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

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

INTRODUCTION ................................................................................................. 5

2

STARTING CI PLAYER ..................................................................................... 6

3

SUPPORTED INPUT MODEL TYPES ............................................................ 7

4

MAIN WINDOW................................................................................................... 8

5 MENU BAR .......................................................................................................... 9
5.1
File | Open ........................................................................................................ 9
5.2
File | Open Recent Files ............................................................................... 10
5.3
File | Close File .............................................................................................. 10
5.4
File | Close All Files ...................................................................................... 10
5.5
File | Export .................................................................................................... 11
5.6
File | Export All ............................................................................................... 11
5.7
File | Look & Feel .......................................................................................... 12
5.8
File | Print Visible Area ................................................................................. 12
5.9
File | Print........................................................................................................ 13
5.10 File | Exit ......................................................................................................... 13
5.11 Edit | Undo ...................................................................................................... 13
5.12 Edit | Redo ...................................................................................................... 13
5.13 Edit | Find........................................................................................................ 14
5.14 Edit | Select All ............................................................................................... 14
5.15 Edit | Select None.......................................................................................... 14
5.16 Edit | Select Inverse ...................................................................................... 14
5.17 Edit | Align To Grid ........................................................................................ 15
5.18 Edit | Align To ................................................................................................. 15
5.19 Edit | Move To ................................................................................................ 15
5.20 Element | Show All ........................................................................................ 16
5.21 Element | Hide ............................................................................................... 16
5.22 Element | Arrange ......................................................................................... 16
5.23 Element | References ................................................................................... 17
5.24 Element | URL Templates ............................................................................ 18
5.25 Element | Create Chart ................................................................................. 18
5.26 Replay | Play .................................................................................................. 18
5.27 Replay | Step Forward .................................................................................. 19
5.28 Replay | Step Backward ............................................................................... 19
5.29 Replay | Pause .............................................................................................. 19
5.30 Replay | Stop And Initialize .......................................................................... 20
5.31 View | Mode.................................................................................................... 20
5.32 View | Zoom In ............................................................................................... 20© 2002-2017 The University of Tokyo. All rights reserved.

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5.33
5.34
5.35
5.36
5.37
5.38
5.39
5.40
5.41
5.42
5.43
5.44
5.45
5.46
5.47
5.48
5.49
5.50
5.51
5.52
5.53
5.54
5.55
5.56
5.57
5.58
5.59
5.60

View | Zoom Out ............................................................................................ 21
View | Actual Size.......................................................................................... 21
View | Fit In Canvas ...................................................................................... 21
View | Show All Charts ................................................................................. 22
View | Hide All Charts ................................................................................... 22
View | Show Grid ........................................................................................... 22
View | Antialiasing ......................................................................................... 22
View | Grid Size ............................................................................................. 23
View | Background Color.............................................................................. 23
Analyze | Select | Downstream ................................................................... 23
Analyze | Select | Upstream ........................................................................ 23
Analyze | Select | Both ................................................................................. 24
Analyze | Keyword Search ........................................................................... 24
Analyze | Path Search .................................................................................. 24
Analyze | Entity List Search ......................................................................... 24
Window | Tile Horizontal .............................................................................. 25
Window | Tile Vertical ................................................................................... 25
Window | Maximize Canvas ........................................................................ 25
Window | Reset Perspective........................................................................ 25
Window | Show Frame ................................................................................. 25
Window | Hide All Frames............................................................................ 26
Window | Restore All Frames ...................................................................... 26
Window | Preferences .................................................................................. 26
Help | Cell Illustrator Help ............................................................................ 26
Help | User Guide .......................................................................................... 27
Help | CSML Online ...................................................................................... 27
Help | Cell Illustrator Web page .................................................................. 27
Help | About Cell Illustrator .......................................................................... 27

6 TOOLBARS ....................................................................................................... 28
6.1
Draw Toolbar.................................................................................................. 28
6.2
File Toolbar .................................................................................................... 28
6.3
Edit Toolbar .................................................................................................... 29
6.4
Replay Toolbar .............................................................................................. 29
7 DRAWING CANVAS ........................................................................................ 30
7.1
Multiple Views ................................................................................................ 30
7.2
Canvas Popup Menus .................................................................................. 30
8 FRAMES ............................................................................................................. 31
8.1
Element Lists.................................................................................................. 31
8.2
Element Settings ........................................................................................... 35
8.3
Navigator ........................................................................................................ 46
8.4
Simulation Settings ....................................................................................... 47© 2002-2017 The University of Tokyo. All rights reserved.

