GFtbox Tutorial pages: Difference between revisions
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#'''Do only some things''' from the GUI. This is the best way to develop ideas. Use the GUI to generate the mesh (canvas) and create growth factors (morphogens - in other words declare the variables) but capturing your ideas on how the regulatory processes work in, what we call, the interaction function. See (3) below. | #'''Do only some things''' from the GUI. This is the best way to develop ideas. Use the GUI to generate the mesh (canvas) and create growth factors (morphogens - in other words declare the variables) but capturing your ideas on how the regulatory processes work in, what we call, the interaction function. See (3) below. | ||
#'''Without the GUI'''. For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We have used this way extensively but the code is not yet ready for general use. | #'''Without the GUI'''. For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We have used this way extensively but the code is not yet ready for general use. | ||
=''' | ='''A''' In the beginning: doing it from the GUI= | ||
{| border="0" cellpadding="5" cellspacing="3" | {| border="0" cellpadding="5" cellspacing="3" | ||
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<small>Note: this model should have many more finite elements</small> | <small>Note: this model should have many more finite elements</small> | ||
|} | |} | ||
=''' | ='''B''' Adding polariser= | ||
{| border="0" cellpadding="5" cellspacing="3" | {| border="0" cellpadding="5" cellspacing="3" | ||
|- valign="top" | |- valign="top" | ||
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|width="200pt"|<wikiflv width="192" height="168" loop="true" background="white">InTheBeginning.flv|GPT in the beginning-2011-05-05-000002-0001.png</wikiflv> | |width="200pt"|<wikiflv width="192" height="168" loop="true" background="white">InTheBeginning.flv|GPT in the beginning-2011-05-05-000002-0001.png</wikiflv> | ||
|} | |} | ||
=''' | ='''C''' Getting serious: doing it with an interaction function= | ||
Interaction functions - programmatic modelling | Interaction functions - programmatic modelling | ||
Revision as of 14:49, 10 May 2011
Three ways to use GFtbox
There are three ways to use the GFtbox.
- Doing everything from the GUI. This is the best way to start. See (1,2) below.
- Do only some things from the GUI. This is the best way to develop ideas. Use the GUI to generate the mesh (canvas) and create growth factors (morphogens - in other words declare the variables) but capturing your ideas on how the regulatory processes work in, what we call, the interaction function. See (3) below.
- Without the GUI. For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We have used this way extensively but the code is not yet ready for general use.
A In the beginning: doing it from the GUI
| For tutorial page click here Consider a disc shaped canvas (tissue) in which the specified growth increases in proportion to the distance from the centre. Into what shape will the disc grow? Already we are into the realms of modelling biological systems. Compare this result with the discussion of Lily petals and Gaussian curvature (Lianga and Mahadevana,Sharon, Marder and Swinney,Nath, Crawford, Carpenter and Coen ). |
<wikiflv width="192" height="168" loop="true" background="white">Fascinator.flv|GPT in the beginning-2011-05-05-000002d76-0001.png</wikiflv>
Note: this model should have many more finite elements |
B Adding polariser
| <wikiflv width="192" height="168" loop="true" background="white">InTheBeginning.flv|GPT in the beginning-2011-05-05-000002-0001.png</wikiflv> |
C Getting serious: doing it with an interaction function
Interaction functions - programmatic modelling