Difference between revisions of "GFtbox Example pages"

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[[Software#GFtbox|Return to BanghamLab software]]<br><br>
 
__NOTOC__
 
__NOTOC__
=The models=
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=Published models=
The models are a part of the GFtbox release in directory'' \GrowthToolbox\Models\Published''. The models can be loaded using the GUI: ''Menus:Projects:Models:Published:Kennaway etal 2011''<br><br>
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==Richard Kennaway, Enrico Coen, Amelia Green, Andrew Bangham, "Generation of diverse biological forms through combinatorial interactions between tissue polarity and growth", PLoS Comp Biol, 2011 (''in press'')==
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<span style="color: DarkRed">'''2013''' Susanna Sauret-Güeto, Katharina Schiessl, Andrew Bangham, Robert Sablowski, Enrico Coen "JAGGED Controls Arabidopsis Petal Growth and Shape by Interacting with a Divergent Polarity Field",''' PLoS Biol 11(4): e1001550. doi:10.1371/journal.pbio.1001550''': [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Susanna Sauret-Güeto et al 2013]</span><br><br>
The models shown here illustrate points about the understanding of growth seen through the lens of the Growing Polarised Tissue Framework. They are not designed to illustrate properties of our implementation of the idea, the ''GFtbox'' (although this might be a by-product). [[GFtbox Tutorial pages|Tutorials on the GFtbox are here]] and [[GFtbox|details about the ''GFtbox'' are here]].<br><br>
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<span style="color: CornflowerBlue">Comparing petal and leaf growth and relating the differences to expression patterns of genes in the petal</span><br>
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The models described in this paper can be downloaded [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip here]. <br><br>
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<span style="color: DarkRed">'''2012''' Erika E. Kuchen, Samantha Fox, Pierre Barbier de Reuille, Richard Kennaway,
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Sandra Bensmihen, Jerome Avondo, Grant M. Calder, Paul Southam, Sarah Robinson, Andrew Bangham, Enrico Coen "Generation of Leaf Shape through Early Patterns of Growth and Tissue Polarity",''' Science''': ([http://www.sciencemag.org/content/335/6072/1092.abstract Kuchen et al 2012])</span><br><br>
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<span style="color: CornflowerBlue">Understanding patterns of leaf growth</span><br>
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The models described in this paper can be downloaded [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip here]. <br><br>
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<span style="color: DarkRed">'''2011''' Richard Kennaway, Enrico Coen, Amelia Green, Andrew Bangham, "Generation of diverse biological forms through combinatorial interactions between tissue polarity and growth",''' PLoS Comp Biol, 7(6)''': e1002071. doi:10.1371/journal.pcbi.1002071</span>http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071<br><br>
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<span style="color: CornflowerBlue">Introducing the Growing Polarised Tissue framework and ''GFtbox''</span><br>
 +
The models described here are included in GFtbox release (directory'' \GrowthToolbox\Models\Published''). They can be loaded using the GUI by selecting ''Menus:Projects:Models:Published:Kennaway etal 2011''. They can also be downloaded [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip here]. <br>
 +
 
 +
The models illustrate points about the understanding of growth seen through the lens of the Growing Polarised Tissue Framework. They are not designed to illustrate properties of our implementation of the idea, the ''GFtbox'' (although this might be a by-product). [[GFtbox Tutorial pages|Tutorials on the GFtbox are here]] and [[GFtbox|details about the ''GFtbox'' are here]].<br><br>
  
 
CASES A to Q have been extracted from the original single project for two reasons, clarity and they have been altered slightly to make them more consistent with the style of programming that we have found makes interaction functions clearer. The results are the same.<br>
 
CASES A to Q have been extracted from the original single project for two reasons, clarity and they have been altered slightly to make them more consistent with the style of programming that we have found makes interaction functions clearer. The results are the same.<br>
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*GPT_CASES_JKLM   
 
*GPT_CASES_JKLM   
 
*GPT_CASES_NOPQ  <br>
 
*GPT_CASES_NOPQ  <br>
These models are those used in the paper.
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The following model is exactly as used in the paper.
 
