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-	function [MinimalGenomes, UnEssentialGeneLists, Models] = FindMinimalGenomes(TheModel, NumberOfMinGenomes, FinalGrowthRate, NumberOfSteps, FirstThreshold)	+
-	%NumberOfMinGenomes: Number of minimal genomes you want the code to find (since there are many possible minimal genomes)	+
-	%FinalGrowthRate: is what the final growth rate will apporximately be.  Lower values result in a lower final	+
-	%growth rate, but this allows for more genes to be deleted (resulting in a smaller allowable minimal genome).	+
-	%FirstThreshold: This is the threshold growth rate for the first iteration of gene deletions.	+
-		+
-	disp('May take 5 mins per NumberOfMinGenomes (default is 1 list)')	+
-	solutionI = optimizeCbModel(TheModel);	+
-	InitialGrowthRate = solutionI.f	+
-		+
-	%Input/Output Error Checking	+
-		+
-	if nargout == 0	+
-	error('You must have at least 1 output argument! For example: MinGenomes = FindMinimalGenomes(model)')	+
-	end	+
-	if FinalGrowthRate > InitialGrowthRate	+
-	disp(['FinalGrowthRate (set by you): ' num2str(FinalGrowthRate)]);	+
-	error('The FinalGrowthRate must be less than the InitialGrowthRate')	+
-	end	+
-	if NumberOfSteps < 1	+
-	error('NumberOfSteps must be greater than or equal to 1!')	+
-	end	+
-	if FirstThreshold >= InitialGrowthRate	+
-	error('FirstThreshold must be less than the InitialGrowthRate')	+
-	end	+
-		+
-	%Initialization of variables	+
-		+
-	switch nargin	+
-	case 1	+
-	FinalGrowthRate = 0.2	+
-	f1 = ((InitialGrowthRate-FinalGrowthRate)*0.87)+FinalGrowthRate	+
-	f2 = FinalGrowthRate;	+
-	n = 2; iterationsPerList = n+1  % n = 2 results in 3 iterations of gene filtering.	+
-	NumberOfMinGenomes = 1;	+
-	case 2	+
-	FinalGrowthRate = 0.2	+
-	f1 = ((InitialGrowthRate-FinalGrowthRate)*0.87)+FinalGrowthRate	+
-	f2 = 0.3	+
-	n = 2; iterationsPerList = n+1	+
-	case 3	+
-	FinalGrowthRate	+
-	f1 = ((InitialGrowthRate-FinalGrowthRate)*0.87)+FinalGrowthRate	+
-	f2 = FinalGrowthRate	+
-	n = 2; iterationsPerList = n+1	+
-	case 4	+
-	if rem(NumberOfSteps,1) ~= 0	+
-	error('NumberOfSteps must be an integer')	+
-	end	+
-	f1 = ((InitialGrowthRate-FinalGrowthRate)*0.87)+FinalGrowthRate	+
-	f2 = FinalGrowthRate	+
-	if NumberOfSteps == 1	+
-	n = 0.000000001; %to cause only 1 iteration & to prevent division by 0 (which only Chuck Norris can do).	+
-	iterationsPerList = 1	+
-	else	+
-	n = NumberOfSteps-1;	+
-	iterationsPerList = NumberOfSteps	+
-	end	+
-	case 5	+
-	if rem(NumberOfSteps,1) ~= 0	+
-	error('NumberOfSteps must be an integer')	+
-	end	+
-	f1 = FirstThreshold	+
-	f2 = FinalGrowthRate	+
-	if NumberOfSteps == 1	+
-	n = 0.000000001; %to cause only 1 iteration & to prevent division by 0	+
-	iterationsPerList = 1	+
-	else	+
-	n = NumberOfSteps-1;	+
-	iterationsPerList = NumberOfSteps	+
-	end	+
-	otherwise	+
-	error('Too many input arguments! Sorry, try again!')	+
-	end	+
-		+
-	fStep = (f1-(f2)-0.0001)/n	+
-	MinimalGenomes = cell(1,NumberOfMinGenomes);	+
-	UnEssentialGeneLists = cell(1,NumberOfMinGenomes);	+
-	TheModelOriginal = TheModel;	+
-	Models = cell(1);	+
-		+
-	w = 1;	+
-		+
-	%Algorithm to find minimal genomes.	+
-		+
-	while w<=NumberOfMinGenomes	+
-	disp(['Finding Minimal Genome List: ' num2str(w)]);	+
-		+
-	geneList = cell(1);	+
-	geneListTEST = cell(1);	+
-	d = 1;	+
-	f = f1;	+
-		+
-	%this part shuffles the TheModel list for randomization	+
-		+
-	RandomGeneList = cell(1,length(TheModelOriginal.genes));	+
-	random = randperm(length(TheModel.genes))';	+
-		+
-	for x = (1:length(TheModel.genes))	+
-	RandomGeneList(x) = TheModelOriginal.genes(random(x));	+
-	end	+
-		+
-	while f >= f2	+
-	disp(['Performing deletions that result in a growth rate of at least ' num2str(f) ' ...']);	+
-		+
-	for c = (1:length(RandomGeneList))	+
-	match = zeros(length(RandomGeneList));	+
-	for a = (1:length(geneList))  %check if gene already on geneList. if so, skip analysis	+
-	if strcmp(geneList(a),RandomGeneList(c)) == 1	+
-	match(a) = 1;	+
-	else	+
-	match(a) = 0;	+
-	end	+
-	end	+
-		+
-	%This part decides whether or not to permanently knockout a gene	+
-		+
-	if sum(match) == 0  %if gene does not exist in geneList yet, test its deletion	+
-	geneListTEST(d) = RandomGeneList(c);	+
-		+
-	deltamodel = deleteModelGenes(TheModelOriginal,geneListTEST);	+
-	solution = optimizeCbModel(deltamodel);	+
-		+
-	if solution.f > f %"if the deletion causes satisfactory growth, commit gene to geneList	+
-	geneList(d) = geneListTEST(d);	+
-	%F(d) = solution.f;	+
-	d = d+1;	+
-	end	+
-	end	+
-	end	+
-	disp(['Genes Deleted So Far for this List is: ' num2str(length(geneList))])	+
-	f = f-fStep;	+
-	end	+
-		+
-	UnEssentialGeneLists{w} = geneList';	+
-		+
-	%This part "inverts" the unessential list to obtain the essential list	+
-		+
-	InvertThis = UnEssentialGeneLists{w};	+
-	WithThis = TheModel.genes;	+
-	InvertedList = cell(1);	+
-		+
-	Match=zeros(length(WithThis));	+
-	for a = (1:length(InvertThis))	+
-	for b = (1:length(WithThis))	+
-	if strcmp(InvertThis(a), WithThis(b)) == 1	+
-	Match(b) = 1;	+
-	end	+
-	end	+
-	end	+
-	d = 1;	+
-		+
-	for c=(1:length(WithThis))	+
-	if Match(c) == 0	+
-	InvertedList(d) = WithThis(c);	+
-	d = d+1;	+
-	end	+
-	end	+
-	MinimalGenomes{w} = InvertedList'	+
-	Models{w} = deleteModelGenes(TheModelOriginal, geneList);	+
-	w = w+1;	+
-	end	+
-		+
-	if nargout == 3	+
-	disp('Access a model of interest like this: model3 = Models{3}, except replace "Models" with your 3rd output argument.')	+
-	end	+
-		+
-	%University of Alberta 2009 iGEM Team	+
-	%Project BioBytes	+
-	%EricB	+

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Latest revision as of 07:52, 18 October 2009

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