CADLIVE Ver.2.15
Operation Manual
2004.03. Kyushu

Instituteof Technology

CONTENTS
1 CADLIVE ........................................................................................................................... 3
2 System Requirements........................................................................................................ 3
3 Installation.......................................................................................................................... 4
3.1 Installing the JavaTM 2 Runtime Environment.............................................................. 4
3.2 Installing CADLIVE...................................................................................................... 44 Start-up .............................................................................................................................. 5
4.1 Start-up of CADLIVE ................................................................................................... 5
4.2 Creating a New Network ............................................................................................. 6
4.3 Loading the Existing Network...................................................................................... 95 Network Constructor ........................................................................................................ 10
5.1 Explanation of Objects on the Network Constructor .................................................. 10
5.1.1 Panel ..................................................................................................................10
5.1.2 Specie Palette..................................................................................................... 10
5.1.3 Reaction Palette ................................................................................................. 10
5.1.4 Modifier Palette................................................................................................... 10
5.1.5 Gene Palette....................................................................................................... 11
5.1.6 Compartment Display Box .................................................................................. 11
5.1.7 Synchronize Button............................................................................................. 11
5.1.8 Edit Compartment Button ................................................................................... 11
5.1.9 Expand Button .................................................................................................... 125.1.10 Zoom Out Button .............................................................................................. 125.1.11 Zoom In Button ................................................................................................. 13
5.1.12 Zoom Magnification Display Box....................................................................... 13
5.2 Positioning the Symbol.............................................................................................. 14
5.2.1 Positioning the Specie ........................................................................................ 14
5.2.2 Positioning the Reaction ..................................................................................... 14
5.2.3 Positioning the Modifier ...................................................................................... 16
5.2.4 Positioning the Gene .......................................................................................... 17
5.2.5 Positioning the Option......................................................................................... 17
5.3 Moving the Symbol.................................................................................................... 20
5.3.1 Moving the Specie .............................................................................................. 20
5.3.2 Moving the Reaction ........................................................................................... 20
5.3.3 Moving the Modifier ............................................................................................ 20
5.3.4 Moving the Gene ................................................................................................ 20
5.3.5 Bending the Symbol............................................................................................ 20
5.4 Deleting the Symbol .................................................................................................. 21
5.4.1 Deleting the Specie............................................................................................. 21
5.4.2 Deleting the Reaction ......................................................................................... 21
5.4.3 Deleting the Modifier........................................................................................... 21
5.4.4 Deleting the Gene............................................................................................... 22
5.5 Connecting the Symbol ............................................................................................. 23
5.5.1 Connecting the Reaction, Modifier and Specie ................................................... 23
5.5.2 Connecting the Gene and Specie ....................................................................... 23
5.5.3 Connecting the Modifier and Reaction................................................................ 23.

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6 Data Editor....................................................................................................................... 24
6.1 Explanation of Objects on the DataEditor.................................................................. 24
6.1.1 Specie Spreadsheet............................................................................................ 24
6.1.2 Reaction Spreadsheet ........................................................................................ 24
6.1.3 Save Button ........................................................................................................ 24
6.2 Explanation of Specie Items ...................................................................................... 25
6.3 Explanation of the Reaction Items............................................................................. 27
7 Explanation of Menu Items .............................................................................................. 29
7.1 File Menu .................................................................................................................. 29
7.1.1 New .................................................................................................................... 29
7.1.2 Open................................................................................................................... 29
7.1.3 Save ................................................................................................................... 29
7.1.4 SaveAs ............................................................................................................... 29
7.1.5 Import ................................................................................................................. 30
7.1.6 Export ................................................................................................................. 30
7.1.7 Print ....................................................................................................................31
7.1.8 Search ................................................................................................................ 31
7.1.9 Exit...................................................................................................................... 32
7.2 Edit Menu ..................................................................................................................33
7.2.1 EditCompartment................................................................................................ 33
7.3 Window Menu ........................................................................................................... 33
7.3.1 DataEditor........................................................................................................... 33
7.3.2 NetworkConstructor ............................................................................................ 34
7.4 Config Menu.............................................................................................................. 34
7.4.1 SmallMolecule .................................................................................................... 34
7.4.2 SymbolColor ....................................................................................................... 35
7.5 Help Menu................................................................................................................. 36
7.5.1 About CADLIVE .................................................................................................. 36

Notice:There are two kinds of CADLIVE editors: the GUI editor and text editor. Users arerecommended to draw a large-scale biochemical network by using the GUI editor and toelaborately edit the generated regulator-reaction equations by using the text editor. The text
editor handles the XML file created by the GUI editor, but the GUI editor cannot read the
XML file edited by the text editor.

