EX NO:10. Cell designer 4.

2: Mathematical pathway model construction and simulation Aim: Design a glycolsis metabolic pathway and simulate pathway to identify the parameter variation Principle: CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Intuitive user-interface helps you to draw a diagram in rich graphical representation with your own design. Understanding of logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks using solidly defined and comprehensive graphical representation (SBGN: Systems Biology Graphical Notation). CellDesigner is SBML compliant,and is SBW-enabled software so that it can import/export SBML described documents and can integrate with other SBW-enabled simulation/analysis software packages.CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ODE Solver, enabling us to simulate through our sophisticated graphical user interface. We could also browse and modify existing SBMLmodels with references to existing databases.CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X.CellDesigner is freely available via the Web. Procedure : Select File - Open in the Menu to open M-Phase.xml in the samples directory. A graphical network model is displayed on the Draw Area. In the Menu, select File Save as to open the Save dialog. In the File name text box, enter a new name, e.g. M-Phase_Test.xml. Click Save. Drag the borders (left or right) of the Draw Area to change the area size.

Select a Component Confirm that Select Mode icon is highlighted. If not, click the arrow icon. Select a component in the Draw Area. For instance, select the green square-shaped component labeled CAK which you will find in the upper left corner of the Draw Area. This shape indicates that the component is a Protein. Observe that the green square, a Protein, and also the linked line, called a Reaction, are highlighted.

components in a Compartment To select a Compartment, click on its border line. See the edge of the border line is turned into magenta and the Species inside are shadowed. A Compartment can hold Species and other Compartments inside. Drag the Compartment, and confirm that the Species inside follow it.

Activate a Species Select a Species. Type a on keyboard. Or, select Component Set Active in the Menu. See the Species is wrapped by a dashed line.

To simulate a model using the Control Panel

1. Open the sample file MAPK.xml in the samples folder. 2. In the Menu, select Simulation - Control Panel. 3. The Control Panel will open. 4. Change the End Time value to 1000,and change the quantity to various value. 5. Click Execute button. 6. You will see the time course plot in the right side of the control panel.

Result : The given mathematical pathway model was done and executed by cell designer software