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8.5
8.6
8.7
8.8

Chart Settings ................................................................................................ 47
View Settings ................................................................................................. 49
Biological Properties ..................................................................................... 50
Path Search Results ..................................................................................... 51

9 DIALOG BOXES ............................................................................................... 53
9.1
Preferences .................................................................................................... 53
9.2
Chart Window ................................................................................................ 54
9.3
Keyword Search ............................................................................................ 55
9.4
Path Search.................................................................................................... 57
9.5
Entity List Search .......................................................................................... 59
9.6
About Cell Illustrator...................................................................................... 60© 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.
Cell Illustrator Player (CI Player) is a part of the Cell Illustrator™ software
package. CI Player enables you to view a Cell Illustrator model and replay asimulation run from a log created with the Cell Illustrator program.
With Cell Illustrator Player, you can:-view pathway models created by Cell Illustrator-

replay a logged simulation run in a step mode, or quickly move
forward and backward to a specific part of a simulation log;-

visualize entity value and process speed/state on the canvas-

display charts with element value changes over time,-compare results of several simulation runs.

Technically, CI Player is a viewer of Cell Illustrator log files. A CI log (CIL)
is an CSML file that consists of two parts: the input model and the time series ofvalues for the logged properties. You cannot edit the model with the Cell Illustrator
Player. Neither can you run the simulation in the CI Player; you can only view the
CSML model created with Cell Illustrator and replay a simulation run recorded with
Cell Illustrator.
CIL is created by the Cell Illustrator during a simulation run if the user
requests logging of simulation results. Each simulation run is stored as a separate file.
The list of log files is available for viewing in the Simulation History dialog in the
Cell Illustrator. Refer to the CI User Guide and CI Reference Manual for instructions
on how to create simulation logs with Cell Illustrator.
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 Player
version 5.0 (CI Player 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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2Starting CI Player
CI Player can be started in three ways:-

from the Cell Illustrator workspace, by pressing the Rerun button in
Simulation History frame. This opens the selected CSV or CIL files in the CI
Player Workspace.

-from the Windows Programs menu, by executing the command Start |Programs | Cell Illustrator | Cell Illustrator Player. This will open an empty CI
Player Workspace. To open a log file, use the File | Open command.

CI Player is a Java Desktop application and can be run directly from the Linux
console or Windows command-line.

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3 Supported Input Model Types
Since the version 3.0, Cell Illustrator Player enables the users to view two
types of models:(i)

Biopathway model dedicated for simulation and modeling of complex
biological processes and systems using Petri Net models(ii)

Gene Relationship Net model dedicated for analysis and exploration ofgene relationship networks.

Biopathway models may include simulation results, which can e viewed andreplayed in CI Player. A typical gene network cannot be simulated, thus it will notinclude the simulation log data.

CI Player can load model from various files formats. The native CI format is
CSML – www.csml.org. CSML file format can be used to represent biopathway andgene net models. It also can store the simulation results. CSML files with simulation
log are called CIL (CI log) files.
Beside CSML files CI player can import other external file formats, such as:-edge file in CSV format
Those non-native files do not include any simulation log data.

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 exploration capabilities.

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

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4 Main Window
The Workspace is the main window of Cell Illustrator Player. The Menu Bar
located at 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
comparison to Cell Illustrator, CI Player does not have menu options for editing amodel and the Simulation menu and toolbar buttons are replaced with the Replay
commands.
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.
During simulation replay, the canvas window is updated with changing entity values
and process states.
In Cell Illustrator Player, the user can open several-

Frames. The contents of these frames 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 chart dialog boxes that
display logged simulation results.

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5 Menu Bar
5.1

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.

-

-

-

-

-

-

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 has the .gon extension. This command opens all versions of CSML
files.
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.
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 Player.
Other File Formats
File | Open command also opens models from other, non-CSML formats, such
as: CSV.
CSV – Edge Files
Imports gene networks from a normal text file with tab separated values.
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.

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-If the file does not include column headers, then the colums will be recognized
as follows:<parent> <child> <edgeScore> <relationType> <bspline>

Constraints:- None5.2

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.

5.3

File | Close File

Description:- Closes the active model file without exiting the program.
- CTRL+W is the keystroke shortcut for this command.
Constraints:- At least one canvas window must be opened in the workspace.

5.4

File | Close All Files

Description:- Closes all model files without exiting the program.
- 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.
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5.5File | Export

5.5.1

Image

Description:- Exports active canvas to JPEG or PNG file
- File name and location is selected by user in dialog window

5.5.2

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.

5.5.3

HTML Report

Description:- Exports the model in the active canvas to a file in HTML format.

5.6

File | Export All
5.6.1

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

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5.6.2JPEG

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

5.7

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

5.8

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.

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5.9

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.

5.10 File | Exit
Description:- Exits the application.

5.11 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.

5.12 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- CTRL+Y is the keystroke shortcut for this command.
Constraints:- There is an action to redo.
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5.13 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.
Constraints:- At least one canvas window must be opened in the workspace.

