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

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
Line 72: Line 72:
* Select the 'Edit Reaction'. A new window pops out with the reaction properties.  
* Select the 'Edit Reaction'. A new window pops out with the reaction properties.  
|
|
[[Image:CellDesigner_Tutorial_Example_6.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_5b.png|300px|CellDesigner]]
|-  
|-  
|
|
Line 80: Line 80:
* Click on: Kinetic Law  'Create'. A new window pops out.
* Click on: Kinetic Law  'Create'. A new window pops out.
|
|
[[Image:CellDesigner_Tutorial_Example_7.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_6.png|300px|CellDesigner]]
|-
|-
|
|
Line 89: Line 89:
* A new window pops out.
* A new window pops out.
|
|
[[Image:CellDesigner_Tutorial_Example_8.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_7.png|300px|CellDesigner]]
|-
|-
|
|
Line 97: Line 97:
* The windows closes. You are now back on the 'Kinetic Law' Window.
* The windows closes. You are now back on the 'Kinetic Law' Window.
|
|
[[Image:CellDesigner_Tutorial_Example_9.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_8.png|300px|CellDesigner]]
|-
|-
|
|
Line 108: Line 108:
* Save your project. File --> Save.
* Save your project. File --> Save.
|
|
[[Image:CellDesigner_Tutorial_Example_10.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_9.png|300px|CellDesigner]]
|}
|}


Line 122: Line 122:
* A new window pops out.
* A new window pops out.
|
|
[[Image:CellDesigner_Tutorial_Example_11.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_10.png|300px|CellDesigner]]
|-
|-
|
|
Line 130: Line 130:
* You can now press the 'Execute' button to launch the simulation.   
* You can now press the 'Execute' button to launch the simulation.   
|
|
[[Image:CellDesigner_Tutorial_Example_12.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_11.png|300px|CellDesigner]]
|}
|}


Line 141: Line 141:
* It allows you to modify species initial amount, or kinetic parameters   
* It allows you to modify species initial amount, or kinetic parameters   
|
|
[[Image:CellDesigner_Tutorial_Example_13.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_12.png|300px|CellDesigner]]
|}
|}


Line 154: Line 154:
* 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.
|
|
[[Image:CellDesigner_Tutorial_Example_14.png|300px|CellDesigner]]
[[Image:CellDesigner_Tutorial_Example_13.png|300px|CellDesigner]]
|}
|}


Revision as of 08:40, 12 January 2008

Synthetic Biology (Spring2008): Computer Modelling Practicals

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

<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 transform 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.

CellDesigner

Defining the reaction network

Main Working Area

  • We want now to create 2 compounds: 'A' and 'B'.
  • Click on the 'Simple Molecule' icon
  • Click then in the working area to create the first compound. Name the compound 'A'.
  • Repeat the operations to create compound 'B' in the working area.

CellDesigner

  • 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

  • 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'. 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 transformed into products.
  • The kinetic law represents how the reactants reacts in time to produce the product.
  • First, you need to create a New parameter. Click on ListOfParameters NEW.
  • A new window pops out.

CellDesigner

'Parameter' Window

  • Set parameter id = k1, name = k1, initial value 1.0. No units, Constant = True.
  • Then click 'Add' to register the new parameter. And then Click 'Close'.
  • The windows closes. You are now back on 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
  • A new window 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.
  • You can now press the 'Execute' button to launch the simulation.

CellDesigner

Interactive Simulation

'Control Panel' Window

  • Select the 'Interactive Simulation' Menu
  • It allows you to modify species initial amount, or kinetic parameters

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.

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.
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/CellDesigner_Tutorial/Example&oldid=178366"