closes the window without saving any changes.
In the middle, a script pad is placed where you can edit a script either byclicking on the function buttons and selecting entities from the table, or by typing intext.
At the bottom there are 3 lists that facilitate the script creation:-

Operators and Functions: list of common algebraic operators andmathematical functions.

-

Entities: List of all entities in the model.

9.2.1 Script Languages
This combo defines allows the user to select the script language that should be
used for the evaluation of the script. If this field is empty the default language of themodel (defined in Simulation Settings frame) will be used for the evaluation of thescriptNote: For usual scripts, it is recommended to leave the language field empty.
The language should be changed for very specific cases only when defining complex
scripts, e.g. when you would like to add some condition processing or use outsidefeature.

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The scripting framework which executes the scripts can be quite slow.
Fortunately, most of the scripts in Cell Illustrator models are simple mathematicalexpression, e.g. m1*m2, 0.1*m1. Thus, highly customized simplemath scripting
language was developed for this project and added to the scripting framework.
Additionally two types of scripting languages based on Java can be used: java andjava-bulk. For those types the scripts are written in Java, then compiled into java bytecode and executed within the scripting framework as normal java method.

All available Scripting Languages are listed in the table below from the fastest(simplemath, java-bulk) to the slowest (js – javascript, pnuts).

Language

Properties

simplemath

Default Scripting Language
Quite restrictive syntax
Allows writing mathematical expressions and some logical expressions
Provides many mathematical functions (basically it allows doing operations as
medium level calculators)
Very fast (basically one java function is invoked for each operation), quite
similar performance to java for not very complex scripts.
Most of the scripts can be used later in SECG
The syntax supported by simplemath script is summarized in the chapter below.

java-bulk

Identical to java, but all scripts are compiled at once, so the generation ofengine is much faster than java.
Fast. Almost as fast as simplemath. Especially for large models with many java
scripts it is much faster than java.
However there is one drawback: If the script has errors, the error report can only
show the compile error but cannot point out the exact place where the error
script is written, i.e. kinetic script in process p1.
The recommended usage is to switch to java script to check the cause of error
and switch back to java-bulk after the model compiles successfully.
Most of the scripts can be used later in SECG.
Requires JDK, JRE is not enough.

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JavaAllows for writing scripts in normal java code. The code is placed inside a java
function for compilation and execution. Each script is placed into a separate
class file.
Not fast, slower than java-bulk. Recommended for small models only. AlthoughJava is fast during execution, it is slow at startup. Creation of the simulationengine may take a lot of time, since each of scripts is compiled separately.
Most of the scripts can be used later in SECG.
Requires JDK, JRE is not enough.

js

Allows for writing scripts in js (javascript) language.
Not fast, not so fast as java at execution time.
More simple syntax than Java.
Not compatible with SECG. Scripts created in js might not run with SECG.

Pnuts

The Pnuts script is supported mainly for the backward compatibility to previous
Cell Illustrator versions. In CI5.0 the running speed of Pnuts is very slow, since
the implementation of Pnuts is not customized to the java scripting framework.
When loading the model created in CI4.0 to CI5.0, it is recommended to switch
to other supported script language in CI5.0.
In most cases the scripts will work just after switching the script from Pnuts toother language in the Simulation Setting dialog or Element Setting dialog.
If a model contains a few complicated scripts, one solution is to set Pnuts as
language for these complex scripts and set the default scripting language as
simplemath in simulation settings dialog. In such a case the slow Pnuts executor
will be used for the few complex scripts only, while rest of the scripts will be
executed by using the fast simplemath executor.

Note: Very simple scripts (such as ‘1’,’true’,’2.434’ or ‘m1’), are not executedby evaluating the script in the selected language, but they simply return the value as itis written. The definition of simple scripts is summarized in the next chapter.

9.2.2 Simple Scripts Syntax

Simple scripts are scripts that are treated as plain text by the simulation engine.
Such scripts are neither compiled nor executed, but the simulation engine replaces the
script by a value. Thank to that simple scripts are independent from scripting© 2002-2017 The University of Tokyo. All rights reserved.

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language selection, they will always return the same value regardless of the selectedlanguage. The simple scripts can be divided into several types, which are defined byregular expressions:

Type

Regular Expression

ExampleNumber"[+-]?([0-9]*\\.?[0-9]+|[0-9]+\\.?[0-9]*)([eE][+]?[0-9]+)?"-98.76
1.234E-56“true”

true“false”

false

String"\"[^\"]*\""“abc”

Variable"[_a-zA-Z][_a-zA-Z0-9]*"m22

BooleanThe simple scripts might be surrounded by “return” and “;”. In such a case theprogram will detect this and neither compile nor execute the script, but replace it withthe proper value

Examples of simple scripts surrounded with “return” and “;”.
return 1.23;
return 4.56e-789
true;
return false;
return “abc”
m22;© 2002-2017 The University of Tokyo. All rights reserved.

