Full freshly minted interaction function - Revision history

AndrewBangham at 19:50, 2 June 2011

2011-06-02T19:50:22Z

← Older revision		Revision as of 20:50, 2 June 2011
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	Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>		Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>
	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	<span style="color: CornflowerBlue">% Section 1</span>		<span style="color: CornflowerBlue">% Section 1</span>
	function m = gpt_tut_interaction_example_20110601( m )		function m = gpt_tut_interaction_example_20110601( m )
	%m = gpt_tut_interaction_example_20110601( m )		<span style="color: Green">%m = gpt_tut_interaction_example_20110601( m )</span>
	% Morphogen interaction function.		<span style="color: Green">% Morphogen interaction function.</span>
	% Written at 2011-06-02 14:55:46.		<span style="color: Green">% Written at 2011-06-02 14:55:46.</span>
	% GFtbox revision 3554, 2011-06-02 12:30:52.789869.		<span style="color: Green">% GFtbox revision 3554, 2011-06-02 12:30:52.789869.</span>

	<span style="color: Green">% The user may edit any part of this function between delimiters</span>		<span style="color: Green">% The user may edit any part of this function between delimiters</span>

AndrewBangham at 19:48, 2 June 2011

2011-06-02T19:48:37Z

← Older revision		Revision as of 20:48, 2 June 2011
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	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	<span style="color: CornflowerBlue">% Section 1</span>		<span style="color: CornflowerBlue">% Section 1</span>
	function m = ~~gpt_temp_fresh_20110602~~( m )		function m = gpt_tut_interaction_example_20110601( m )
	~~<span style="color: Green">~~%m = ~~gpt_temp_fresh_20110602~~( m )~~</span>~~		%m = gpt_tut_interaction_example_20110601( m )
	~~<span style="color: Green">~~% Morphogen interaction function.~~</span>~~		% Morphogen interaction function.
	~~<span style="color: Green">~~% Written at 2011-06-02 20:43:56.~~</span>~~		% Written at 2011-06-02 14:55:46.
	~~<span style="color: Green">~~% GFtbox revision 0, .~~</span>~~		% GFtbox revision 3554, 2011-06-02 12:30:52.789869.

	<span style="color: Green">% The user may edit any part of this function between delimiters</span>		<span style="color: Green">% The user may edit any part of this function between delimiters</span>

AndrewBangham at 19:45, 2 June 2011

2011-06-02T19:45:44Z

Show changes

AndrewBangham at 19:18, 30 May 2011

2011-05-30T19:18:41Z

← Older revision		Revision as of 20:18, 30 May 2011
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	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	<span style="color: CornflowerBlue">Section 1</span>		<span style="color: CornflowerBlue">Section 1</span>
	function m = ~~gpt_tut_fresh_interaction_function_20110530~~( m )		function m = gpt_tut_interaction_20110530( m )
	<span style="color: Green">%m = ~~gpt_tut_fresh_interaction_function_20110530~~( m )</span>		<span style="color: Green">%m = gpt_tut_interaction_20110530( m )</span>
	<span style="color: Green">% Morphogen interaction function.</span>		<span style="color: Green">% Morphogen interaction function.</span>
	<span style="color: Green">% Written at 2011-05-30 20:10:22.</span>		<span style="color: Green">% Written at 2011-05-30 09:42:07.</span>
	<span style="color: Green">% GFtbox revision 0, .</span>		<span style="color: Green">% GFtbox revision 0, .</span>

	<span style="color: Green">% The user may edit any part of this function between delimiters</span>		<span style="color: Green">% The user may edit any part of this function between delimiters</span>

