Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/CellDesigner Tutorial/Kinetic Simulation: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(New page: __NOTOC__ {{Template:ImperialCollege Spring2008 SyntheticBiologyCourse ComputerModellingPractical}} <div style="padding: 10px; width: 720px; border: 5px solid #B3CD4E;"> <div class="...) |
No edit summary |
||
Line 18: | Line 18: | ||
''...under development...'' | ''...under development...'' | ||
=Set-up a Kinetic Simulation= | |||
===Overview=== | |||
* this section deals with preparing your model to kinetic simulations (time evolving simulations). | |||
* CellDesigner offers a link to an ODE Solver. | |||
===Minimum requirements for a simulation=== | |||
* Compounds: 'initialAmount' might need to be changed for some compounds (zero by default) | |||
* Reactions : define a kineticLaw for all reactions defined, write a formula with appropriate parameters. | |||
===Defining a kinetic law for your reaction=== | |||
* Double click on an item in the reaction list to display the “Reaction” dialog. | |||
* You can also display “Reaction” dialog” by clicking on the reaction on canvas with right mouse button, then select “Edit Reaction” menu. | |||
* Click “KineticLaw” Edit button to display “KineticLaw” dialog | |||
* Enter “math” formulae and edit parameters by clicking in the “listofParameters” section | |||
* '''Note''': In “math” formulae, Species ID, not Species Name, should be specified | |||
* To enter Species ID, you can click the target Species on canvas, and press [copy] button below the “math” field. The ID will be automatically input to the field. | |||
===Defining a parameter used in the kinetic law=== | |||
* Local parameter: To set a local parameter for the kinetic law formula, click [New] button in the above KineticLaw dialog window to specify the parameter id, name, value and units. | |||
* Global parameter: From the "Parameters" tab in the list window, select [NEW] to create a new global parameter. | |||
===References=== | |||
* [http://www.systems-biology.org/cd/simulation.html CellDesigner Simulation tutorial] |
Revision as of 10:31, 7 January 2008
<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>
...under development...
Set-up a Kinetic Simulation
Overview
- this section deals with preparing your model to kinetic simulations (time evolving simulations).
- CellDesigner offers a link to an ODE Solver.
Minimum requirements for a simulation
- Compounds: 'initialAmount' might need to be changed for some compounds (zero by default)
- Reactions : define a kineticLaw for all reactions defined, write a formula with appropriate parameters.
Defining a kinetic law for your reaction
- Double click on an item in the reaction list to display the “Reaction” dialog.
- You can also display “Reaction” dialog” by clicking on the reaction on canvas with right mouse button, then select “Edit Reaction” menu.
- Click “KineticLaw” Edit button to display “KineticLaw” dialog
- Enter “math” formulae and edit parameters by clicking in the “listofParameters” section
- Note: In “math” formulae, Species ID, not Species Name, should be specified
- To enter Species ID, you can click the target Species on canvas, and press [copy] button below the “math” field. The ID will be automatically input to the field.
Defining a parameter used in the kinetic law
- Local parameter: To set a local parameter for the kinetic law formula, click [New] button in the above KineticLaw dialog window to specify the parameter id, name, value and units.
- Global parameter: From the "Parameters" tab in the list window, select [NEW] to create a new global parameter.