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1 CADLIVECADLIVE is a system for constructing large-scale biological networks (metabolic and gene
regulatory networks) using GUI (Graphic User Interface) and saving them as regulator
reaction equations in a database in the format compatible to a simulator. It has beendeveloped by Professor Kurata at the Kyushu Institute of Technology together with staffs at
Mitsui Knowledge Industry Co., Ltd.
There are two kinds of CADLIVE editors: the GUI editor and text editor. Users arerecommended to draw a large-scale biochemical network by using the GUI editor and toelaborately edit the generated regulator-reaction equations by using the text editor. The text
editor handles the XML file created by the GUI editor, but the GUI editor cannot read the
XML file edited by the text editor.

2 System Requirements
Hardware Configuration:
CPU:Pentium3 500M Hz or higher
Memory:128MB or more (256MB or more recommended)
HDD:1Gb or more recommended
Software Configuration:
Windows 98, NT4.0, 2000, XP
JavaTM 2 Runtime Environment 1.3.

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3 Installation
3.1 Installing the JavaTM 2 Runtime Environment
Double-click the j2re-1_3_1_03-win-i.exe on the CD-ROM.
Follow the on-screen instructions to complete the installation process.
Skip this process if JavaTM 2 Runtime Environment or JavaTM 2 Standard Development Kit
1.3 or later is already installed.
3.2 Installing CADLIVE
Double-click the setup.exe. icon on the CD-ROM.
Follow the on-screen instructions to install CADLIVE directly below the C drive.
(Installation will be completed by pressing the NEXT button and Install button.)

To uninstall CADLIVE, double-click the unins000.exe icon installed on the directory. OnceCADLIVE is uninstalled, all the existing files as well as the existing network data will bedeleted. If you need the network data, make sure to save it as backup on another directory
before uninstalling.

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44 Start-up
4.1 Start-up of CADLIVE
Make sure that JavaTM 2 Runtime Environment (1.3) has been installed.
Select CADLIVE from the Program menu or double-click the "CADLIVE32.exe" on the
directory (C:¥CADLIVE) where CADLIVE is installed.
Note that CADLIVE needs more than 4000 kB memory allocation.

Start-up Screen.

54.2 Creating a New Network- OpeningDialog box

Select "Network Construction."
Click the [Next>] button.

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- Component layout using the Cell Comp Dialog box

Select Components from the select box for editing cellular components.
*There are nine types of Components: Environment, Cytoplasm, Nucleoplasm, ER,
Mitochondria, Golgi, Chloroplast, Membrane and Others.
*If "Others" is selected, its name can be edited arbitrarily.
Select the form (circle or rectangle).
If the panel is clicked, the object will be placed in the designated form of the designatedComponent.
*By dragging the object, it can be moved to a new location.
*By dragging the toggle button on the object, its size can be changed.
*When two objects are overlapped, the overlapping object will have priority over theother. The overlapped part will then be invalid.
* By right-clicking on the object and selecting Delete, the object will be deleted.

- VolumeDialog.

7In order to define the Volume of Compartment, select the specified Compartment and click
the Volume on the right-click menu. Put an appropriate value in the Volume box and click
the [OK] Button.
* Regarding Compartment whose name is the same, setting the value of Volume reflects
all the values of Compartment Volume.
After finishing placing all objects, click the [OK] button.

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84.3 Loading the Existing Network- OpeningDialog

Select the Existing Network
Click the [Next>] button.
- OpenNetWorkDialog

ModelName and ModelInfo will be displayed in a list.
Select the ModelName of the network to load.
Click the OK button.

