Steps for creating and visualizing a simple network using CellDesigner :

 

Step 1: Open CellDesigner.

 

Click on CellDesigner icon from your desktop. Goto simulator tab to know more about the installation of CellDesigner.

 

Step 2: Create new model.

 

Go to file menu from the GUI and click on “New”. A new dialogue box appears with the information like Name, Width, and Height to create a new model. New model will be created by the name given by the user.

 

 

figure 1: Creating a new model

 

 

Step 3: Create a simple network and simulate the model

 

Out of the drawing features, from the species menu select the node to create , like a protein or gene if the user wants to rename the node by giving right click on the node to edit name. Connect the nodes together with suitable reactions from the reaction menu and make it as a perfect network .

 

 

 

FIgure 2: Species menu

 

Figure 3:  Reaction menu 

 

 

Figure 4: Reaction of simple network

 

 

The mathematical equations can be edited by the user according to the reactant and the product of the model. Math equations are edited by clicking the reactions from the list menu, and double click on the math option according to user’s choice. One popup window named as reaction will appear on the screen, By clicking the edit from the popup window it will redirect to another popup named as KineticLaw, there user can edit the math equation depends on the kinetic law. Which is shown in below Figure.

 

 

 Figure 5: Representation of Mathematical representation

 

Step 4: Running simulation for the reaction

 

Go to simulation from the menu, select the control panel, save the file in .xml format and execute it. Before that, user needs to change the initial quantities in species menu according to the reaction in network as based upon the requirement .. The user can view the scatter plot by selecting the two species from the species menu in the simulation tab.

 

Hence mathematical equation is depends upon the

 

V= k* conc.of the reactants

 

Where :

 

V= Rate of reaction
K= Rate constant
 

 

 

Graphical representation of the reaction. 

 

Simulate the reaction by changing conditions of time vs substance.This helps us to understand what would be the expression of a particular substance at a particular time, based on an equation.In general all models have an input, processor and output of expected results

 

 

 Figure 6:Graphical representation of reaction.

 

 

Scatter plot can be shown by selecting of two species.

 

 

 

Figure 7: scatter plot representation.

 

 

 

This experiment uses: CellDesigner, www.celldesigner.org.