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SBML-A markup language for mathematical models in systems biology using cell designer
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Procedure

 

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

 

To import/export SBML file:

 

CellDesigner can stores all the model information and interaction informations in SBML file format. The model which has been created in the CellDesigner, will saved it in the complete SBML document.

 

To import SBML file :

 

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: select the file :

 

Go to CellDesigner file menu and click on open. It is easy to open the SBML file which has been saved previously. If user want to import the SBML file which is created by using any other applications, as the valid graphical information for CellDesigner is missing, it will generate the model automatically. File importing can be represented shown below.

 

 

 Figure 1: Select the file. 

 

Step 2: Select the file to be open :

 

Select the SBML file which has to be open. If the valid graphical information for CellDesigner is missing in the SBML file, CellDesigner will generate the model automatically.

 

Figure 2: Select the file to be open

 

 

Step 3: Visualizing the SBML model using CellDesigner :

 

Click on the file which has to be open using CellDesigner. The model example is shown below.

 

 

 

 Figure 3: Visualizing the model.

 

 Exporting a model:

 

 Step 1:  Exporting a model 

 

Go to export pure SBML from the file menu, and export the pure SBML file from the database where the file stored.

 

 

Figure 4:  Exporting the model

 

Step 2: Exporting actual SBML format of  Glycolysis represents as shown below.

 

 

 Figure 5: Exporting actual SBML format of a model

Step 3: Exporting a SBML file using Level 1 Version 2 :

 

SBML Level 1 Version 2 should accept input for all elements and attributes where the term occurs. Each species in the pathway is replaced by specie id , like in glycolysis glucose can be represented as [S1]. In this level, all the enzymes are represented away from the reactions [mentioned separately].

 

Figure 6 : Exporting a SBML file using Level 1 Version 2 

 

Step 4: Exporting a SBML file using Level2 Version 1 

 

In SBML Level 2, the specie spelling will be removed entirely and only species will be used. Finally, note that the deļ¬nition of Species in SBML requires a species in a model to be located within a compartment. That compartment should defines any species. One exception in this case is degenerative models does not have any species or reactions.

 

 

Figure 7 : Exporting a SBML file using Level2 Version 1

 

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

 

 

  

 

 

 

 

 

 

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