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95 Network Constructor
5.1 Explanation of Objects on the Network Constructor

5.1.1 Panel
This is the field used to position and draw Symbols.
have been selected from the Component Dialog box.

One sees the Components that

5.1.2 Specie PaletteThis palette is used to position RNA, protein, metabolite, environmental factor, ion
signal, or others.
5.1.3 Reaction PaletteThis palette is used to position binding, binding_with_stoichiometric_changes,
homo_association_or_modification,
homo_association_or_modification_with_stoichiometric_changes,
reversible_conversion, irreversible_conversion, transitionState, degradation,transport, or translation.
5.1.4 Modifier PaletteThis palette is used to position activator, inhibitor,or enzyme.

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105.1.5 Gene PaletteThis palette is used to position transcription, protein_synthesis, or regulatory regions ofa gene (enhancer, promoter, other).
5.1.6 Compartment Display Box
This box displays the Component that is selected in the panel.
5.1.7 Synchronize Button
Clicking this button will synchronize data on the Network Constructor with the other
Windows.
5.1.8 Edit Compartment Button
Clicking this button will display the Window to reedit Compartment.

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5.1.9 Expand Button

Clicking this button will expand the drawing area of the panel in the upper left or lower
right direction. Since the area of the environment is enlarged, one can change the sizeof area of cellular compartments of interest.
5.1.10 Zoom Out Button

Clicking this button will reduce the viewing area of the panel (Individual Symbols will be
reduced accordingly.) The area can be zoomed out up to 25%.

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5.1.11 Zoom In Button

Clicking this button will expand the viewing area of the panel (Individual Symbols will beenlarged accordingly.) The area can be zoomed in up to 400%.
5.1.12 Zoom Magnification Display Box
The box displays the current zoom magnification.

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5.2 Positioning the Symbol
5.2.1 Positioning the Specie
The Specie is an element that expresses a biomolecule and can become a node of
biological networks.
- Positioning the Specie
Click any Specie to be positioned on the Specie palette, making it "selected."
Click the Specie once again at the location that you want to position it in the panel. The
Specie will be positioned in the panel.
The Specie data that is set in the spreadsheet of the Data Editor is displayed at thesame time as the Specie is placed on the panel.

RNA

Denotes RNA

protein

Denotes Protein

metabolite

Denotes Metabolite

environmental_factor

Denotes Environmental Factor

ion_signal

Denotes Ion Signal

othersDenotes Others"DNA" denotes DNA.
* Use Gene (5.2.4) for layout.
"complex" denotes a complex.
* Position Complex using binding, homo_association_or_modification.
(5.2.2)"modified" denotes a modified substance.
*Position Modified substance, use binding_with_stoichiometric_changes,
homo_association_or_modification_with_stoichiometric_changes(5.2.2)"text_option" denotes text data necessary for detailed reactions.
* Position text_option using Option (5.2.7) of Reaction.
"small_molecule" denotes small compound.
* Position small_molecule_option using Option (5.2.7) of Reaction.

5.2.2 Positioning the Reaction
Reactions are the elements that are described as lines of biological networks, denoting
various biochemical reactions and formations of complexes.
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- Positioning the Reaction
Click any Reaction to be positioned on the Reaction palette, making it "selected."
Click the Reaction one more time at the location where you want to position it on thepanel. The reaction is placed on the panel. By dragging either node of the reaction onto
the Symbol of the Specie, reaction can be connected with the specie. Both ends of thearrows turn red in color when the specie is successfully connected to the reaction. The
reaction data appear in the spreadsheet of the Data Editor in the timing of connecting
the reaction arrow to the Specie that satisfies the reaction equation.
binding
denotes the reaction that forms a complex.
binding_with_stoichiometric_changes
denotes the reaction that forms a complex
with a chemical process (stoichiometric).
homo_association_or_modification
denotes the association of identical molecules.
homo_ association_or_modification_with_stoichiometric_changes
denotes the modification of small molecules.
reversible_conversion
denotes reversible conversion.
irreversible_conversion
denotes irreversible conversion.
degradation
denotes degradation reaction.
translation
denotes translation reaction.
transport
denotes transport reaction.
*If Transport is used, a Specie identical to its reactant willautomatically be registered in the Compartment where thespecie is transported.
elimination
denotes eliminating a molecule from the complex.
elimination_with_stoichiometric_changes
denotes eliminating a molecule from the modified
molecule.
* Use Option (5.2.7) for elimination andelimination_with_stoichiometric_changes.
reversible_conversion_regarding_multicompornent
denotes reversible conversion regarding
multiple species.
irreversible_conversion_regarding_multicompornent
denotes irreversible conversion regarding
multiple species*Position
reversible_conversion_regarding_multicompornent
and irreversible_conversion_regarding_multicompornent using
the Symbol of TransitionState.

