In the beginning - Revision history

AndrewBangham at 14:23, 10 May 2011

2011-05-10T14:23:04Z

← Older revision		Revision as of 14:23, 10 May 2011
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	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- 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. <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?'''		'''What will be the result of growth on just the bottom side of the canvas, KAPAR?'''
	[[File:gftboxGUIB_3detailB.jpg\|300px]]		[[File:gftboxGUIB_3detailB.jpg\|300px]]
	\|width="500px"\|[[File:gftboxGUIB_3.jpg\|500px\|GFtbox interface]]		\|width="500px"\|[[File:gftboxGUIB_3.jpg\|500px\|GFtbox interface]]
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	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.<br><br>		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.<br><br>
	<small>Warning: saving is essential if you want to ''Restart'' the simulation.<br>		<small>Warning: saving is essential if you want to ''Restart'' the simulation.<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"\|[[File:~~gftboxGUIB_4~~.~~jpg~~\|500px\|GFtbox interface]]		\|width="500px"\|[[File:GPT_in_the_beginning-2011-05-05-000002d76-0001.png\|500px\|GFtbox interface]]
	\|}		\|}

AndrewBangham at 07:22, 6 May 2011

2011-05-06T07:22:13Z

AndrewBangham at 17:40, 5 May 2011

2011-05-05T17:40:21Z

← Older revision		Revision as of 17:40, 5 May 2011
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			[[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.
	==First view==		==First view==

AndrewBangham: Created page with '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. ==First view== {| border="1" c…'

2011-05-05T17:14:46Z

Created page with '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. ==First view== {| border="1" c…'

New page

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.
==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. 
[[File:gftboxGUIB_3detailB.jpg|300px]]
|width="500px"|[[File:gftboxGUIB_3.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 a the files needed for the project. 
''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: 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"|[[File:gftboxGUIB_4.jpg|500px|GFtbox interface]]
|}

← Older revision		Revision as of 07:22, 6 May 2011
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	\|- valign="top"		\|- 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. <br>		\|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. <br>
	[[File:gftboxGUIB_1detailB.jpg\|300px]]<br>		[[File:gftboxGUIB_1detailB.jpg\|300px]]<br><br>
	<small>Idea: change all ''GFtbox'' font sizes using ''Menu Misc:Gui Format''</small>		<small>Idea: change all ''GFtbox'' font sizes using ''Menu Misc:Gui Format''</small>
	\|width="500px"\|[[File:gftboxGUIB_1.jpg\|500px\|GFtbox interface]]		\|width="500px"\|[[File:gftboxGUIB_1.jpg\|500px\|GFtbox interface]]
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	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- valign="top"		\|- 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.<small>Idea: Special shapes can be imported as ''OBJ'' files. ''</small>		\|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.<br><small>Idea: Special shapes can be imported as ''OBJ'' files. ''</small>
	\|width="500px"\|[[File:gftboxGUIB_2.jpg\|500px\|GFtbox interface]]		\|width="500px"\|[[File:gftboxGUIB_2.jpg\|500px\|GFtbox interface]]
	\|}		\|}
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	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- 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. <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. <br><br>
			'''What will be the result of growth on just the bottom side of the canvas?'''
	[[File:gftboxGUIB_3detailB.jpg\|300px]]		[[File:gftboxGUIB_3detailB.jpg\|300px]]
	\|width="500px"\|[[File:gftboxGUIB_3.jpg\|500px\|GFtbox interface]]		\|width="500px"\|[[File:gftboxGUIB_3.jpg\|500px\|GFtbox interface]]
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	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- valign="top"		\|- 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.<br>A directory is created with the project name which contains a the files needed for the project.<br>		\|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.<br>A directory is created with the project name which contains all the files needed for the project and any results (snapshots, movies) we create.<br>
	''Select Tool:Simulation'' makes the ''Simulation'' Panel visible. <br>		''Select Tool:Simulation'' makes the ''Simulation'' Panel visible. <br>
	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.<br>		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.<br><br>
	<small>Warning: saving is essential if you want to ''Restart'' the simulation.<br>		<small>Warning: saving is essential if you want to ''Restart'' the simulation.<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"\|[[File:gftboxGUIB_4.jpg\|500px\|GFtbox interface]]		\|width="500px"\|[[File:gftboxGUIB_4.jpg\|500px\|GFtbox interface]]
	\|}		\|}