AndrewBangham at 19:14, 30 May 2011

2011-05-30T19:14:23Z

← Older revision		Revision as of 20:14, 30 May 2011
Line 9:		Line 9:
	Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>		Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>
	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	~~'''Section 1 Automatic'''</span>~~		<span style="color: CornflowerBlue">Section 1</span>
	~~function m = gpt_freshly_minted_20110529( m )~~		function m = gpt_tut_fresh_interaction_function_20110530( m )
	~~%m = gpt_freshly_minted_20110529( m )~~		<span style="color: Green">%m = gpt_tut_fresh_interaction_function_20110530( m )</span>
	~~% Morphogen interaction function.~~		<span style="color: Green">% Morphogen interaction function.</span>
	~~% Written at 2011-05-29 08:38:05.~~		<span style="color: Green">% Written at 2011-05-30 20:10:22.</span>
	~~% GFtbox revision 0, .~~		<span style="color: Green">% GFtbox revision 0, .</span>
	~~% The user may edit any part of this function between delimiters~~
	~~% of the form "USER CODE..." and "END OF USER CODE...". The~~		<span style="color: Green">% The user may edit any part of this function between delimiters</span>
	~~% delimiters themselves must not be moved, edited, deleted, or added.~~		<span style="color: Green">% of the form "USER CODE..." and "END OF USER CODE...". The</span>
	~~if isempty(m), return; end~~		<span style="color: Green">% delimiters themselves must not be moved, edited, deleted, or added.</span>
	~~fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );~~
	~~try~~		if isempty(m), return; end
	~~m = local_setproperties( m );~~
	~~catch~~		fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span>
	~~end~~
	~~realtime = m.globalDynamicProps.currenttime;~~		try
	~~%%% USER CODE: INITIALISATION~~		m = local_setproperties( m );
	~~<span style="color: CornflowerBlue">'''Section 2'''</span>~~		catch
			end
	~~% In this section you may modify the mesh in any way whatsoever.~~
	~~if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration~~		realtime = m.globalDynamicProps.currenttime;
	~~% Zero out a lot of stuff to create a blank slate.~~
	~~% If no morphogens are set in the GUI it may be useful to~~		<span style="color: CornflowerBlue">Section 2</span>
	~~% zero some arrays by uncommenting the following.~~		<span style="color: Green">%%% USER CODE: INITIALISATION</span>
	~~% m.morphogens(:) = 0;~~
	~~% m.morphogenclamp(:) = 0;~~		<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
	~~% m.mgen_production(:) = 0;~~		if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% First iteration</span>
	~~% m.mgen_absorption(:) = 0;~~		<span style="color: Green">% Zero out a lot of stuff to create a blank slate.
	~~% m.seams(:) = false;~~
	~~% m.mgen_dilution(:) = false;~~
	~~% Set up names for variant models. Useful for running multiple models on a cluster.~~
	~~m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' }; % CLUSTER~~
	~~m.userdata.ranges.~~

AndrewBangham at 09:22, 29 May 2011

2011-05-29T09:22:06Z

← Older revision		Revision as of 10:22, 29 May 2011
Line 1:		Line 1:
	[[GFtbox_Tutorial_pages\|Back to tutorial pages]]<br>		[[GFtbox_Tutorial_pages#Modelling using a combination of GUI and interaction function\|Back to tutorial pages]]<br>
	[[Tutorial on the basic interaction function\|Tutorial on the basic interaction function]]		[[Tutorial on the basic interaction function\|Tutorial on the basic interaction function]]
	<br><br>		<br><br>

AndrewBangham at 09:20, 29 May 2011

2011-05-29T09:20:51Z

← Older revision		Revision as of 10:20, 29 May 2011
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	<br><br>		<br><br>
	<span style="color: CornflowerBlue">'''This file is output automatically on clicking Panel: Edit in a newly saved project. '''<br>		<span style="color: CornflowerBlue">'''This file is output automatically on clicking Panel: Edit in a newly saved project. '''<br>
	Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>'''Section 1'''</span>		Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>
			The code has been divided into Sections to help with the tutorial.<br><br>
			'''Section 1 Automatic'''</span>
	function m = gpt_freshly_minted_20110529( m )		function m = gpt_freshly_minted_20110529( m )
	%m = gpt_freshly_minted_20110529( m )		%m = gpt_freshly_minted_20110529( m )
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	% 'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')		% 'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')

	<span style="color: CornflowerBlue">'''Section 3'''</span>		<span style="color: CornflowerBlue">'''Section 3 Automatic'''</span>
	%%% END OF USER CODE: INITIALISATION		%%% END OF USER CODE: INITIALISATION

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	% If this happens, maybe you forgot a model.		% If this happens, maybe you forgot a model.
	end		end
	<span style="color: CornflowerBlue">'''Section 11'''</span>		<span style="color: CornflowerBlue">'''Section 11 Automatic'''</span>

