Tutorial on the basic interaction function - Revision history

AndrewBangham at 17:36, 6 June 2011

2011-06-06T17:36:46Z

← Older revision		Revision as of 17:36, 6 June 2011
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	\|width="150pt"\|Steps(m)\|\| current step number in Mesh m		\|width="150pt"\|Steps(m)\|\| current step number in Mesh m
	\|-		\|-
	\|width="150pt"\|pro(k,id)\|\| promote by k in regions designated by factor, id		\|width="150pt"\|pro(k,id)\|\| promote by k in regions designated by factor, id (''pro(k,'''x''')=1+k'''x'')
	\|-		\|-
	\|width="150pt"\|inh(k,id)\|\| inhibit by k in regions designated by factor, id		\|width="150pt"\|inh(k,id)\|\| inhibit by k in regions designated by factor, id (''inh(k,'''x''')=1/(1+k'''x''')'')
	\|-		\|-
	\|width="150pt"\|local_setproperties( m )\|\| initialise Mesh properties		\|width="150pt"\|local_setproperties( m )\|\| initialise Mesh properties

AndrewBangham at 11:17, 3 June 2011

2011-06-03T11:17:53Z

← Older revision		Revision as of 11:17, 3 June 2011
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	[[GFtbox_Tutorial_pages\|Back to tutorial pages]]		[[GFtbox_Tutorial_pages#2 Modelling using a combination of GUI and interaction function\|Back to tutorial pages]]
	=Creating an interaction function=		=Creating an interaction function=
	The goal is to re-create the model used to illustrate [[GFtbox#What does GFtbox require?\|why we use matlab]]. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why?[[Tutorial on the basic interaction function#Variables and utility functions\| see below]]). The ''x,y,z'' coordinates of mesh nodes (vertices) are stored in the Mesh data structure in a field called ''nodes''. Thus the ''x'' coordinate of node 1 is stored in ''m.nodes(1,1)'', the ''y'' coordinate in ''m.nodes(1,2)'' and ''z'' coordinate in ''m.nodes(1,3)''.		The goal is to re-create the model used to illustrate [[GFtbox#What does GFtbox require?\|why we use matlab]]. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why?[[Tutorial on the basic interaction function#Variables and utility functions\| see below]]). The ''x,y,z'' coordinates of mesh nodes (vertices) are stored in the Mesh data structure in a field called ''nodes''. Thus the ''x'' coordinate of node 1 is stored in ''m.nodes(1,1)'', the ''y'' coordinate in ''m.nodes(1,2)'' and ''z'' coordinate in ''m.nodes(1,3)''.

AndrewBangham at 11:16, 3 June 2011

2011-06-03T11:16:23Z

← Older revision		Revision as of 11:16, 3 June 2011
Line 1:		Line 1:
	[[GFtbox_Tutorial_pages\|Back to tutorial pages]]		[[GFtbox_Tutorial_pages\|Back to tutorial pages]]
	=Creating an interaction function=		=Creating an interaction function=
	The goal is to re-create the model used to illustrate [[GFtbox#What does GFtbox require?\|why we use matlab]]. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why?[[Tutorial on the basic interaction function#Variables and utility functions\| see below]]). The model is articulated in the following code.		The goal is to re-create the model used to illustrate [[GFtbox#What does GFtbox require?\|why we use matlab]]. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why?[[Tutorial on the basic interaction function#Variables and utility functions\| see below]]). The ''x,y,z'' coordinates of mesh nodes (vertices) are stored in the Mesh data structure in a field called ''nodes''. Thus the ''x'' coordinate of node 1 is stored in ''m.nodes(1,1)'', the ''y'' coordinate in ''m.nodes(1,2)'' and ''z'' coordinate in ''m.nodes(1,3)''.
			The patterns of morphogens A and B are set up by <br>

			id_a_p(m.nodes(:,1)<-0.03)=1;
			id_b_p(m.nodes(:,2)<-0.01)=1;
			where ''id_a_p'' is the A morphogen. ''m.node(:,1)'' refers to the ''x'' coordinates of all nodes (vertices) in the mesh<br>
			The expression ''(m.nodes(:,1)<-0.03)'' means find all vertices with ''x'' coordinates that are less than -0.03.<br><br>
			Similarly, ''(m.nodes(:,2)<-0.01)'' means find all vertices with ''y'' coordinates that are less than -0.01.<br><br>
			The model is articulated in the following code.

	if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.		if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.

AndrewBangham at 14:21, 31 May 2011

2011-05-31T14:21:29Z

← Older revision		Revision as of 14:21, 31 May 2011
Line 1:		Line 1:
	[[GFtbox_Tutorial_pages\|Back to tutorial pages]]		[[GFtbox_Tutorial_pages\|Back to tutorial pages]]
	=Creating an interaction function=		=Creating an interaction function=
	The goal is to re-create the model used to illustrate why we use matlab. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why? see below). The model is ~~as follows~~.		The goal is to re-create the model used to illustrate [[GFtbox#What does GFtbox require?\|why we use matlab]]. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why?[[Tutorial on the basic interaction function#Variables and utility functions\| see below]]). The model is articulated in the following code.

	if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.		if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.