5.14 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.

5.15 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.

5.16 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.
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5.17 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.
Constraints:- At least one element must be selected in the active canvas.

5.18 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.

5.19 Edit | Move To Top Bottom Left Right
 Top (1px) Bottom (1px) Left (1px) Right (1px)© 2002-2017 The University of Tokyo. All rights reserved.

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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
Constraints:- At least one element must be selected.

5.20 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.

5.21 Element | Hide

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.

5.22 Element | Arrange
 Bring to Front© 2002-2017 The University of Tokyo. All rights reserved.

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 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.

5.23 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.
- External References menu item opens the Error! Reference source not found.
frame where you can view and manage the list of references associated withthe 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.

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

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5.24 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.

5.25 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.

5.26 Replay | Play
Description:- If the model in the active canvas is in the “initialized” or “paused” state, thecommand starts the simulation.
- The Log Update Interval, Replay Speed, Sampling Interval, Simulation Timeand all other simulation settings are properties of the model (CIL file). You
can see these parameters in the Simulation Settings frame.
- 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, one or more Chart Window are
opened when the command 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 theReplay | Stop And Initialize command, or (2) the user has executed theReplay | Pause command, or (3) the simulation time has reached the value
specified (in pt units) by the Simulation time setting in the Simulation Settings
frame.
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Constraints:- At least one canvas is opened in the workspace- The model in the active canvas includes a simulation log- The model in the active canvas is not in the “simulation end” state

5.27 Replay | Step Forward
Description:- The command replays one step from the simulation log for the model in theactive canvas.
- The replay status is displayed at the top of the CI canvas.
Constraints:- At least one canvas is opened in the workspace- The model in the active canvas includes a simulation log

5.28 Replay | Step Backward
Description:- The command replays one step backward from the simulation log for themodel in the active canvas.
- The replay status is displayed at the top of the CI canvas.
Constraints:- At least one canvas is opened in the workspace- The model in the active canvas includes a simulation log

5.29 Replay | Pause
Description:- Pauses a running simulation.
- The simulation can be resumed with the Replay | Play and other playcommands: Step Play, Fast Play, Max Speed Play.
Constraints:- The model in the active canvas includes a simulation log© 2002-2017 The University of Tokyo. All rights reserved.

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5.30 Replay | 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 replay for the model in the active
canvas has been paused or completed.

5.31 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:- None5.32 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.
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Constraints:- At least one canvas window must be opened in the workspace.

5.33 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
Constraints:- At least one canvas window must be opened in the workspace.
5.34 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.

5.35 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.

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

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

5.38 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
Constraints:- At least one canvas window must be opened in the workspace.

5.39 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.

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

5.40 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.
5.41 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.

5.42 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.

5.43 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.

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5.44 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.

5.45 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.

5.46 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.
5.47 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.

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

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

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

5.50 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.

5.51 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:- None5.52 Window | Show Frame
Description:- Display and activate the selected frame.
- This command drops down the list of all frames available in Cell Illustrator.

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

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Constraints:- None5.53 Window | Hide All Frames
Description:- Hide all frames and display the canvas window in maximal size.
Constraints:- None5.54 Window | Restore All Frames
Description:- Restore the frames which were hidden, e.g. by Window | Hide All Framescommand or other user actions.
Constraints:- None5.55 Window | Preferences
Description:- Opens the Preferences dialog box, in which the user can view/edit the global
settings.
Constraints:- None5.56 Help | Cell Illustrator Help
Description:- Opens the HTML help system for Cell Illustrator.
Constraints:-

Internet connection is required© 2002-2017 The University of Tokyo. All rights reserved.

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5.57 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
5.58 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 and OWL
ontology that is used in Cell Illustrator to store and exchange models.
Constraints:- The Internet connection must be available.

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

5.60 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 27 of 60

6 Toolbars

6.1

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

Description

Zoom In

Push this button to zoom in.

Zoom Out

Push this button to zoom in.

Reset Zoom

See View | Actual Size

Fit in Canvas

See View | Fit In Canvas

Toggle theAntialiasing Status
Toggle the Grid
Visible Status
Set View Mode

6.2

See View | Antialiasing
See View | Show Grid
With this button, you can set
global view mode. See
View | Mode

File 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

Open Canvas File

See File | OpenNo

Close FileNo

Close All Files

See File | Close File
See
File | Close All Files© 2002-2017 The University of Tokyo. All rights reserved.

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6.3

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

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

Align Vertical
Align Horizontal
Space Evenly VerticalSpace Evenly Horizontal

6.4

Replay 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
Replay Simulation

Description
See Replay | Play

Step Forward

See Replay | Step

Fast Play Simulation

See Replay | Step Backward

Pause Simulation
Stop Simulation andInitialize

See Replay | Pause
See Replay | Stop And Initialize© 2002-2017 The University of Tokyo. All rights reserved.