*GPT_CASE_RST     
 
*GPT_CASE_RST     
A Matlab script to run all three submodels and check that ''dt'' is reasonable is as follows:
 
  
        SilentGFtboxV2('State','Start','Path','/GrowthToolbox/Models/Published/Kennaway-etal-2011/','Name','GPT_CASE_RST',...
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*GPT_InvagEmbryo <br>
        'Stages',[20 100 140 180 200],'dt',[0.5,1,2,5],'modelname',[1:3]);
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The Snapdragon model is given in Green et. al. shown below.<br><br>
        VMSreport('Path','/GrowthToolbox/Models/Published/Kennaway-etal-2011/','Project','GPT_CASE_RST',...
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<span style="color: DarkRed">'''2010''' Amelia A. Green, J. Richard Kennaway, Andrew I. Hanna, J. Andrew Bangham, Enrico Coen, "Genetic Control of Organ Shape and Tissue Polarity",''' PLoS Biol vol.8, no.11''', http://dx.doi.org/10.1371/journal.pbio.1000537.</span><br><br>
        'Experiment','All','flattentime',572.5,'morphogen','KPAR','SNAPFIG',true);
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<span style="color: CornflowerBlue">Relating gene activity to growing shapes </span><br>
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The GFtbox project is a part of the ''GFtbox'' and is accessed through the Project menu. It also be downloaded [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip here]. <br>
 +
 
 +
The project is the unabridged interaction function used to produce all the Figures. As result, it is very long. To understand it requires a good understanding of the GFtbox environment, the paper and its supplemental Text 1. The submodels capture the development of the scientific argument made in the paper. The same model is used for Cui et al.
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*GPT_Snapdragon_2010_Green_et_al.<br><br>
  
where the ''Path'' parameter specifies the location of GPT_CASE_RST directory, included in the GFtbox download. ''Name'' and ''Project'' both refer to the name of the GPT_CASE_RST directory itself. The first command (SilentGFtboxV2...) will sequentially run 12 5-stage simulations, comprising three models, generated using four different values of ''dt''. The second command (VMSreport...) will generate images of the locally simulated models.
 
  
*GPT_InvagEmbryo <br>
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<span style="color: DarkRed">'''2010''' Min-Long Cui, Lucy Copsey, Amelia A. Green, J. Andrew Bangham, Enrico Coen, "Quantitative Control of Organ Shape by Combinatorial Gene Activity", PLoS Biol, 2010, vol.8, no.11, http://dx.doi.org/10.1371/journal.pbio.1000538.</span><br><br>
The Snapdragon model is given in Green et. al. shown below.
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<span style="color: CornflowerBlue">Relating hypothetical patterns of gene activity to observed growing shapes</span><br>
==Amelia A. Green, J. Richard Kennaway, Andrew I. Hanna, J. Andrew Bangham, Enrico Coen, "Genetic Control of Organ Shape and Tissue Polarity", PLoS Biol, 2010, vol.8, no.11, http://dx.doi.org/10.1371/journal.pbio.1000537.==
 
The following project is the unabridged interaction function used to produce all the Figures. As result, it is very long. To understand it requires a good understanding of the GFtbox environment, the paper and its supplemental Text 1. The submodels capture the development of the scientific argument made in the paper. The same model is used for Cui et al.
 
*GPT_Snapdragon_2010_Green_et_al.
 
==Min-Long Cui, Lucy Copsey, Amelia A. Green, J. Andrew Bangham, Enrico Coen, "Quantitative Control of Organ Shape by Combinatorial Gene Activity", PLoS Biol, 2010, vol.8, no.11, http://dx.doi.org/10.1371/journal.pbio.1000538.==
 
 
The models used in this paper are all a part of the project GPT_Snapdragon_2010_Green_et_al.  However, to run the models requires an understanding of how to script GFtbox to run on a cluster.
 
