GPT tut interaction 20110530 second edit - Revision history

AndrewBangham at 20:11, 2 June 2011

2011-06-02T20:11:08Z

← Older revision		Revision as of 20:11, 2 June 2011
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	<span style="color: Green">% the activity (_a) is set to zero</span>		<span style="color: Green">% the activity (_a) is set to zero</span>

	id_a_p(m.nodes(:,1)<-0.03)=1; <span style="color: Green">% setup region for A where identity factor A is represented by id_a_p</span>		<span style="color: Magenta"> id_a_p(m.nodes(:,1)<-0.03)=1; <span style="color: Green">% setup region for A where identity factor A is represented by id_a_p</span>
	id_b_p(m.nodes(:,2)<-0.01)=1; <span style="color: Green">% setup region for B</span>		id_b_p(m.nodes(:,2)<-0.01)=1; </span><span style="color: Green">% setup region for B</span>

	<span style="color: Green">% One way to set up a morphogen gradient is by ...</span>		<span style="color: Green">% One way to set up a morphogen gradient is by ...</span>
	<span style="color: Green">% Setting up a gradient by clamping the ends (execute only once)</span>		<span style="color: Green">% Setting up a gradient by clamping the ends (execute only once)</span>
	P((m.nodes(:,1)<-0.05)&(m.nodes(:,2)>0.03))=1;		<span style="color: MediumBlue">P((m.nodes(:,1)<-0.05)&(m.nodes(:,2)>0.03))=1;
	m.morphogenclamp( P==1, polariser_i ) = 1;		m.morphogenclamp( P==1, polariser_i ) = 1;
	m = leaf_mgen_conductivity( m, 'POLARISER', 0.001 ); <span style="color: Green">%specifies the diffusion rate of polariser</span>		m = leaf_mgen_conductivity( m, 'POLARISER', 0.001 ); <span style="color: Green">%specifies the diffusion rate of polariser</span>
	m = leaf_mgen_absorption( m, 'POLARISER', 0.1 ); <span style="color: Green">% specifies degradation rate of polariser</span>		m = leaf_mgen_absorption( m, 'POLARISER', 0.1 ); <span style="color: Green">% specifies degradation rate of polariser</span></span>

	<span style="color: Green">% Fixing vertices, i.e. fix z for the base to prevent base from moving up or down</span>		<span style="color: Green">% Fixing vertices, i.e. fix z for the base to prevent base from moving up or down</span>

AndrewBangham at 19:56, 2 June 2011

2011-06-02T19:56:21Z

← Older revision		Revision as of 19:56, 2 June 2011
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	<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>		<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>
	m.userdata.ranges.modelname.range = { 'NoPolariser', 'WithPolariser' }; <span style="color: Green">% CLUSTER</span>		m.userdata.ranges.modelname.range = { <span style="color: Magenta">'NoPolariser'</span>, <span style="color: MediumBlue">'WithPolariser'</span> }; <span style="color: Green">% CLUSTER</span>
	<span style="color: Crimson">m.userdata.ranges.modelname.index = 2;</span> <span style="color: Green">% CLUSTER</span>		<span style="color: Crimson">m.userdata.ranges.modelname.index = 2;</span> <span style="color: Green">% CLUSTER</span>
	end		end

AndrewBangham at 16:09, 2 June 2011

2011-06-02T16:09:34Z

← Older revision		Revision as of 16:09, 2 June 2011
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	[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>		[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>
	The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>		The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed. If you copy this function we recommend removing all the comments that you no longer need to see.<br><br>
	There are two submodels. The two are the same except that the first has isotropic growth (see lines shown in <span style="color: Magenta">magenta</span>) and the second has anisotropic growth (see lines shown in <span style="color: MediumBlue">MediumBlue</span>). The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>		There are two submodels. The two are the same except that the first has isotropic growth (see lines shown in <span style="color: Magenta">magenta</span>) and the second has anisotropic growth (see lines shown in <span style="color: MediumBlue">MediumBlue</span>). The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>
	<span style="color: CornflowerBlue">% Section 1</span>		<span style="color: CornflowerBlue">% Section 1</span>

AndrewBangham at 16:05, 2 June 2011

2011-06-02T16:05:54Z

← Older revision		Revision as of 16:05, 2 June 2011
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	[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>		[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>
	The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>		The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>
	There are two submodels. The two are the same except that the first has isotropic growth (see lines shown in magenta) and the second has anisotropic growth (see lines shown in ~~cyan~~). The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>		There are two submodels. The two are the same except that the first has isotropic growth (see lines shown in <span style="color: Magenta">magenta</span>) and the second has anisotropic growth (see lines shown in <span style="color: MediumBlue">MediumBlue</span>). The choice of submodel (1 or 2) is made on the line highlighted in RED.<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 )
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	<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>
	<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>
	<span style="color: ~~Cyan~~">kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>		<span style="color: MediumBlue">kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
	kaper_p(:) = 0.1*kapar_p; <span style="color: Green">% anisotropic growth</span>		kaper_p(:) = 0.1*kapar_p; <span style="color: Green">% anisotropic growth</span>
	kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>		kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>

AndrewBangham at 16:02, 2 June 2011

2011-06-02T16:02:39Z

AndrewBangham at 15:58, 2 June 2011

2011-06-02T15:58:44Z

AndrewBangham at 15:55, 2 June 2011

2011-06-02T15:55:55Z

Show changes

AndrewBangham at 14:49, 31 May 2011

2011-05-31T14:49:21Z

← Older revision		Revision as of 14:49, 31 May 2011
Line 1:		Line 1:
	[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]]		[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>
	The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>		The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>
	There are two submodels. The first has isotropic growth and the second has anisotropic growth. The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>		There are two submodels. The first has isotropic growth and the second has anisotropic growth. The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>

