Identify Conserved Moieties

Author(s): Ronan M.T. Fleming, School of Medicine, University of Galway

Reviewer(s):

INTRODUCTION

Given an atom transition multgraph for a metabolic model, this tutorial identifies its conserved moieties, as described elsewhere [1,2].

These tutorials should generally be used in the following order:

1. Initialise and set the paths to inputs and outputs

COBRA.tutorials/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')

Acknowledgments

Co-funded by the European Union's Horizon Europe Framework Programme (101080997)

REFERENCES

Ghaderi, S., Haraldsdóttir, H. S., Ahookhosh, M., Arreckx, S., & Fleming, R. M. T. (2020). Structural conserved moiety splitting of a stoichiometric matrix. Journal of Theoretical Biology, 499, 110276. https://doi.org/10.1016/j.jtbi.2020.110276
Rahou, H., Haraldsdóttir, H. S., Martinelli, F., Thiele, I., & Fleming, R. M. T. (2026). Characterisation of conserved and reacting moieties in chemical reaction networks. Journal of Theoretical Biology, 112348. https://doi.org/10.1016/j.jtbi.2025.112348