The models used in this paper are all a part of the project GPT_Snapdragon_2010_Green_et_al.  However, to run the models requires an understanding of how to script GFtbox to run on a cluster.

Latest revision as of 13:20, 2 May 2013

Return to BanghamLab software

Published models

2013 Susanna Sauret-Güeto, Katharina Schiessl, Andrew Bangham, Robert Sablowski, Enrico Coen "JAGGED Controls Arabidopsis Petal Growth and Shape by Interacting with a Divergent Polarity Field", PLoS Biol 11(4): e1001550. doi:10.1371/journal.pbio.1001550: Susanna Sauret-Güeto et al 2013

Comparing petal and leaf growth and relating the differences to expression patterns of genes in the petal

The models described in this paper can be downloaded here.

2012 Erika E. Kuchen, Samantha Fox, Pierre Barbier de Reuille, Richard Kennaway, Sandra Bensmihen, Jerome Avondo, Grant M. Calder, Paul Southam, Sarah Robinson, Andrew Bangham, Enrico Coen "Generation of Leaf Shape through Early Patterns of Growth and Tissue Polarity", Science: (Kuchen et al 2012)

Understanding patterns of leaf growth
The models described in this paper can be downloaded here.

2011 Richard Kennaway, Enrico Coen, Amelia Green, Andrew Bangham, "Generation of diverse biological forms through combinatorial interactions between tissue polarity and growth", PLoS Comp Biol, 7(6): e1002071. doi:10.1371/journal.pcbi.1002071http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071

Introducing the Growing Polarised Tissue framework and GFtbox
The models described here are included in GFtbox release (directory \GrowthToolbox\Models\Published). They can be loaded using the GUI by selecting Menus:Projects:Models:Published:Kennaway etal 2011. They can also be downloaded here.

The models illustrate points about the understanding of growth seen through the lens of the Growing Polarised Tissue Framework. They are not designed to illustrate properties of our implementation of the idea, the GFtbox (although this might be a by-product). Tutorials on the GFtbox are here and details about the GFtbox are here.

CASES A to Q have been extracted from the original single project for two reasons, clarity and they have been altered slightly to make them more consistent with the style of programming that we have found makes interaction functions clearer. The results are the same.
The models are to be understood in conjuction with the paper.

  • GPT_CASE_A
  • GPT_CASE_B
  • GPT_CASE_C
  • GPT_CASE_E
  • GPT_CASES_FGHI
  • GPT_CASES_JKLM
  • GPT_CASES_NOPQ

The following model is exactly as used in the paper.

  • GPT_CASE_RST
  • GPT_InvagEmbryo

The Snapdragon model is given in Green et. al. shown below.

2010 Amelia A. Green, J. Richard Kennaway, Andrew I. Hanna, J. Andrew Bangham, Enrico Coen, "Genetic Control of Organ Shape and Tissue Polarity", PLoS Biol vol.8, no.11, http://dx.doi.org/10.1371/journal.pbio.1000537.

Relating gene activity to growing shapes
The GFtbox project is a part of the GFtbox and is accessed through the Project menu. It also be downloaded here.

The project is the unabridged interaction function used to produce all the Figures. As result, it is very long. To understand it requires a good understanding of the GFtbox environment, the paper and its supplemental Text 1. The submodels capture the development of the scientific argument made in the paper. The same model is used for Cui et al.

  • GPT_Snapdragon_2010_Green_et_al.


2010 Min-Long Cui, Lucy Copsey, Amelia A. Green, J. Andrew Bangham, Enrico Coen, "Quantitative Control of Organ Shape by Combinatorial Gene Activity", PLoS Biol, 2010, vol.8, no.11, http://dx.doi.org/10.1371/journal.pbio.1000538.

Relating hypothetical patterns of gene activity to observed growing shapes
The models used in this paper are all a part of the project GPT_Snapdragon_2010_Green_et_al. However, to run the models requires an understanding of how to script GFtbox to run on a cluster.