AndrewBangham at 14:48, 31 May 2011

2011-05-31T14:48:44Z

← Older revision		Revision as of 14:48, 31 May 2011
Line 1:		Line 1:
	[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]]		[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]]
	The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>		The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>
	There are two submodels. The first has isotropic growth and the second has anisotropic growth. The choice of submodel is made ~~with~~ the ~~index -~~ highlighted in RED.<br><br>		There are two submodels. The first has isotropic growth and the second has anisotropic growth. The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>
	<span style="color: CornflowerBlue">Section 1</span>		<span style="color: CornflowerBlue">Section 1</span>
	function m = gpt_tut_interaction_20110530( m )		function m = gpt_tut_interaction_20110530( m )
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	<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>		<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>
	m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' }; <span style="color: Green">% CLUSTER</span>		m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' }; <span style="color: Green">% CLUSTER</span>
	<span style="color: ~~DarkRed~~">m.userdata.ranges.modelname.index = 2;</span> <span style="color: Green">% CLUSTER</span>		<span style="color: Crimson">m.userdata.ranges.modelname.index = 2;</span> <span style="color: Green">% CLUSTER</span>
	end		end
	modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; <span style="color: Green">% CLUSTER</span>		modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; <span style="color: Green">% CLUSTER</span>

AndrewBangham: Created page with 'Back to tutoral on the interaction function details The green comments have not been removed in this copy - to allow you to see t…'

2011-05-31T14:47:29Z

Created page with 'Back to tutoral on the interaction function details The green comments have not been removed in this copy - to allow you to see t…'

Show changes

← Older revision		Revision as of 16:02, 2 June 2011
Line 1:		Line 1:
	[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>		[[Tutorial on the interaction function details\|Back to tutoral on the interaction function details]].<br><br>
	The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>		The green comments have not been removed in this copy - to allow you to see the context in which the new code has been placed.<br><br>
	There are two submodels. The first has isotropic growth and the second has anisotropic growth. The choice of submodel (1 or 2) is made on the line highlighted in RED.<br><br>		There are two submodels. The two are the same except that the first has isotropic growth (see lines shown in magenta) and the second has anisotropic growth (see lines shown in cyan). The choice of submodel (1 or 2) is made on the line highlighted in RED.<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 )
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	<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>
	<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>
	kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>		<span style="color: Magenta"> kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
	kaper_p(:) = kapar_p; <span style="color: Green">% isotropic growth</span>		kaper_p(:) = kapar_p; <span style="color: Green">% isotropic growth</span>
	kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>		kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>
	kbper_p(:) = kapar_p; <span style="color: Green">% same</span>		kbper_p(:) = kapar_p; <span style="color: Green">% same</span></span>
	knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>		knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>
	<span style="color: CornflowerBlue">% Section 11</span>		<span style="color: CornflowerBlue">% Section 11</span>
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	<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% kbper_p(:) = 0; % @@ Eqn xx</span>
	<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>		<span style="color: Green">% knor_p(:) = 0; % @@ Eqn xx</span>
	kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>		<span style="color: Cyan">kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
	kaper_p(:) = 0.1*kapar_p; <span style="color: Green">% anisotropic growth</span>		kaper_p(:) = 0.1*kapar_p; <span style="color: Green">% anisotropic growth</span>
	kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>		kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>
	kbper_p(:) = 0.1*kapar_p; <span style="color: Green">% also anisotropic</span>		kbper_p(:) = 0.1*kapar_p; </span><span style="color: Green">% also anisotropic</span>
	knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>		knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>
	otherwise		otherwise

← Older revision		Revision as of 15:58, 2 June 2011
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	<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>		<span style="color: Green">% Set up names for variant models. Useful for running multiple models on a cluster.</span>
	m.userdata.ranges.modelname.range = { 'NoPolariser', 'WithPolariser' }; <span style="color: Green">% CLUSTER</span>		m.userdata.ranges.modelname.range = { 'NoPolariser', 'WithPolariser' }; <span style="color: Green">% CLUSTER</span>
	m.userdata.ranges.modelname.index = 2; <span style="color: Green">% CLUSTER</span>		<span style="color: Crimson">m.userdata.ranges.modelname.index = 2;</span> <span style="color: Green">% CLUSTER</span>
	end		end
	modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; <span style="color: Green">% CLUSTER</span>		modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; <span style="color: Green">% CLUSTER</span>
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	switch modelname		switch modelname
	<span style="color: CornflowerBlue">% Section 10</span>		<span style="color: CornflowerBlue">% Section 10</span>
	case 'NoPolariser' <span style="color: Green">% @@model MODEL1</span>		<span style="color: Crimson">case 'NoPolariser' </span><span style="color: Green">% @@model MODEL1</span>
	<span style="color: Green">% @@PRN Polariser Regulatory Network</span>		<span style="color: Green">% @@PRN Polariser Regulatory Network</span>
	<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>		<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
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	knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>		knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>
	<span style="color: CornflowerBlue">% Section 11</span>		<span style="color: CornflowerBlue">% Section 11</span>
	case 'WithPolariser' <span style="color: Green">% @@model MODEL2</span>		<span style="color: Crimson">case 'WithPolariser' </span><span style="color: Green">% @@model MODEL2</span>
	<span style="color: Green">% @@PRN Polariser Regulatory Network</span>		<span style="color: Green">% @@PRN Polariser Regulatory Network</span>
	<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>		<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>