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Click the Transition State on the Reaction palette, making it "selected."

Click it once again at the location that you want to position it in the panel.
Transition State will be positioned in the panel.

If Transition State is right-clicked, Set SmallMoleculeOption, Set TextOption,
Delete, reversible-conversion out, reversible-conversion in,irreversible-conversion out, irreversible-conversion in will be displayed.
Thus, when creating reversible_conversion_regarding_multicompornent,
use reversible-conversion out and reversible-conversion in,
and when creating irreversible_conversion_regarding_multicompornent,
use irreversible-conversion out and irreversible-conversion in.
transcription
protein_synthesis* Position transcription and protein_synthesis using Gene (5.2.4).
5.2.3 Positioning the Modifier
The Modifier is an enzyme that catalyzes reaction, or a regulator that activates or inhibits areaction. Regulators can also express the reaction for activation or inhibition of the Specie or
another Modifier.
- Positioning the Modifier
Click Modifier on the Modifier palette, making it "selected."
Click it once again at the location that you want to position it in the panel. Modifier will
be positioned in the panel.
activation
denotes Activation
inhibition denotes Inhibition
enzymedenotes Enzyme Reaction* Enzyme can be connected only to protein, complex, modified.

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5.2.4 Positioning the Gene
Functions of Gene are Specie elements such as DNA and transcription, as well as reaction
elements such as protein synthesis.
- Positioning the Gene
Click Gene on the DNA palette, making it "selected."
Click it once again at the location that you want to position it in the panel. Gene will bepositioned in the panel.
transcription

Collectively denotes the coding region
and transcription reaction
protein_synthesis Collectively denotes the coding region,transcription and translation reaction.
other_gene
denotes the regulatory region(enhancer or promoter).
* Transcription is connected only to RNA.
* "protein_synthesis" is connected only to protein. When using protein_synthesis, RNAwill be registered as Specie while transcription and translation will be registered as
Reaction.
5.2.5 Positioning the Option- Positioning the elimination, elimination _with_stoichiometric_changes
Right-click homo_association_or_modification or
homo_association_or_modification_with_stoichiometric_changes, andselect SetElimination or SetEliminationWithStoichiometicChanges.

- Positioning the Text Option
Right-click the arrow for Reaction (homo_association_or_modification,
homo_association_or_modification_with_stoichiometric_changes, elimination,
elimination_with_stoichiometric_changes,reversible_conversion,
irreversible_conversion, reversible_conversion_regarding_multi_component, or
irreversible_conversion_regarding_multi_component)
to open Text Option and select Set Text Option.

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Input Option data by following the Text Option Dialog box.

*Input the number of Species on the Reactant side of Reaction to which Text Option
will be added (can be selected from numbers from 2 to 10, or Poly, Hyper or Hypo).
*Input the number of Specie on the Product side of Reaction to which Text Option will
be added (can be selected from numbers from 2 to 10, or Poly, Hyper or Hypo).
*Input the Specie data to which Text Option will be added.
If the data is "+," it will be registered in Reactant.
If it is "-," it will be registered in Product.
However, it will always be positive in Homo_association_or_modification or
Homo_association_or_modification and it will always be negative in
Elimination, Elimination_with_stoichiometric_changes
The number of Text Option of Specie can be selected from numbers between 2 and10, or Poly, Hyper or Hypo. The name input in the lower box will be registered asSpecie Name.
- Layout of Small Molecule Option

Right-click Reaction that can position SmallMoleculeOption
and select "Set SmallMoleculeOption."
In order to add Option to ReversibleConversion, IrreversibleConversion,
reversible_conversion_regarding_multi_component or
irreversible_conversion_regarding_multi_component, the specie name before and after
the reaction can be edited. The default is Reactant and Product as follows.

