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Getting Started

Make sure you have completed the installation process before continuing.

Examples are given for both MATLAB (using the RAVEN Toolbox) and Python (using COBRApy); select the corresponding tab in each code block. Unless otherwise noted, the MATLAB commands are run from the MATLAB command prompt.

Loading Human-GEM

Important

The Human-GEM model files are provided in a RAVEN-friendly format. If you intend on using COBRA in MATLAB, see the Using Human-GEM with COBRA section below. In Python, COBRApy reads the SBML (.xml) file directly.

Note

All the model file formats described below are on the main branch of the Human-GEM repository. Note that only the .yml version is available on branches other than main (e.g., devel), to facilitate tracking of model changes.

From the Human-GEM.mat file (MATLAB) or SBML file (Python)

The quickest and easiest way to load the Human-GEM model is from the .mat file. 

load('Human-GEM.mat');

This will load the model as a structure named humanGEM. 

humanGEM

% humanGEM = 
% 
%   struct with fields:
% 
%                      id: 'HumanGEM'
%                    name: 'Generic genome-scale metabolic model of Homo sapiens'
%             description: ''
%                 version: '2.0.0'
%                    date: '2026-03-26'
%              annotation: [1×1 struct]
%                    rxns: {12931×1 cell}
%                rxnNames: {12931×1 cell}
%                    mets: {8461×1 cell}
%                metNames: {8461×1 cell}
%                       S: [8461×12931 double]
%                      lb: [12931×1 double]
%                      ub: [12931×1 double]
%                     rev: [12931×1 double]
%                       c: [12931×1 double]
%                       b: [8461×1 double]
%                   genes: {2848×1 cell}
%                 grRules: {12931×1 cell}
%              rxnGeneMat: [12931×2848 double]
%              subSystems: {12931×1 cell}
%                 eccodes: {12931×1 cell}
%                rxnNotes: {12931×1 cell}
%           rxnReferences: {12931×1 cell}
%     rxnConfidenceScores: [12931×1 double]
%                metComps: [8461×1 double]
%                  inchis: {8461×1 cell}
%             metFormulas: {8461×1 cell}
%              metCharges: [8461×1 double]
%                   comps: {9×1 cell}
%               compNames: {9×1 cell}
%          geneShortNames: {2848×1 cell}
%                 metFrom: {8461×1 cell}
%                 rxnFrom: {12931×1 cell}

In Python, load the SBML (.xml) version of Human-GEM with COBRApy. (Reading the SBML file takes up to a minute.) 

import cobra

model = cobra.io.read_sbml_model('Human-GEM.xml')
len(model.reactions), len(model.metabolites), len(model.genes)

# (12931, 8461, 2848)

From the Human-GEM.yml file

The YAML version is the format tracked across all branches, and is recommended if you are not on the main branch.

The YAML version of Human-GEM is loaded using the RAVEN readYAMLmodel function. 

humanGEM = readYAMLmodel('Human-GEM.yml');

COBRApy does not read the RAVEN YAML format directly; use the SBML (.xml) file as shown above.

From the Human-GEM.xml (SBML) file

The .xml (SBML) version of Human-GEM is loaded using the RAVEN importModel function. 

humanGEM = importModel('Human-GEM.xml');

% Warning: The following fields have prefixes removed from all entries. If this is
% undesired, run importModel with removePrefix as false. Example:
%         importModel('filename.xml',[],false);

Note

The warning regarding removed prefixes can be ignored for normal use. If you need the original identifier prefixes preserved, load the model with importModel('Human-GEM.xml', [], false).

import cobra

model = cobra.io.read_sbml_model('Human-GEM.xml')

From the Human-GEM.txt file

There is no function to import the .txt version of the model. The Human-GEM.txt file is supplied for those who need or prefer a more human-readable plain-text format, but is not intended for loading into MATLAB or Python.

Using Human-GEM with COBRA

In Python, COBRApy is itself a COBRA implementation, so the SBML file loaded above is already a COBRA model — no conversion is needed.

In MATLAB, the provided Human-GEM models can generally be used directly with the COBRA Toolbox, though there may remain some incompatibilities that cause errors or unexpected behavior. We suggest to first convert the model to a COBRA-friendly format before using the COBRA Toolbox.

1. Load the model into MATLAB

Use one of the methods described above to load Human-GEM into MATLAB. 

load('Human-GEM.mat');  % loads model as structure named "humanGEM"

2. Convert the model into COBRA format

Use the RAVEN ravenCobraWrapper function to convert the model into a COBRA-friendly format. 

model = ravenCobraWrapper(humanGEM);

%  Converting RAVEN structure to COBRA..

The resulting model output should now be ready for use with the COBRA Toolbox.