	%%% END OF USER CODE: MORPHOGEN INTERACTIONS		%%% END OF USER CODE: MORPHOGEN INTERACTIONS
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	%%% USER CODE: SUBFUNCTIONS		%%% USER CODE: SUBFUNCTIONS
	<span style="color: CornflowerBlue">'''Section 13'''</span>		<span style="color: CornflowerBlue">'''Section 13 Semi-automatic'''</span>

	function m = local_setproperties( m )		function m = local_setproperties( m )

AndrewBangham at 09:18, 29 May 2011

2011-05-29T09:18:24Z

← Older revision		Revision as of 10:18, 29 May 2011
Line 6:		Line 6:
	Remember: a GFtbox model comprises two parts, the Mesh and the Interaction function. At the point that the interaction function is created the Mesh exists (shape and general physical properties) but the regulatory systems do not - it is these that you add to the interaction function. A loose analogy is to say that the Mesh corresponds to the cell membranes and cytoplasm (the structure) and the Interaction function corresponds to the nucleus and DNA. You need both to grow - and they must be compatible with each other.		Remember: a GFtbox model comprises two parts, the Mesh and the Interaction function. At the point that the interaction function is created the Mesh exists (shape and general physical properties) but the regulatory systems do not - it is these that you add to the interaction function. A loose analogy is to say that the Mesh corresponds to the cell membranes and cytoplasm (the structure) and the Interaction function corresponds to the nucleus and DNA. You need both to grow - and they must be compatible with each other.
	<br><br>		<br><br>
			<span style="color: CornflowerBlue">'''This file is output automatically on clicking Panel: Edit in a newly saved project. '''<br>
			Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>'''Section 1'''</span>
	function m = gpt_freshly_minted_20110529( m )		function m = gpt_freshly_minted_20110529( m )
	%m = gpt_freshly_minted_20110529( m )		%m = gpt_freshly_minted_20110529( m )
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	realtime = m.globalDynamicProps.currenttime;		realtime = m.globalDynamicProps.currenttime;
	%%% USER CODE: INITIALISATION		%%% USER CODE: INITIALISATION
			<span style="color: CornflowerBlue">'''Section 2'''</span>

	% In this section you may modify the mesh in any way whatsoever.		% In this section you may modify the mesh in any way whatsoever.
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	% 'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')		% 'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')

			<span style="color: CornflowerBlue">'''Section 3'''</span>
	%%% END OF USER CODE: INITIALISATION		%%% END OF USER CODE: INITIALISATION

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	% In this section you may modify the mesh in any way that does not		% In this section you may modify the mesh in any way that does not
	% alter the set of nodes.		% alter the set of nodes.
			<span style="color: CornflowerBlue">'''Section 4'''</span>

	if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.		if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
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	end		end
			<span style="color: CornflowerBlue">'''Section 5'''</span>

	% Second way to generate a gradient		% Second way to generate a gradient
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	% 'add', true ); % These discs are added to any discs existing already		% 'add', true ); % These discs are added to any discs existing already
	% end		% end
			<span style="color: CornflowerBlue">'''Section 6'''</span>

	% Directives for creating latex representation directly from Matlab code		% Directives for creating latex representation directly from Matlab code
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	% @@after t		% @@after t
	% @@between t1 t2		% @@between t1 t2
			<span style="color: CornflowerBlue">'''Section 7'''</span>

	% % If you want to define different phases according to the absolute		% % If you want to define different phases according to the absolute
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	%		%
	% mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth		% mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth
			<span style="color: CornflowerBlue">'''Section 8'''</span>

	% Code common to all models.		% Code common to all models.
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	% Code for specific models.		% Code for specific models.
	switch modelname		switch modelname
			<span style="color: CornflowerBlue">'''Section 9'''</span>
	case 'MODEL1' % @@model MODEL1		case 'MODEL1' % @@model MODEL1
	% @@PRN Polariser Regulatory Network		% @@PRN Polariser Regulatory Network
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	% kbper_p(:) = 0; % @@ Eqn xx		% kbper_p(:) = 0; % @@ Eqn xx
	% knor_p(:) = 0; % @@ Eqn xx		% knor_p(:) = 0; % @@ Eqn xx
			<span style="color: CornflowerBlue">'''Section 10'''</span>
	case 'MODEL2' % @@model MODEL2		case 'MODEL2' % @@model MODEL2
	% @@PRN Polariser Regulatory Network		% @@PRN Polariser Regulatory Network
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	% If this happens, maybe you forgot a model.		% If this happens, maybe you forgot a model.
	end		end
			<span style="color: CornflowerBlue">'''Section 11'''</span>