AndrewBangham at 14:18, 31 May 2011

2011-05-31T14:18:25Z

← Older revision		Revision as of 14:18, 31 May 2011
Line 1:		Line 1:
	[[GFtbox_Tutorial_pages\|Back to tutorial pages]]		[[GFtbox_Tutorial_pages\|Back to tutorial pages]]
			=Creating an interaction function=
			The goal is to re-create the model used to illustrate why we use matlab. We will create two new variables A and B - in the interaction function they are labelled'' id_a_p'' and ''id_b_p'' (why? see below). The model is as follows.

			if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
			id_a_p(m.nodes(:,1)<-0.03)=1; % setup region for A where identity factor A is represented by id_a_p
			id_b_p(m.nodes(:,2)<-0.01)=1; % setup region for B
			else
			% @@KRN Growth Regulatory Network
			kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
			kaper_p(:) = kapar_p; % isotropic growth
			kbpar_p(:) = kapar_p; % same on both sides of the sheet
			kbper_p(:) = kapar_p; % same
			knor_p(:) = 0; % thickness not growing
			end

	==Creating the interaction function from the GUI==		==Creating the interaction function from the GUI==
	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- valign="top"		\|- valign="top"
	\|width="300px"\|The ''GFtbox'' user interface. ~~Save~~ a new project, with a disc shaped mesh and add two new morphogens ''id_a'' and ''id_b'' (Panel: Morphogens: New).<br><br>		\|width="300px"\|The ''GFtbox'' user interface. Start a new project, with a disc shaped mesh and add two new morphogens ''id_a'' and ''id_b'' (Panel: Morphogens: New).<br><br>
	Now create the interaction function by clicking on Panel: Interaction function: Edit (bottom left) <br><br>		Save As<br><br>
			Now create and edit the interaction function by clicking on (Panel: Interaction function: Edit) (bottom left) <br><br>
			There is lots of 'green stuff' - lines that are comments. Just for the moment we will more than ignore them - delete them. Look at the listing below to get an idea of what to delete.
			Now in Section 4 add the code shown above - it is shown in the listing below.
	<br><br>		<br><br>

	A free-text file with the same name as the interaction function is also created automatically on pressing Panel:Interaction function: notes. This makes it easier to keep notes on what you are doing.<br><br>		A free-text file with the same name as the interaction function is also created automatically on pressing Panel:Interaction function: notes. This makes it easier to keep notes on what you are doing.<br><br>
	<small>Note: you can see the internal data structure by clicking Menu: Wizard: Export mesh and follow the instructions shown at the command line.<br>Another way to see Mesh m is to set a break point in the interaction function and running (e.g. Panel: Run: Step, or Panel: Interaction function: Call, etc.)<br>Note: a history of commands that have been run recently can be displayed (can be used to help write custom modelling programs that exploit the GFtbox library) </small>		<small>Note: you can see the internal data structure by clicking Menu: Wizard: Export mesh and follow the instructions shown at the command line.<br>Another way to see Mesh m is to set a break point in the interaction function and running (e.g. Panel: Run: Step, or Panel: Interaction function: Call, etc.)<br>Note: a history of commands that have been run recently can be displayed (can be used to help write custom modelling programs that exploit the GFtbox library) </small>

AndrewBangham at 13:17, 31 May 2011

2011-05-31T13:17:49Z

← Older revision		Revision as of 13:17, 31 May 2011
Line 3:		Line 3:
	{\| border="1" cellpadding="5" cellspacing="5"		{\| border="1" cellpadding="5" cellspacing="5"
	\|- valign="top"		\|- valign="top"
	\|width="300px"\|The ''GFtbox'' user interface. ~~Having saved~~ a new project, ~~click~~ on Panel: Interaction function: Edit (bottom left) ~~and the initial interaction function will be generated automatically.~~<br><br>		\|width="300px"\|The ''GFtbox'' user interface. Save a new project, with a disc shaped mesh and add two new morphogens ''id_a'' and ''id_b'' (Panel: Morphogens: New).<br><br>
			Now create the interaction function by clicking on Panel: Interaction function: Edit (bottom left) <br><br>
			<br><br>
	A free-text file with the same name as the interaction function is also created automatically on pressing Panel:Interaction function: notes. This makes it easier to keep notes on what you are doing.<br><br>		A free-text file with the same name as the interaction function is also created automatically on pressing Panel:Interaction function: notes. This makes it easier to keep notes on what you are doing.<br><br>
	<small>Note: you can see the internal data structure by clicking Menu: Wizard: Export mesh and follow the instructions shown at the command line.<br>Another way to see Mesh m is to set a break point in the interaction function and running (e.g. Panel: Run: Step, or Panel: Interaction function: Call, etc.)<br>Note: a history of commands that have been run recently can be displayed (can be used to help write custom modelling programs that exploit the GFtbox library) </small>		<small>Note: you can see the internal data structure by clicking Menu: Wizard: Export mesh and follow the instructions shown at the command line.<br>Another way to see Mesh m is to set a break point in the interaction function and running (e.g. Panel: Run: Step, or Panel: Interaction function: Call, etc.)<br>Note: a history of commands that have been run recently can be displayed (can be used to help write custom modelling programs that exploit the GFtbox library) </small>

