GFtbox Tutorial pages: Difference between revisions
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|width="700pt"|[[In the beginning|For tutorial | |width="700pt"|[[In the beginning Uniform|For tutorial on uniform growth click here]]<br>Consider a disc shaped canvas (tissue) in which the '''specified growth is uniform''', isotropic and on both sides.<br>'''Into what shape will the disc grow?'''<br>This model is as simple as it gets. Notice that, during growth, the mesh is automatically subdivided. Notice also that the final surface is not quite flat. This is because it is not flat initially. This is to allow it to deform in 3D. It can be made flat and forced to remain flat - see options on the GUI (hover over controls to get prompts). | ||
|width="200pt"|<wikiflv width="192" height="168" loop="true" background="white">UniformGrowth.flv|GPT_in_the_beginning_2_20110510-000000-0001.png</wikiflv> | |||
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|width="700pt"|[[In the beginning|For tutorial on radially increasing growth click here]]<br>Consider a disc shaped canvas (tissue) in which the''' non-uniform specified growth''' increases in proportion to the distance from the centre.<br>'''Into what shape will the disc grow?'''<br>Already we are into the realms of modelling biological systems. Compare this result with the discussion of Lily petals and Gaussian curvature ([http://www.pnas.org/content/early/2011/03/14/1007808108.abstract Lianga and Mahadevana],[http://www.americanscientist.org/issues/feature/leaves-flowers-and-garbage-bags-making-waves Sharon, Marder and Swinney],[http://rico-coen.jic.ac.uk/uploads/0/0f/Nath_Science.pdf Nath, Crawford, Carpenter and Coen] ). | |||
|width="200pt"|<wikiflv width="192" height="168" loop="true" background="white">Fascinator.flv|GPT in the beginning-2011-05-05-000002d76-0001.png</wikiflv> | |width="200pt"|<wikiflv width="192" height="168" loop="true" background="white">Fascinator.flv|GPT in the beginning-2011-05-05-000002d76-0001.png</wikiflv> | ||
<small>Note: this model should have many more finite elements</small> | <small>Note: this model should have many more finite elements</small> | ||
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='''B''' Adding polariser= | ='''B''' Adding polariser= | ||
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Revision as of 16:48, 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 on uniform growth click here Consider a disc shaped canvas (tissue) in which the specified growth is uniform, isotropic and on both sides. Into what shape will the disc grow? This model is as simple as it gets. Notice that, during growth, the mesh is automatically subdivided. Notice also that the final surface is not quite flat. This is because it is not flat initially. This is to allow it to deform in 3D. It can be made flat and forced to remain flat - see options on the GUI (hover over controls to get prompts). |
<wikiflv width="192" height="168" loop="true" background="white">UniformGrowth.flv|GPT_in_the_beginning_2_20110510-000000-0001.png</wikiflv> |
| For tutorial on radially increasing growth click here Consider a disc shaped canvas (tissue) in which the non-uniform 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