	%%% END OF USER CODE: MORPHOGEN INTERACTIONS		%%% END OF USER CODE: MORPHOGEN INTERACTIONS
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	m.morphogens(:,arrest_i) = arrest_p;		m.morphogens(:,arrest_i) = arrest_p;
	%%% USER CODE: FINALISATION		%%% USER CODE: FINALISATION
			<span style="color: CornflowerBlue">'''Section 12'''</span>

	% In this section you may modify the mesh in any way whatsoever.		% In this section you may modify the mesh in any way whatsoever.
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	%%% USER CODE: SUBFUNCTIONS		%%% USER CODE: SUBFUNCTIONS
			<span style="color: CornflowerBlue">'''Section 13'''</span>

	function m = local_setproperties( m )		function m = local_setproperties( m )
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	% m = leaf_setproperty( m, 'lengthscale', 0.200000 );		% m = leaf_setproperty( m, 'lengthscale', 0.200000 );
	end		end
			<span style="color: CornflowerBlue">'''Section 14'''</span>

	% Here you may write any functions of your own, that you want to call from		% Here you may write any functions of your own, that you want to call from

AndrewBangham at 08:06, 29 May 2011

2011-05-29T08:06:42Z

← Older revision		Revision as of 09:06, 29 May 2011
Line 3:		Line 3:
	<br><br>		<br><br>
	The large number of comments do two things. Firstly, they provide '''guidence on how to structure a growth mode'''l - in other words how one might organise thoughts on how things grow - the polarity regulation network, the gene regulation network and the specified growth regulation network. Secondly, they '''help us remember how''' to do certain things without having to look them up in the manual (that is not always complete and up to date). It is easier to delete what is not wanted than to look up and add what is wanted.		The large number of comments do two things. Firstly, they provide '''guidence on how to structure a growth mode'''l - in other words how one might organise thoughts on how things grow - the polarity regulation network, the gene regulation network and the specified growth regulation network. Secondly, they '''help us remember how''' to do certain things without having to look them up in the manual (that is not always complete and up to date). It is easier to delete what is not wanted than to look up and add what is wanted.
			<br><br>
			Remember: a GFtbox model comprises two parts, the Mesh and the Interaction function. At the point that the interaction function is created the Mesh exists (shape and general physical properties) but the regulatory systems do not - it is these that you add to the interaction function. A loose analogy is to say that the Mesh corresponds to the cell membranes and cytoplasm (the structure) and the Interaction function corresponds to the nucleus and DNA. You need both to grow - and they must be compatible with each other.
	<br><br>		<br><br>
	function m = gpt_freshly_minted_20110529( m )		function m = gpt_freshly_minted_20110529( m )

AndrewBangham at 07:56, 29 May 2011

2011-05-29T07:56:45Z

← Older revision		Revision as of 08:56, 29 May 2011
Line 2:		Line 2:
	[[Tutorial on the basic interaction function\|Tutorial on the basic interaction function]]		[[Tutorial on the basic interaction function\|Tutorial on the basic interaction function]]
	<br><br>		<br><br>
	The large number of comments do two things. Firstly, they provide guidence on how to structure a growth ~~model~~ - in other words how one might organise thoughts on how things grow - the polarity regulation network, the gene regulation network and the specified growth regulation network. Secondly, they help us remember how to do certain things without having to look them up in the manual (that is not always complete and up to date). It is easier to delete what is not wanted than to look up and add what is wanted.		The large number of comments do two things. Firstly, they provide '''guidence on how to structure a growth mode'''l - in other words how one might organise thoughts on how things grow - the polarity regulation network, the gene regulation network and the specified growth regulation network. Secondly, they '''help us remember how''' to do certain things without having to look them up in the manual (that is not always complete and up to date). It is easier to delete what is not wanted than to look up and add what is wanted.
	<br><br>		<br><br>
	function m = gpt_freshly_minted_20110529( m )		function m = gpt_freshly_minted_20110529( m )