In the beginning non-uniform - Revision history

AndrewBangham at 11:04, 3 June 2011

2011-06-03T11:04:11Z

← Older revision		Revision as of 12:04, 3 June 2011
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	Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>		Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>
	Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. Compressors can be selected using the Menu: Movie: Codec option and the result can be converted to a flash movie (for the web) by Menu: Movie: Convert to flash this, however, requires ffmpeg to be installed on the computer.</small>		Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. Compressors can be selected using the Menu: Movie: Codec option and the result can be converted to a flash movie (for the web) by Menu: Movie: Convert to flash this, however, requires ffmpeg to be installed on the computer.</small>
	\|width="500px"\|[[Image:tut_non_uniform_growth_final.png\|500px\|GFtbox interface]]		\|width="500px"\|[[Image:tut_non_uniform_growth_final.png\|500px\|GFtbox interface]]Extra growth around the perimeter introduces Gaussian curvature. The canvas is readily able to distort out the plane because it started out with a small amount of random noise in the Z direction. (If the canvas started perfectly flat, residual strain (stress) would build up at each step rather than the surface distorting to accommodate the extra growth.)
	\|}		\|}

AndrewBangham at 07:03, 28 May 2011

2011-05-28T07:03:48Z

← Older revision		Revision as of 08:03, 28 May 2011
Line 32:		Line 32:
	Idea: set the axes manually (here to +-3) and turn off Panel:Plot Options: Auto axis range and Menu:Plot:Auto zoom and centre. This enables growth to be seen as a change of size rather than change of axis range.		Idea: set the axes manually (here to +-3) and turn off Panel:Plot Options: Auto axis range and Menu:Plot:Auto zoom and centre. This enables growth to be seen as a change of size rather than change of axis range.
	Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>		Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>
	Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. ~~We normally compress~~ the ~~movies using Microsoft Live~~ Movie ~~Maker or Quicktime~~.</small>		Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. Compressors can be selected using the Menu: Movie: Codec option and the result can be converted to a flash movie (for the web) by Menu: Movie: Convert to flash this, however, requires ffmpeg to be installed on the computer.</small>
	\|width="500px"\|[[Image:tut_non_uniform_growth_final.png\|500px\|GFtbox interface]]		\|width="500px"\|[[Image:tut_non_uniform_growth_final.png\|500px\|GFtbox interface]]
	\|}		\|}

AndrewBangham at 07:00, 28 May 2011

2011-05-28T07:00:35Z

← Older revision		Revision as of 08:00, 28 May 2011
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	\|- valign="top"		\|- valign="top"
	\|width="300px"\|''Select Tool:Factors'' makes the ''Morphogen'' Panel visible. Currently we are controlling the ''KAPAR'' factor. It has been selected from a drop down list top right (''Plot current factor''). We add a radially increasing gradient of ''KAPAR''. Make sure that the ''Panel Plot Options:Monochrome'' is ticked and the gradient of ''KAPAR'' will be as shown. Do the same for the top face, KBPAR. <br><br>		\|width="300px"\|''Select Tool:Factors'' makes the ''Morphogen'' Panel visible. Currently we are controlling the ''KAPAR'' factor. It has been selected from a drop down list top right (''Plot current factor''). We add a radially increasing gradient of ''KAPAR''. Make sure that the ''Panel Plot Options:Monochrome'' is ticked and the gradient of ''KAPAR'' will be as shown. Do the same for the top face, KBPAR. <br><br>
	'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''		'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''<br><small>Note: the different ways to fix the levels of morphogens - 'Add constant', 'Add random', 'Add to rim', 'Add radial' centred on x,y,z position, 'Add linear'. In addition, if Panel: Plot Options: FE edges is ticked to reveal the mesh, clicking on a node will add the specified amount (slider) to that node alone. To set values (as opposed to adding) use 'Set zero' or select 'Set' in the list box. <br><br>Colours are set by clicking on the colour boxes.</small>
	\|width="500px"\|[[File:tut_non_uniform_growth_initial.png\|500px\|GFtbox interface]]		\|width="500px"\|[[File:tut_non_uniform_growth_initial.png\|500px\|GFtbox interface]]
	\|}		\|}