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To set up SmallMoleculeOption regarding
Homo_association_or_modification_with_stoichiometric_changes, select Reactant
and Product from the dialog box.

The substance in JunctionKey will be added to Modified.
- Positioning the Option Transport
By right-clicking on the Transport and selecting SetOptionTransport, users are able to draw
the reversed transport.

Since Option transport is able to connect not only to the transported Reactant but also to therelated Specie, users are able to draw the transportation between multiple compartments.

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195.3 Moving the Symbol
5.3.1 Moving the Specie
By dragging the Symbol viewing area of the Specie , it can be moved.
However, TextOption and SmallMoleculeOption cannot move individually.
They move according to the movement of the added Reaction.
5.3.2 Moving the Reaction
By dragging one end node of Reaction, one can rotate, expand and contract Reaction
using the opposite node as an axis. However, TransitionState will move in line with theSpecie. The Reaction connected to the Specie moves in accordance with the
movement of its connecting end of the Specie.
5.3.3 Moving the Modifier
By dragging one end node of the Modifier, one can rotate, expand or contract theModifier using the other end node as an axis. However, TransitionState will be moved
in line with the Modifier. The Modifier connected to Specie, Reaction or another Modifier
move in accordance with the movement of its connecting end of the Symbol.
5.3.4 Moving the GeneBy dragging the Symbol viewing area of the Gene, it can be moved. By dragging theone end node of the Gene, one can rotate, expand and contract Reaction using theSpecie as an axis. The Reaction area of the Gene connected to Specie can movefollowing the movement of its connecting end of the Specie.
5.3.5 Bending the Symbol
To draw a polygonal line, right-click the line segment you want to change, and select"PolygonalLine" from the Popup menu.

A handle (Red Squares) will appear in the center of the designated line. By dragging
the handle, a polygonal line can be drawn. A polygonal line can be bent up to fourtimes.

To make the polygonal line back to a straight line, right-click the line segment and selectStraightLine from the Popup menu.

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If there is Modifier attached to that line segment, right-click to draw a polygonal line on
the Reactant side. Modifier will move towards the Product side. Likewise, if one
draws a polygonal line by right-clicking on the Product side, Modifier will move towards
the Reactant side.

Right-clicking on the Reactant side

Right-clicking on the Product side

5.4 Deleting the Symbol
5.4.1 Deleting the Specie

By right-clicking on the Symbol viewing area of the Specie and selecting "Delete," theSpecie can be deleted. To delete TextOption or SmallMoleculeOption, right-click theReaction viewing area where Option has been positioned, and select"DeleteTextOption" or "DeleteSmallMoleculeOption." Also, if one deletes the Reaction
where Option has been positioned, Option will be deleted as well.
5.4.2 Deleting the Reaction

By right-clicking on the Reaction and selecting "Delete," Reaction can be deleted. If
both end nodes are connected, Reaction can be deleted by right-clicking the line andselecting "Delete."
5.4.3 Deleting the Modifier

By right-clicking on the Modifier and selecting "Delete," Reaction can be deleted. If
both end nodes are connected, Modifier can be deleted by right-clicking the line andselecting "Delete.".

215.4.4 Deleting the GeneBy right-clicking the Specie viewing area of Gene and selecting "Delete," Gene canbe deleted. However, one cannot do so by right-clicking the Reaction area.

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5.5 Connecting the Symbol

5.5.1 Connecting the Reaction, Modifier and Specie
By dragging the either node of the Reaction and Modifier onto the Symbol of the Specie,
Reaction and Modifier can be connected with the Specie.
Both ends of the arrows turn red in color when the Specie is successfully connected to
the Reaction.
5.5.2 Connecting the Gene and Specie
By dragging the end node of Transcription and Protein_synthsis onto the Symbol ofSpecie, DNA (Transcription, Protein_synthsis) and Specie can be connected.
5.5.3 Connecting the Modifier and Reaction
By dragging the tip of Modifier onto the Reaction or another Modifier 's line, Modifier,
Reaction, or another Modifier can be connected.

