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

From OpenWetWare

Jump to: navigation, search
Synthetic Biology (Spring2008): Computer Modelling Practicals

Home        CellDesigner Tutorial        Practical 1        Practical 2        Practical 3        Schedule        Back to Synthetic Biology Course       

web metrics

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  : A \xrightarrow{k_{1}} B
  • Kinetic Law for 'A':  \frac{d[A]}{dt} = -k_{1}[A] ;   [A]_{t=0} = A_{0} > 0
  • Kinetic Law for 'B':  \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.

CellDesigner

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 Image:CellDesigner_Tutorial_Example_2.png
  • 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.

CellDesigner

Main Working Area: Defining the reaction

  • To create the reaction linking 'A' to 'B', click on the 'State Transition' icon Image:CellDesigner_Tutorial_Example_4.png
  • 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.

CellDesigner

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.

CellDesigner

'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.

CellDesigner

'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.

CellDesigner

'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.

CellDesigner

'Kinetic Law' Window

  • The actual mathematical description of the reaction is now needed.
  • Use the field called 'Math' to enter the kinetic law: k1[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.

CellDesigner

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.

CellDesigner

'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.

CellDesigner

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

CellDesigner

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

CellDesigner

Additional features

To finish this first part of the tutorial, take the time to explore some features that will be useful for you to write your reports:

  • Save image
  • Export data
  • >> more info from the CellDesigner Tutorial.
Personal tools