AndrewBangham at 06:47, 28 May 2011

2011-05-28T06:47:40Z

← Older revision		Revision as of 07:47, 28 May 2011
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	[[GFtbox Tutorial pages\|Back to Tutorial pages]]<br><br>		[[GFtbox Tutorial pages\|Back to Tutorial pages]]<br><br>
	We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFtbox'' graphical interface.		We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFtbox'' graphical interface.
	=Modelling uniform growth using the GUI alone=		=Modelling non-uniform growth using the GUI alone=
	==First view==		==First view==
	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
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	\|width="300px"\|''Select Tool:Factors'' makes the ''Morphogen'' Panel visible. Currently we are controlling the ''KAPAR'' factor. It has been selected from a drop down list top right (''Plot current factor''). We add a radially increasing gradient of ''KAPAR''. Make sure that the ''Panel Plot Options:Monochrome'' is ticked and the gradient of ''KAPAR'' will be as shown. Do the same for the top face, KBPAR. <br><br>		\|width="300px"\|''Select Tool:Factors'' makes the ''Morphogen'' Panel visible. Currently we are controlling the ''KAPAR'' factor. It has been selected from a drop down list top right (''Plot current factor''). We add a radially increasing gradient of ''KAPAR''. Make sure that the ''Panel Plot Options:Monochrome'' is ticked and the gradient of ''KAPAR'' will be as shown. Do the same for the top face, KBPAR. <br><br>
	'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''		'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''
	\|width="500px"\|[[File:~~UniformGrowthOnAB~~.~~jpg~~\|500px\|GFtbox interface]]		\|width="500px"\|[[File:tut_non_uniform_growth_initial.png\|500px\|GFtbox interface]]
	\|}		\|}
	==And grow==		==And grow==
Line 33:		Line 33:
	Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>		Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls)<br>
	Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. We normally compress the movies using Microsoft Live Movie Maker or Quicktime.</small>		Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. We normally compress the movies using Microsoft Live Movie Maker or Quicktime.</small>
	\|width="500px"\|[[Image:~~GPT_in_the_beginning_2_20110510-000001d61-0001~~.png\|500px\|GFtbox interface]]		\|width="500px"\|[[Image:tut_non_uniform_growth_final.png\|500px\|GFtbox interface]]
	\|}		\|}

AndrewBangham: Created page with 'Back to Tutorial pages

We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFt…'

2011-05-27T20:18:25Z

Created page with 'Back to Tutorial pages We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFt…'

New page

[[GFtbox Tutorial pages|Back to Tutorial pages]] 
We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFtbox'' graphical interface.
=Modelling uniform growth using the GUI alone=
==First view==
{| border="1" cellpadding="5" cellspacing="5"
|- valign="top"
|width="300px"|The ''GFtbox'' user interface. Focus on the ''Select Tool'' Panel. Here the ''Mesh Editor'' has been selected and the ''Mesh Editor'' panel is visible. 
[[File:gftboxGUIB_1detailB.jpg|300px]] 
Idea: change all ''GFtbox'' font sizes using ''Menu Misc:Gui Format''
|width="500px"|[[File:gftboxGUIB_1.jpg|500px|GFtbox interface]]
|}
==Add a mesh (canvas that represents tissue)==
{| border="1" cellpadding="5" cellspacing="5"
|- valign="top"
|width="300px"|Create a canvas by clicking on ''Panel Mesh Editor:new''. A variety of preset shapes are available, here we choose a Circle with 4 concentric rings of nodes that is 2 mm in diameter. Idea: Special shapes can be imported as ''OBJ'' files. ''
|width="500px"|[[File:gftboxGUIB_2.jpg|500px|GFtbox interface]]
|}
==Add a pattern of growth factor==
{| border="1" cellpadding="5" cellspacing="5"
|- valign="top"
|width="300px"|''Select Tool:Factors'' makes the ''Morphogen'' Panel visible. Currently we are controlling the ''KAPAR'' factor. It has been selected from a drop down list top right (''Plot current factor''). We add a radially increasing gradient of ''KAPAR''. Make sure that the ''Panel Plot Options:Monochrome'' is ticked and the gradient of ''KAPAR'' will be as shown. Do the same for the top face, KBPAR. 
'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''
|width="500px"|[[File:UniformGrowthOnAB.jpg|500px|GFtbox interface]]
|}
==And grow==
{| border="1" cellpadding="5" cellspacing="5"
|- valign="top"
|width="300px"|'''Now save the project''' using the ''Save As'' button. A dialogue box will open - here we keyed in ''in_the_beginning'' and the prefix ''GPT_'' and the suffix ''_date'' was added automatically. A directory is created with the project name which contains all the files needed for the project and any results (snapshots, movies) we create. 
''Select Tool:Simulation'' makes the ''Simulation'' Panel visible. 
Change the ''Panel Run:Run until'' box to 2 and click the ''Panel Run:Run until'' button. The canvas will grow in steps set by the ''Panel Simulation:Timescale'' box. 
Warning: saving is essential if you want to ''Restart'' the simulation. 
Idea: set the axes manually (here to +-3) and turn off Panel:Plot Options: Auto axis range and Menu:Plot:Auto zoom and centre. This enables growth to be seen as a change of size rather than change of axis range.
Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls) 
Idea: to create an uncompressed movie of your simulation, before running click the ''Record movie'' and when it is finished click ''Stop movie''. The movie will be in the Project directory. We normally compress the movies using Microsoft Live Movie Maker or Quicktime.
|width="500px"|[[Image:GPT_in_the_beginning_2_20110510-000001d61-0001.png|500px|GFtbox interface]]
|}

In the beginning non-uniform - Revision history

AndrewBangham at 11:04, 3 June 2011

AndrewBangham at 07:03, 28 May 2011

AndrewBangham at 07:00, 28 May 2011

AndrewBangham at 06:47, 28 May 2011

AndrewBangham: Created page with 'Back to Tutorial pages We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFt…'

AndrewBangham: Created page with 'Back to Tutorial pages

We start with a number of very large screenshots (don't be daunted they are just here to orient you). They show the ''GFt…'