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6 Data Editor
6.1 Explanation of Objects on the DataEditor

6.1.1 Specie Spreadsheet
This is the spreadsheet used to display, input and edit attribute data of the Specie andBlackBox positioned by NetworkConstructor. Before inputting texts, make sure that the
input cell is "selected." After inputting text, press the return key to define it.
6.1.2 Reaction Spreadsheet
This is the spreadsheet to display, input and edit attribute data of Reaction positioned
by NetworkConstructor. Before inputting text, make sure that the cell to input data in is"selected." After inputting text, press the return key to define it.
6.1.3 Save Button
Network data created and edited by NetworkConstructor or DateEditor will be saved in
the model folder on the XML database (C: ¥CADLIVE¥data)
It is the same function as the Save in the File menu.

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246.2 Explanation of Specie Items- SpecieName
The Specie positioned will be given as a temporary name in the system, which can beedited by DataEditor.
*The name connecting the SpecieName with colons like "A:B:" is given as a Complex;
the name connecting SpecieName with hyphens like "A-B-" is given as a Modified.
Such generated Specie name cannot be changed. However, the name of RNA
generated by ProteinSynthesis can be edited.
- SpecieClass
Material denotes material attributes of the Specie generated by
NetworkConstructor.
DNA
RNA
proteinmetabolite
environmental_factor
ion_signal
complexmodifier_complex(Enzyme-substrate complex: Specie that is
automatically created by the system, cannot beedited by users)
modified (Modified Substance)
text_option(Specie Generated by a text_option)
small_molecule (Specie Generated by a small_molecule_option)others- BindingSite
It selects the classification of the DNAs that neither encode any protein nor RNAs asa material attribute.
enhancer: activating factor binding site of DNAs
promoter: inhibiting factor binding site of DNAsother
: non-specific binding sites of DNAs
The default is other. Depending on the selection box, the displayed content can bechanged.
- Compartment
Component denotes location attributes of the Specie generated by
NetworkConstructor.NetworkConstructor.
environment
cytoplasm
nucleoplasmERmitochondria
golgi
chloroplast
membrane
other

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- MassBalance
Select MassBalacne attribute in the ListOfSpecies.
off: It does not require any mass balance equation.
on: It requires a mass balance equation.
When the SpecieClass is RNA, Protein, Metabolite, Complex or Modified, the default
will display "on," if not, the default will display "off." The viewing content can bechanged using the selection box.
- TotalAmount
Select TotalAmount attribute in the ListOfSpecies.
constant: constant in a differential equation
variable: variable in a differential equation
If the SpecieClass is DNA, metabolite, environmentl_factor, ion_sygnal,
small_molecule and other, the default “constant” will appear. If not, the default“variable” will appear. Depending on the selection box, the displayed content
can be changed.
- Decomposition
Select Decomposition attribute in the ListOfSpecies.
on: generates the decomposition term in a mathematical modeloff: does not generate the decomposition term in a mathematical model
When the SpecieClass is RNA, Protein, Metabolite, Complex or Modified, the default
will display "on," if not, the default will display "off." The viewing content can bechanged using the selection box.
- InitialAmount
Input the initial value of species.

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6.3 Explanation of the Reaction Items- ReactionName
The Reaction name is displayed that is attached by the symbol “#” preceding
Reaction ID.
- ModifierReactionEquation
The regulator reaction equations corresponding to the map are displayed. (Theyappear in the order of Modifier Specie, ModifierType, ReactantReaction Specie,
Reaction, and ProductReaction Specie.)- Layer
Select the reaction layer.
metabolic: reaction at the metabolic layer
protein: reaction at the protein interaction layergene: reaction at the gene expression layer
The default is given according to ReactioType.
The viewing content can be modified using the selection box.
- ReactionType
Reaction attributes generated by NetworkConstructor are displayed.
bindingbinding_with_stoichiometric_changes
homo_association_or_modification
homo_association_or_modification_with_stoichiometric_changes
elimination
elimination_with_stoichiometric_changes
reversible_conversion
irreversible_conversion
reversible_conversion_regarding_multicompornent
irreversible_conversion_regarding_multicompornent
transport
option_transporttranscription
translation
degradation
activation_of_specie
inhibition_of_specie
activation_of_modifier
inhibition_of_ modifier- isConvertible
Select if a simulator converts the reaction into mathematical equations or not.
true
: It is convertible.
false: It is not convertible.
The default is true.
Depending on the selection box, the displayed content can be changed.
Note that the reaction that is not able to generate any regulator reaction equation is“false” and it cannot be changed by users.

