4.1 Components

This section will introduce the various components of the modelling environment and the associated functionality. Figure 4-1 gives screen shot of the entire application.

Figure 4-1: Screenshot of Cellware

The application window consists of the following components:

Menu, Tool bar and Model kit : These are described in the next section.

Model workspace : This is the ‘canvas’ on which the various species of a pathway are placed and their interactions described diagrammatically.

Project Browser : This tab page (Figure 3-1: Cellware Graphic User Interface. Item 6) organizes the various species of a model in a tree structure for quick access. Clicking on any one of the species opens the Species Editor (4.1.2).

Project Properties: This tab page, next to the project browser, displays some properties associated with a model. Figure 4-2 shows the project properties tab.

Figure 4-2: Project Properties

4.1.1 Menu, Toolbar and Model Kit

Menu, Toolbar and model kit may be used for quick access to various components of Cellware. The menu options are listed in the Table 4-1.

Main Menu	Option		Description
File	New		Create a new model workspace
	Open		Open an existing model saved in the .cwm format
	Close		Close current model
	Save		Save the model in .cwm format. This will save the current model along with the diagrammatic layout
	Save as		Save as another .cwm file
	Import SBML		Import a SBML model file. The imported model may automatically be laid out on the model workspace using two layout algorithms – Force directed and hierarchical. See section 4.3.2 .
	Export SBML		Export a model to a SBML file.
	Print		Print the model diagram
	Exit		Exit Cellware
Add	Gene, Protein, Modifier, mRNA, Metabolite		Adds new specie corresponding to the category to the model and displays on the workspace.
	Reaction		Add a reaction link to the model workspace ( Reaction Editor )
	Text		Add free text to the model workspace
Edit	Undo		Undo last operating on model workspace. At most 10 operations can be undone.
	Cut		Cut an object on the workspace
	Copy		Copy an object from the workspace
	Paste		Paste an object on the workspace
	Delete		Delete an object from the workspace
View	Tool Bar		Enable/Disable the Toolbar
	Model kit		Enable/Disable the Model kit
	Status Bar		Enable/Disable the Status Bar at the bottom on the application
	Description		Enable/Disable the project description window
	Model Species		Edit a summary of properties of all species in the model.
	Model Reactions		Edit a summary of properties of all reactions in the model.
Simulation	Set Up...		Open the Simulation setup window ( Setup )
	Run on Local		Runs the simulation on the local computer. Depending on simulation setup options a plotting window or a progress bar opens up
	Run on Grid		Submits the simulation job to the Grid. The progress can be monitored by the (Job Manager).
Analysis	Parameter Estimation		Opens the parameter estimation setup window for setting up and submitting a parameter estimation job to the Grid.
	Network	Statistics…	Show network statistic information
		Find cycles…	Find independent cycles in the whole network
		Transverse	Highlight transferable nodes from a selected node
		Find path	Find shorted path between two nodes
		Blast	Show conversed pathways among networks
Tool	Result Plot		Opens a plotting window to view results saved in PlotML format
	Job Manager		Opens the Job manager for viewing the status and results of jobs submitted to the Grid
	Layout Manager		Arranges the network drawn using either Force-Directed or Hierarchical-Embedding algorithms
	Options…		Change preference
Figure	Delete line…		Delete a line from the active figure
	Insert line…		Insert a line to the active figure
	Line properties…		Change line properties, such as colour, thickness, style and expression
	Y-axis Properties...		Change y-axis properties
	X-axis Properties...		Change x-axis properties
	Figure Properties...		Change figure properties
	Data Statistics...		Show data statistics
Help	Help Topics		Opens the Java help window containing most of this user manual
	About Cellware		Information on Cellware

Table 4-1: Menu Options in Cellware

The toolbar contains the shortcuts for some of commonly used menu option like open, save, print, help etc which are activated by clicking on the corresponding icons.

Figure 4-3 shows the toolbar and the model tool kit. The model tool kit contains mouse short cuts for operations related to model building.

Figure 4-3 gives a short description of the each icon in the model tool kit. More details on using them would be provided in following sections.

Figure 4-3: Cellware Toolbar and Model Kit

4.1.2 Species Editor

In any model the species may be one of Gene, Protein, Modifier, Metabolite or mRNA. For easy identification each category has a different icon associated with it as shown in Figure 4-3 . The Species Editor exists in two forms. One is a tabbed pane which is located at the left of the main window and another is a dialog which will be triggered by double clicking on the species in the model tree viewer. Species Editor may be opened in one of the following ways:

Double Click on the species in the model tree viewer.
Click on the species in the model canvas (shown in Section 4.1).
Right click on the species and choose edit.

Figure 4-4 shows a snapshot of the species editor. Following information can be entered through the species editor:

Figure 4-4: Species Editor

Label	Name displayed on the model workspace
Full Name	Full Name
Concentration	Concentration specified in Moles/litre
Volume	Volume of the compartment to which the specie belongs. Volume is entered through the project properties tab ( 4.1).
Total Quantity	Number of moles of the specie
No. of Molecules	Number of molecules of the specie
Value Fixed	Check this check box for keeping the concentration fixed during simulation
Notes	Annotation of the specie

Only one of concentration and number of Molecules need to be entered. The rest is calculated using formula:

Total Quantity = Concentration x Volume	Equation 4-1
No. of Molecules = Total Quantity x Avogadro’s Number	Equation 4-2

4.1.3 Reaction Editor

An in-silico model of a biological system is abstracted as a network of chemical reactions. Section 3.3 describes steps to be followed for constructing a model on the model workspace.

Reaction Editor is an interface (Figure 4-5) for changing the properties of a reaction such as stoichiometry, rate laws etc.

The reaction editor consists of three tabs:

Reaction : Through this tab the reaction name, reversibility and stoichiometry can be entered. Stoichiometry can be entered through the drop down list of positive integers prefixed to each species involved in the reaction. Also a quick view of the properties of species, which form the reaction, can be obtained by pressing the View Species Details button as shown in (Figure 4-5: Reaction Editor).

Kinetics : The kinetic law associated with the reaction and the associated rate constants are entered through this tab. In this version only Mass action rate law is supported.

Figure 4-5: Reaction Editor - Reaction Tab

4.1.4 Compartment Editor

Chemical reactions may take place in different compartments. Compartment Editor is an interface ( Figure 4-6 ) for changing the properties of a compartment.

Figure 4-6: Compartment Editor