# Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/CellDesigner Tutorial/Example

Synthetic Biology (Spring2008): Computer Modelling Practicals

<html> <body> <!-- Start of StatCounter Code --> <script type="text/javascript"> var sc_project=3315875; var sc_invisible=0; var sc_partition=36; var sc_security="779debd0"; </script> <script type="text/javascript" src="http://www.statcounter.com/counter/counter_xhtml.js"></script><noscript><div class="statcounter"><a class="statcounter" href="http://www.statcounter.com/"><img class="statcounter" src="http://c37.statcounter.com/3315875/0/779debd0/0/" alt="web metrics" /></a></div></noscript> <!-- End of StatCounter Code --> </body> </html>

CellDesigner Tutorial

# Example: A --> B

## Toy model for this example

• We are considering a very simple reaction network.
• It takes a compound 'A' to be converted into a compound 'B'.
• Following mass action laws, the kinetic law associated to the reaction is a first order reaction, with parameter k1.
• Model described  : $\displaystyle{ A \xrightarrow{k_{1}} B }$
• Kinetic Law for 'A': $\displaystyle{ \frac{d[A]}{dt} = -k_{1}[A] ; [A]_{t=0} = A_{0} \gt 0 }$
• Kinetic Law for 'B': $\displaystyle{ \frac{d[B]}{dt} = k_{1}[A] ; [B]_{t=0} = 0 }$

## Starting a new CellDesigner Project

 Open CellDesigner Application: Double-click on the icon found on the desktop. Open a New Project: File --> New. Name your project 'test_1', for example. No need to change the dimensions of the work area.

## Defining the reaction network

 Main Working Area: Creating Compounds We want now to create 2 compounds: 'A' and 'B'. Click on the 'Simple Molecule' icon Click then in the working area, where you want to create the first compound. Name the compound 'A'. Repeat the previous operations to create compound 'B'. Save your project. File --> Save. Main Working Area: Defining the reaction To create the reaction linking 'A' to 'B', click on the 'State Transition' icon Back to the working area, Click first on compound 'A', and then on compound 'B'. A reaction link is created. The topology of your reaction network is now created. Save your project. File --> Save.

## Defining the reaction kinetic

 Main Working Area: Defining the kinetic law We want now to set the kinetic property of the defined reaction Right-click on the reaction link. It turns blue when you click on it. Select the 'Edit Reaction' fom the pop-up menu. A new window pops out with the reaction properties. 'Reaction' Window This window describes the attributes of the selected reaction link. A kinetic law has to be described to allow us to simulate the reactions. Click on: Kinetic Law 'Create'. A new window pops out. 'Kinetic Law' Window The reaction link describes how reactants are converted into products. The kinetic law represents how the reactants reacts in time to form the products. First, you need to create a New parameter K1. Click on ListOfParameters NEW. A new window pops out. 'Parameter' Window Set parameter id = k1, name = k1, initial value .01 . No units, Constant = True. Then click 'Add' to register the new parameter. And then, Click 'Close'. The window closes. You are now back to the 'Kinetic Law' Window. 'Kinetic Law' Window The actual mathematical description of the reaction is now needed. Use the field called 'Math' to enter the kinetic law: $\displaystyle{ k_{1}[A] }$ [A] must be represented by its id, not its name ! If you Click on the compound 'A' in the main working area, its 'id' will pop out in the Kinetic Law window. Once you are done, Click on 'Update'. And then 'Close'. Save your project. File --> Save.

## Simulating the reactions

### Main Simulation Features

 Main Working Area Your reaction network is now ready to run a simulation. Select within the Menu 'Simulation' --> Control Panel The 'Control Panel' for the simulations pops out. 'Control Panel' Window At the moment, both compounds, 'A' and 'B', have a default initial value of zero. Nothing interesting could happen. Change 'A' initial amount from the 'Species' menu. Set it to 100. Set EndTime = 1000, NbPoints = 1000. You can now press the 'Execute' button to launch the simulation.

### Interactive Simulation

 'Control Panel' Window This function helps you to vary a parameter, or a compound amount interactively. Select the 'Interactive Simulation' Menu, in the left area of the control panel. Select the 'parameter' button, and the slide menu gives you the option to vary k1. >>> more info

### Parameter Scan

 'Control Panel' Window Select the 'Parameter Scan' Menu It allows you to run multiple simulation while varying a specific parameter. This function is useful to run a simple sensitivity analysis on a given model. Check how the k1, or initial amount of A, are impacting the simulations. >>> more info