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- isTotal
Select the method for calculation of modifier by a simulator.
true: the modifier is the Total amountfalse: the modifier is not the Total amountThe default is true. Depending on the selection box, the displayed content can bechanged.
- ChemicalReactionEquation
Displays chemical reaction equations of the Reaction.
The reaction whose attribue of "isConvertible" is “false” does not create any
ChemicalReactionEquation.

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7 Explanation of Menu Items
7.1 File Menu

7.1.1 New
Start the NewDialog box.
Positioning the Component in the dialog box. (4.2)
7.1.2 OpenStart the OpenDialog box.
Loading the Existing Network Data in the dialog box. (4.3)
7.1.3 Save
Save the network data created and edited by NetworkConstructor or DateEditor on
XML. If the network is newly created, it will be always saved as "SaveAs."
7.1.4 SaveAs
Network data can be saved as ModelName.
The input content is ModelName and ModelInfo as follows.

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7.1.5 Import

Load the XML file that is created by another launched CADLIVE by selecting from
dialog.
- Important a new network : a new XML file will be imported.
- Marge another network to the current network : the XML file designated for thecurrently-edited network will be added.
7.1.6 Export

The NetworkConstructor panel will be exported as a PNG image.
Full : The whole panel of NetworkConstructor will be exported as a PNG image.
View : The panel area of NetworkConstructor will be exported as a PNG image.
Specie data and Reaction data of the network viewed in DataEditor will be exported asa PNG image.
XML Form : will be saved in the XML format.
CSV Form : will be saved in the CSV format (comma-delimited text format).

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7.1.7 Print- Printing the NetworkConstructor screen
Full : The whole panel area of NetworkConstructor will be printed on one page.
View : The panel viewing area of NetworkConstructor will be printed on one page.
- Printing the DataEditor screen
The spreadsheet of DataEditor will be printed.
7.1.8 Search
Press the Search button on SearchDataEditor to display the Search Dialog box.

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- ModelName
Select the ModelName to search.
- SpecieClass
Select the SpeciesName of species to search.
With no input data all SpeciesClass are target [/object].
- SearchTerm
Up to 3 SearchTerms can be input to search.
- And/Or Radio Button
Select whether the character line input in SearchTerm will be searched on the "And" or"Or" condition.
- Search Button
Search the Reaction and Specie applicable to the conditions input from XML networks
and display them in spreadsheets of SearchedReaction and Searched Specie.

7.1.9 Exit

You are exiting CADLIVE.

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7.2 Edit Menu

7.2.1 EditCompartment

The Window is displayed to reedit the Compartment.
7.3 Window Menu

7.3.1 DataEditor
When the DataEditor screen is visible, the menu is set to "Invisible." When it isinvisible, it is set to "Visible." The check mark is displayed when the screen isvisible.

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7.3.2 NetworkConstructor
When the NetworkConstructor screen is visible, the menu is set to "Invisible." When
it is invisible, it is set to "Visible." The check mark is displayed when the screen isvisible.
7.4 Config Menu

7.4.1 SmallMolecule

Configure Specie and JunctionKey, which are viewed when SmallMoleculeOption is added
to the homo_association_wih_stoichimetric_change reaction.
- Configuration
Input a character line in Reactant, Product and JunctionKey, and press the Entry button.
- Deletion
After selecting the viewed Specie and JunctionKey, press the Delete button.

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7.4.2 SymbolColor

The viewing color of the Specie can be changed.
- Configuration
After selecting the Specie to configure on the left, select the color from the right anddefine it by pressing OK. A plural number of Species can be configured simultaneously.
To set color as the initial color, press the Default button after selecting the Specie on the
left.

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7.5 Help Menu

7.5.1 About CADLIVEThe version information of CADLIVE is displayed.

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