Difference between revisions of "GFtbox Example pages"

From BanghamLab
Jump to navigation Jump to search
Line 17: Line 17:
 
*GPT_CASE_RST     
 
*GPT_CASE_RST     
 
A Matlab script to run all three submodels and check that ''dt'' is reasonable is as follows:
 
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',...
 +
        'Stages',[20 100 140 180 200],'dt',[0.5,1,2,5],'modelname',[1:3]);
 +
 +
where the 'Path' and 'Name' parameters specify the location and name of GPT_CASE_RST folder, included in the GFtbox download. This command will sequentially run 12 simulations. By adding the 'Use','Cluster' parameter pair, it possible to run the simulations in parallel (and therefore, more quickly) on a Linux cluster.
  
 
*GPT_InvagEmbryo <br>
 
*GPT_InvagEmbryo <br>

Revision as of 11:45, 7 June 2011

The 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

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)

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). 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

These models are those used in the paper.

  • 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',...
       'Stages',[20 100 140 180 200],'dt',[0.5,1,2,5],'modelname',[1:3]);

where the 'Path' and 'Name' parameters specify the location and name of GPT_CASE_RST folder, included in the GFtbox download. This command will sequentially run 12 simulations. By adding the 'Use','Cluster' parameter pair, it possible to run the simulations in parallel (and therefore, more quickly) on a Linux cluster.

  • GPT_InvagEmbryo

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

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.