Identify Conserved Moieties

These tutorials should generally be used in the following order:

1. Initialise and set the paths to inputs and outputs

driver_initConservedMoietyPaths.mlx

2. Build an atom transition graph

tutorial_buildAtomTransitionMultigraph.mlx

3. Identify conserved moieties, given an atom transition graph

tutorial_identifyConservedMoieties.mlx

4. Analyse the output of #3

tutorial_analyseConservedMoieties.mlx

5. Prepare for visualisation of individual conserved moieties (beta)

tutorial_visualiseConservedMoieties.mlx

if ~exist('resultsDir','var')
    driver_initConservedMoietyPaths
end

if ~recompute %|| isequal(modelName,'iDopaNeuro1')
    load([resultsDir modelName '_arm.mat'])
    return
end

1.2.3. Conserved moieties

With the atom mappings we obtained, we can compute the conserved moieties for the iDopaNeuro metabolic network using the atom transition network and the COBRA function identifyConservedMoieties.

switch modelName
    case 'DAS'
        load([dataDir filesep 'models' filesep modelName '.mat'])
        load([resultsDir filesep modelName '_dATM.mat'])
    case 'iDopaNeuro1'
        load([resultsDir filesep modelName '.mat'])
        load([resultsDir filesep modelName '_dATM.mat'])
        
    case {'centralMetabolism','centralMetabolism_fastCore','centralMetabolism_thermoKernel'}
        load([resultsDir filesep modelName '.mat'])
        load([resultsDir filesep modelName '_dATM.mat'])
    otherwise
        load([dataDir filesep modelName '.mat'])
end
 

options.sanityChecks=1;
[arm, moietyFormulae] = identifyConservedMoieties(model, dATM, options);

save([resultsDir filesep modelName '_arm.mat'],'arm', 'moietyFormulae','options')