Page 29 of 60

7 Drawing Canvas

The canvas window is the place where you view the model. During simulation,
the canvas window is updated with entity value changes. In some simulation modes,
processes that fire are marked with color and animated tokens 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.

7.1

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 make elements visible,
execute Element | Show All command or change the Visible flag in Element Lists
frame

7.2

Canvas Popup Menus

In addition to commands available in the Menu Bar and the toolbars, you canright click (CTRL click on a Macintosh) on selected element(s) in the canvas toaccess a popup menu customized to your selection.

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

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8 Frames

8.1

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,-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

8.1.1

Entity Table

Each row in the table corresponds to an entity in the active canvas. The
following properties are listed in the table:o Element Id – unique identifier (not editable)o Name – entity name© 2002-2017 The University of Tokyo. All rights reserved.

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o CSO Class – Cell System Ontology Classo 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.
o Variable – name of variable associated with the entityo Initial Value – initial value or script for simulationo Eval Once – tells whether the Initial Value script is evaluated only
once at the simulation start up, or many times at each simulation stepo Max Value – maximum value of the entity during simulationo Min Value – minimum value of the entity during simulationo 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.
o 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.
o Visible – toggles element visibility on the canvas.
o Show Name – toggles visibility of name label on the canvas.
o Show Variable – toggles visibility of variable label on the canvas.
o Show Value – toggles visibility of value label on the canvas.
o Show Biological Property – toggles visibility of biological property
label on the canvas.
o Depth – changes how deep will be the entity painted.
o Location – biological location of the entity.
o GO, PubMed - display database IDs defined in external references(read-only)
o TRANSFAC, TRANSPATH – display Transpath database ID definedin external references (read-only)

8.1.2

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
connectors of type Inhibitor or Association. For the “Or” firing style atleast one Inhibitor or Association connector must fulfill the firing© 2002-2017 The University of Tokyo. All rights reserved.

Page 32 of 60

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

8.1.3

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

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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.
8.1.4 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 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)
8.1.5 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 Visible – toggles visibility of selected element.
o Depth – changes how deep will be the entity painted.
8.1.6 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.
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© 2002-2017 The University of Tokyo. All rights reserved.

Page 34 of 60

8.2

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 35 of 60

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 36 of 60

8.2.1

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 Error! Reference source not found..

8.2.1.1 Entity
Property NameType
Variable

Initial Value

Eval Once

Max Value
Min Value
Log
GlobalDescription
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 Error!
Reference source not found..
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.

8.2.1.2 Process
Property Name

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

Description

Page 37 of 60

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 38 of 60

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 Error! Reference source not found..
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

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

Page 39 of 60

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

8.2.1.4 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 40 of 60

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.

Check

8.2.1.5 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 41 of 60

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 42 of 60

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)

8.2.2

delta = rate * stoichiometry

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 43 of 60

8.2.3Custom 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

8.2.4

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.

Page 44 of 60

8.2.5Model 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

Property Name
Name
Modified
Loaded

8.2.5.1 File Section
Description
Full path to the file
Date of the last file modification
Date when the file was opened from filesystem

Property Name
EditedTotal Count
Entity Count
Process Count
Connector Count
Fact Vertex Count
Fact Edge Count
Group Count

8.2.5.2 Model Section
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

Property Name
View Size
Actual Size
Antialias Status
Grid Status

8.2.5.3 Canvas Section
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

Property Name
Organism
Cell Type
Tissue8.2.5.4 Biological Section
Description
Defines the CSO property for the model
Defines the CSO property for the model
Defines the CSO property for the model© 2002-2017 The University of Tokyo. All rights reserved.

Page 45 of 60

8.3

Navigator

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.

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

Page 46 of 60

8.4

Simulation Settings

-

-

-

8.5

The Simulation Settings frame displays simulation parameters 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).

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.

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

Page 47 of 60

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.

8.6

View Settings

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.

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

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

8.7

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

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.

Biological Properties

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

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

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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-

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

8.8

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

Search.

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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.

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

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9 Dialog Boxes

9.1

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.

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

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9.2

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.

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.
9.2.1

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.
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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.
9.2.2

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.
9.2.3

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-

9.3

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

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

-

Press the Find button.

-

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.
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-

9.4

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.

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 Error! Reference source
not found. frame

The Path Search dialog consists of the following controls© 2002-2017 The University of Tokyo. All rights reserved.

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9.4.1

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.

9.4.2 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.

9.4.3

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.
9.4.4

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.
9.4.5

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.

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9.4.6

Execute Button

This starts the search with the specified options. The discovered paths are
displayed in the Path Search Results frame.

9.5

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

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-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.

-

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.

9.6

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 user’s license details, including
license type, expiration date, etc.
- 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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