AndrewBangham at 13:02, 31 May 2011

2011-05-31T13:02:55Z

AndrewBangham at 12:28, 31 May 2011

2011-05-31T12:28:18Z

Show changes

AndrewBangham at 10:15, 30 May 2011

2011-05-30T10:15:37Z

← Older revision		Revision as of 10:15, 30 May 2011
Line 52:		Line 52:
	\|}		\|}
	=The interaction function in more detail=		=The interaction function in more detail=
	A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. [[~~Editing~~ Tutorial on the interaction function details\|It is discussed in more detail here.]])<br><br>		A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. [[Tutorial on the interaction function details\|It is discussed in more detail here.]])<br><br>
	<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>		<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
	The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control,		The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control,

AndrewBangham at 10:14, 30 May 2011

2011-05-30T10:14:35Z

← Older revision		Revision as of 10:14, 30 May 2011
Line 52:		Line 52:
	\|}		\|}
	=The interaction function in more detail=		=The interaction function in more detail=
	A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. It is discussed in more detail here.)<br><br>		A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. [[Editing Tutorial on the interaction function details\|It is discussed in more detail here.]])<br><br>
	<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>		<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
	The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control,		The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control,

← Older revision		Revision as of 13:02, 31 May 2011
Line 53:		Line 53:
	=The interaction function in more detail=		=The interaction function in more detail=
	A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. [[Tutorial on the interaction function details\|It is discussed in more detail here.]])<br><br>		A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, [[Full freshly minted interaction function\| here is a full freshly minted interaction function]]. [[Tutorial on the interaction function details\|It is discussed in more detail here.]])<br><br>
	<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>		<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
	The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to		The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to
	our source code control, lines starting with % are comments</span>		our source code control, lines starting with % are comments</span>

	~~<span style="color: CornflowerBlue">Section 1 '''This part is generated automatically''' from the GUI~~
	~~The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our~~
	~~source code control, lines starting with % are comments</span>~~
	function m = gpt_why_matlab_2011_05_05( m )		function m = gpt_why_matlab_2011_05_05( m )
	<span style="color: Green">%m = gpt_why_matlab_2011_05_05( m )</span>		<span style="color: Green">%m = gpt_why_matlab_2011_05_05( m )</span>
Line 80:		Line 76:

	realtime = m.globalDynamicProps.currenttime;		realtime = m.globalDynamicProps.currenttime;

	<span style="color: Green">%%% USER CODE: INITIALISATION</span>		<span style="color: Green">%%% USER CODE: INITIALISATION</span>
	<span style="color: CornflowerBlue">Section 2 This part could contain user code		<span style="color: CornflowerBlue">Section 2 This part could contain user code
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	[id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );		[id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
	[id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );		[id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );

	<span style="color: Green">% Mesh type: circle</span>		<span style="color: Green">% Mesh type: circle</span>
	<span style="color: Green">% centre: 0</span>		<span style="color: Green">% centre: 0</span>
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	<span style="color: CornflowerBlue">Section 4 This part contains user code that articulates the model</span>		<span style="color: CornflowerBlue">Section 4 This part contains user code that articulates the model</span>

	<span style="color: Green">%%% USER CODE: MORPHOGEN INTERACTIONS</span>		<span style="color: Green">%%% USER CODE: MORPHOGEN INTERACTIONS</span>
	if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% Initialisation code.</span>		if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% Initialisation code.</span>
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	<span style="color: CornflowerBlue">Section 5 This part is generated automatically from the GUI		<span style="color: CornflowerBlue">Section 5 This part is generated automatically from the GUI
	Variables are put back into the data structure (Mesh).		Variables are put back into the data structure (Mesh).
	Note: only variables with the _p suffix (promotors) are stored (levels _l can be computed on the fly and activities _a are generally set in the GUI - they can only be changed in the interaction function by altering the data structure itself.</span>		Note: only variables with the _p suffix (promotors) are stored (levels _l can be computed on the fly and activities _a are
			generally set in the GUI - they can only be changed in the interaction function by altering the data structure itself.</span>
	<span style="color: Green">%%% END OF USER CODE: MORPHOGEN INTERACTIONS</span>		<span style="color: Green">%%% END OF USER CODE: MORPHOGEN INTERACTIONS</span>

	<span style="color: Green">%%% SECTION 6: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE</span>		<span style="color: Green">%%% SECTION 6: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE</span>
	<span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>		<span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
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	m.morphogens(:,id_a_i) = id_a_p;		m.morphogens(:,id_a_i) = id_a_p;
	m.morphogens(:,id_b_i) = id_b_p;		m.morphogens(:,id_b_i) = id_b_p;

	<span style="color: Green">%%% USER CODE: FINALISATION</span>		<span style="color: Green">%%% USER CODE: FINALISATION</span>

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	end		end


	<span style="color: Green">%%% USER CODE: SUBFUNCTIONS</span>		<span style="color: Green">%%% USER CODE: SUBFUNCTIONS</span>