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9.2.3 Simplemath Syntax

The simplemath language is dedicated for writing math scripts, which will be
executed very fast by the simulation engine. A simplemath script consist of exactly
one expression that may include tokens listed in the table below:

Simplemath tokens
TOKEN

Description

Definition

ExampleVARIABLE

Variable Label
identifying an
entity value( 'a'..'z'|'A'..'Z'|'_' )( 'a'..'z'|'A'..'Z'|'_'|'0'..'9' )*m1, m2, m3, etc

VALUE

Number('0'..'9')+('.'('0'..'9')*)?| '.'('0'..'9')+

123.456

OPERATOR

Algebraic
operator:

ADDITIVEOP

m1+2

: '+'

m2*m3

| '-'

m2/m3

MULTIPLICATIVEOP

m1%m2
: '*'
| '/'
| '%'

UNARY

Unary signoperator:

ADDITIVEOP

-m1

: '+'

-6.5

| '-'
COMPARATOR

Comparator
operators: equal,
not equal, lessthan, greater than

EQUALOP

m1 == m2

: '=='

m1 >= 2| '!='NOTEQUALOP
: '<'
| '>'
| '<='| '>='© 2002-2017 The University of Tokyo. All rights reserved.

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LOGICAL

Logical operators

OROP

m1 > 1 || m2 > 1: '||'

m1 > 1 && m2 > 1

ANDOP: '&&'
FUNC

Functions andConstants,rand

rand()

randomsin(m1)gauss
gaussianPIE

PI

pow(m1,2)E
sinhill(1,2,3,4)

cos
tan
asin
acos
atan
ceil
floor
round
exp
log
abs
sgn
signum
min
max
pow
atan2
beta
gamma
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medianSMass
LSMass
LSMass2
hill
err
IF

Question markoperator

QMARK

m1 > 0.5 ? 0 : 1

: '?'
ELSE
: ':'

Parentheses

Brackets)

LPAREN(1+m2)/2: '(';RPAREN: ')';WHITESPACESpaces

WHITESPACE: ( '\t' | ' ' | '\r' | '\n'| '\u000C' )+{ $channel = 99; };© 2002-2017 The University of Tokyo. All rights reserved.

Page 108 of 112

9.3

Kinetic Styles Editor

The kinetic style is a property of the process. It allows to define themathematical formula for the process speed, i.e. how the value of the input/output
entities will be increased/decreased after each simulation step the simulation.

The are several kinetic styles which can be divided into following groups:-

User defined Kinetic Script – in these styles (custom, connectorcustom) theuser may define the process speed by its own custom script.

-

Predefined Kinetic Script – in these styles the script is generated automaticallyfrom the parameters provided by the user.

-

Process specific styles – in these styles (custom, MichealisMenten, Hill) the
speed is the same for all connected connectors, i.e. all connected entities will
be increased/decreased by the same value (delta)-

Connector specific styles - in these styles the speed for each connectedconnector can be different, i.e. each connected entities might beincreased/decreased by a different value (delta). The number of parameters forsuch a connector specific styles is proportional to the number of connectors
connected to this process.

Each kinetic styles requires one or more parameters that are defined in the
Kinetic Script tree below.

The table below gives more details on the kinetic style concept by describing
the mathematical formula that is used to calculate the entity value change (delta) for
all the different kinetic styles. Also, the parameters used for each kinetic style arelisted in the table.

© 2002-2017 The University of Tokyo. All rights reserved.

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Kinetic style

Process type

Customcontinuous(speed calc
style)

delta = speed * sampling interval

discrete(add calc
style)

delta = add

continuous(speed calc
style)

delta = connector_speed *sampling_interval

discrete(add calc
style)

delta = connector_add

continuous(speed calc
style)

delta = m_product * coefficient1 *coefficient2^[number_of_input_entities] * stoichiometry *sampling_interval

parameter:
speed / add

connector
customparameters:
speed / add /update for
eachconnector

Massparameters:
coefficient1,
coefficient2,
stoichiometryfor eachconnector

Formula for the change value delta

where m_product is the product of all input entity
values. For the input entity variables (m1, m2, ..., mn)
m_product = m1 * m2 * ... * mn
discrete(add calc
style)

delta = m_product * coefficient1 *coefficient2^[number_of_input_entities] * stoichiometry
where m_product is the product of all input entity
values. For the input entity variables (m1, m2, ..., mn)
m_product = m1 * m2 * ... * mn

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stochastic
masscontinuous(speed calc
style)

parameters:
coefficient1,
coefficient2,
standard
deviation andstoichiometryfor eachconnectordelta is randomly generated using the Gaussian
distribution with the calculated delta_mean andspecified standard deviation.
delta_mean is calculated using the formula for themass kinetic style:delta_mean = delta_mass(coefficient1, coefficient2,
stoichiometry)

discrete(add calc
style)

delta is randomly generated using the Gaussian
distribution with the calculated delta_mean andspecified standard deviationdelta_mean is calculated using the formula for themass kinetic style:delta_mean = delta_mass(coefficient1, coefficient2,
stoichiometry)

connector
rate

continuous(speed calc
style)

delta = rate * stoichiometry *sampling_interval

parameters:
rate andstoichiometryfor eachconnector
discrete(add calc
style)

delta = rate * stoichiometry© 2002-2017 The University of Tokyo. All rights reserved.

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9.4

SECG
Simulation Engine Code Generator (SECG) is a simulation engine that enables
you to simulate the selected model in a special way. SECG performs the simulation in
the following steps:-

Generate the Java source code that represents the Petri Net model of theselected canvas-Compile the source code using Java Compiler (javac)-

Execute the compiled program-

Save simulation log

Thanks to this approach large models can be simulated much faster than using
the default simulation engine included in CI.
Note: For SECG the java compiler must be available and path to it should be setup
correctly in Preferences dialog box, Simulation Settings panel.

© 2002-2017 The University of Tokyo. All rights reserved.

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