A framework for retinotopic map formation modelling and evaluation. Currently four models are fully supported (Gierer, Koulakov, Whitelaw and Willshaw). There is also code to run the Grimbert and Cang model.
URL for github repository, this will create a RetinalMap directory: https://github.com/Hjorthmedh/RetinalMap.git
##Installation
To be able to run all the models you need to compile the C routines. They are located in the RetinalMap/@RetinalMap directory, and in the base directory. The first one is for the Koulakov model, the second one for the Willshaw model.
mex stepFastGlobal.c
mex stepMarkerInductionC.c
The Gierer and Whitelaw models are distributed as R packages. The detailed instructions for them can be found in a PDF in respective subdirectory.
In R:
install.packages(c("sjevor"), contriburl="http://damtp.cam.ac.uk/user/eglen/r/")
install.packages(c("fields"))
In the shell (make sure you are in the RetinalMap directory):
R CMD INSTALL gierer
R CMD INSTALL WhitelawCowan
Finally you need to install the Lattice analysis in the parent directory of RetinalMap. To get the Lattice analysis code:
git clone git://github.com/davidwillshaw/map-analysis.git
You should now have the two packages installed in the same directory, ie. YOUR_PATH/RetinalMap and YOUR_PATH/map-analysis.
##Running the models
To run a simulation using the framework we use:
report = ComparePhenotypeModelling(phenotype,action,expNum,plotFigures,kMask,model);
Here phenotype specifies which phenotype you want to simulate, your
standard options are 'WT','Isl2heterozygous', 'Isl2homozygous',
'ephrinA2mm', 'ephrinA5mm', 'ephrinA2mmA5mm' and 'TKO'; action is
either 'run' or 'analyse'; plotFigures can be set to true or false;
kMask is normally 0, it specifies if we should use any cis-interaction
to mask the gradients (not used in this study); model is one of 'Gierer2D', 'koulakov',
'WhiteCow' or 'Markerinduction'.
For example:
report = ComparePhenotypeModelling('WT','run',1,1,0,'koulakov');
Once the simulation finishes you can use the same command but with 'analyse' as the action to get our first version of plots and summary sheets. However there is another version which has replaced it:
report = makeFiguresForCompareArticle(phenotype,expRange,model,plotFigures)
In our earlier example:
report = makeFiguresForCompareArticle('WT',1,'koulakov',1)
I would recommend using this second option, as it generates the figures relevant to the paper.
##Generating the figures in the paper
If you want to regenerate all the modelling figures for the paper there are two commands you need to do.
To run all simulations (called from matlab)
runCompareArticleKoulakov
runCompareArticleGierer
runCompareArticleWhitelaw
runCompareArticleWillshaw
To analyse all simulations: runCompareArticleMacAnalyseAll
This will output the figures to FIGS/ComparePhenotype
##Running your first own simulation
If you want more freedome in defining your own simulations, then you
can work directly with the RetinalMap class.
r = RetinalMap('experiments/myfirstexperiment.txt');
r.run();
r.plotMapForward(1);
For more instructions see the readme.rtf file.