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Import and simulate models from different databases
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Procedure:

 

Please go to SImulator tab for informtion about how to install and run CellDesigner.

 

Steps for importing a model from JWS online database

 

 

Step 1: Open CellDesigner.

 

Click on CellDesigner icon from your Desktop or go to programs and select the CellDesigner on a windows machine.

 

Step 2: Create new Document.

 

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: Createing a new model

Step 3: Import a model from the database :

 

Go to database from the menu and select “import model from the JWS online database”. By clicking that it will redirect to the database, from their user can select the model of their interest. It is easy to retrieve the model and simulate the model from the database. All the mathematical calculations will be predefined. It can be possible to change the parameters and run the simulation. In database popup window, it have an information like description and Import, by clicking the description it will connect to the webpage which contains the description about the model, and by clicking import it can lead to import the model from the database. The screenshot is shown below.

 

 

Figure 2 : Screenshot of loading model from database

 

Changing the parameters are, by clicking the reactions from the species menu and double clicking on the reaction will redirect to modify the equation. Simulation can be run by changing the parameters.

 

 

Figure 3: Changing the parameters

 

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

 

 

Figure 4: Creating mathematical equation for reaction

 

Running a simulation for the reaction

 

Go to simulation from the menu, select the control panel, save the file in .xml format and execute it. simulation can run by changing the parameters. The user can view the scatter plot by selecting the two species from the species menu in the simulation window. 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 5: Graphical representation of the reaction.

 

 

Figure 6: Scatter plot can be shown by selecting of two species.  

 

 

Procedure to import the model from the Biomodels.net :

 

Go to database from the menu and select the “import model from the biomodels.net”. By clicking that it will redirect to the database, from their user can select the model of their interest. It is easy to retrieve the model and simulate the model from the database. All the mathematical calculations will be predefined. It can be possible to change the parameters and run the simulation. In database popup window it have an information like description and Import and reference ,by clicking the description it will connect to the webpage which contains the description about the model, and by clicking import it can lead to import the model from the database. The reference will give the reference according to the model. The screenshot is shown below.

 

 

Figure 7: import the model from the Biomodels.net

 

Changing the parameters are, by double clicking the reactions from the species menu will redirect to modify the equation. Simulation can be run by changing the parameters.

 

 

 

Figure 8 : Changing Parameters

 

The mathematical equations can be edited by the user according to the reactant and 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 users’ 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 9.

 

 

Figure 9: Changing of mathematical equations.

 

Running a simulation for the reaction

 

Go to simulation from the menu, select the control panel, save the file in .xml format and execute it. simulation can run by changing the parameters. The user can view the scatter plot by selecting the two species from the species menu in the simulation window. 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 10: Graphical representation of the reaction 

 


 

Figure 11: Scatter plot can be shown by selecting of two species. 

 

 

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


 

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