Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/CellDesigner Tutorial/Example: Difference between revisions

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==Toy model for this example==
==Toy model for this example==


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


==Starting a new CellDesigner Project==
==Starting a new CellDesigner Project==
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{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
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* Open CellDesigner Application: Double-click on the icon found on the desktop.
* Open '''CellDesigner''' Application: '''Double-click''' on the '''icon''' found on the desktop.
* Open a New Project: File --> New.
* Open a '''New''' Project: File --> New.
* Name your project 'test_1', for example. No need to change the dimensions.
* Name your project 'test_1', for example. No need to change the dimensions of the work area.
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[[Image:CellDesigner_Tutorial_1.tiff]]
[[Image:CellDesigner_Tutorial_Example_1.png|300px|CellDesigner]]
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{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
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'''Main Working Area'''
'''Main Working Area: Creating Compounds'''
* We want now to create 2 compounds: 'A' and 'B'.
* We want now to '''create 2 compounds''': 'A' and 'B'.
* Click on the 'Simple Molecule' icon [[Image:CellDesigner_Tutorial_Example_2.tiff]]
* Click on the ''''Simple Molecule'''' icon [[Image:CellDesigner_Tutorial_Example_2.png]]
* Click then in the working area to create the first compound. Name the compound 'A'.
* Click then in the working area, where you want to create the first compound. Name the compound 'A'.
* Repeat the operations to create compound 'B' in the working area.
* Repeat the previous operations to create compound 'B'.
* To create the reaction linking 'A' to 'B', click on the 'State Transition' icon [[Image:CellDesigner_Tutorial_Example_3.tiff]]
* Save your project. File --> Save.
* Back to the working area, Click first on compound 'A' and then on compound 'B'. A reaction link is created.
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[[Image:CellDesigner_Tutorial_Example_3.png|300px|CellDesigner]]
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'''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.
* The topology of your reaction network is now created.
* Save your project. File --> Save.
* Save your project. File --> Save.
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[[Image:CellDesigner_Tutorial_4.tiff]]
[[Image:CellDesigner_Tutorial_Example_5.png|300px|CellDesigner]]
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{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
{| border="1" cellpadding="10" cellspacing="2" style="width:700px"
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'''Main Working Area'''
'''Main Working Area: Defining the kinetic law'''
* We want now to set the kinetic property of the defined reaction
* 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.
* '''Right-click''' on the reaction link. It turns blue when you click on it.
* Select the 'Edit Reaction'. A new window pops out with the reaction properties.  
* Select the ''''Edit Reaction'''' fom the pop-up menu. A new window pops out with the reaction properties.  
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[[Image:CellDesigner_Tutorial_5.tiff]]
[[Image:CellDesigner_Tutorial_Example_5b.png|300px|CellDesigner]]
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|-  
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* This window describes the attributes of the selected reaction link.
* This window describes the attributes of the selected reaction link.
* A kinetic law has to be described to allow us to simulate the reactions.
* A kinetic law has to be described to allow us to simulate the reactions.
* Click on: Kinetic Law  'Create'. A new window pops out.
* Click on: Kinetic Law  ''''Create''''. A new window pops out.
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[[Image:CellDesigner_Tutorial_6.tiff]]
[[Image:CellDesigner_Tutorial_Example_6.png|300px|CellDesigner]]
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''''Kinetic Law' Window'''
''''Kinetic Law' Window'''
* The reaction link describes how reactants are transformed into products.
* The reaction link describes how reactants are converted into products.
* The kinetic law represents how the reactants reacts in time to produce the product.
* The kinetic law represents how the reactants reacts in time to form the products.
* First, you need to create a New parameter. Click on ListOfParameters NEW.  
* First, you need to create a '''New parameter''' K1. Click on '''ListOfParameters NEW'''.  
* A new window pops out.
* A new window pops out.
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[[Image:CellDesigner_Tutorial_6.tiff]]
[[Image:CellDesigner_Tutorial_Example_7.png|300px|CellDesigner]]
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''''Parameter' Window'''
''''Parameter' Window'''
* Set parameter id = k1, name = k1, initial value 1.0. No units, Constant = True.
* 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'.
* Then click 'Add' to register the new parameter. And then, Click 'Close'.
* The windows closes. You are now back on the 'Kinetic Law' Window.
* The window closes. You are now back to the 'Kinetic Law' Window.
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[[Image:CellDesigner_Tutorial_6.tiff]]
[[Image:CellDesigner_Tutorial_Example_8.png|300px|CellDesigner]]
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* If you Click on the compound 'A' in the main working area, its 'id' will pop out in the Kinetic Law window.
* 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'.
* Once you are done, Click on 'Update'. And then 'Close'.
* Save your project. File --> Save.
* Save your project. '''File --> Save'''.
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[[Image:CellDesigner_Tutorial_6.tiff]]
[[Image:CellDesigner_Tutorial_Example_9.png|300px|CellDesigner]]
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'''Main Working Area'''
'''Main Working Area'''
* Your reaction network is now ready to run a simulation.
* Your reaction network is now ready to run a simulation.
* Select within the Menu 'Simulation' --> Control Panel
* Select within the '''Menu 'Simulation' --> Control Panel'''
* A new window pops out.
* The 'Control Panel' for the simulations pops out.
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[[Image:CellDesigner_Tutorial_4.tiff]]
[[Image:CellDesigner_Tutorial_Example_10.png|300px|CellDesigner]]
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''''Control Panel' Window
''''Control Panel' Window
* At the moment, both compounds, 'A' and 'B', have a default initial value of zero. Nothing interesting could happen.
* 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.
* Change 'A' initial amount from the 'Species' menu. Set it to 100.
* You can now press the 'Execute' button to launch the simulation.   
* Set EndTime = 1000, NbPoints = 1000.
* You can now press the ''''Execute'''' button to launch the simulation.   
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[[Image:CellDesigner_Tutorial_4.tiff]]
[[Image:CellDesigner_Tutorial_Example_11.png|300px|CellDesigner]]
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''''Control Panel' Window
''''Control Panel' Window
* Select the 'Interactive Simulation' Menu
* This function helps you to vary a parameter, or a compound amount interactively.
* It allows you to modify species initial amount, or kinetic parameters  
* 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.
* [http://www.systems-biology.org/cd/help/CP/CDH_CP-6.html >>> more info]  
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[[Image:CellDesigner_Tutorial_4.tiff]]
[[Image:CellDesigner_Tutorial_Example_12.png|300px|CellDesigner]]
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''''Control Panel' Window
''''Control Panel' Window
* Select the 'Parameter Scan' Menu
* Select the ''''Parameter Scan'''' Menu
* It allows you to run multiple simulation while varying a specific parameter.
* 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.
* 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.
* Check how the k1, or initial amount of A, are impacting the simulations.
* [http://www.systems-biology.org/cd/help/CP/CDH_CP-5.html >>> more info]
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[[Image:CellDesigner_Tutorial_4.tiff]]
[[Image:CellDesigner_Tutorial_Example_13.png|300px|CellDesigner]]
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Latest revision as of 10:02, 12 January 2008

Synthetic Biology (Spring2008): Computer Modelling Practicals

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

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

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
  • 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
  • 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: [math]\displaystyle{ k_{1}[A] }[/math]
  • [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.
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