3.2 Import template models

RAVEN creates a draft GEM by using models of phylogenetically related organisms as templates. For H. polymorpha, the S. cerevisiae model (yeast-GEM) is the primary template and the R. toruloides model (rhto-GEM) the complementary one.

Load the primary template

importModel loads an SBML file into a RAVEN-format MATLAB structure:

modelSce = importModel('yeastGEM.xml');

yeast-GEM is written by the COBRA Toolbox, which appends the compartment to each metabolite ID. RAVEN keeps the compartment in a separate field (.metComps), so the redundant suffix is removed, and the model is given the id sce (used later by getModelFromHomology to match the model with its protein FASTA):

modelSce.mets = regexprep(modelSce.mets, '\[[a-z]+\]$', '');
modelSce.id = 'sce';

Inspect the model

It is often easier to browse a model as a spreadsheet. exportToExcelFormat writes an .xlsx with five sheets — RXNS, METS, COMPS, GENES and MODEL:

exportToExcelFormat(modelSce, 'modelSce.xlsx');

Use a scrap folder

During reconstruction you often write files you don't want to track in git. The hanpo-GEM repository keeps these in a scrap/ folder that is excluded from version control.

Make changes to the model in MATLAB, not in the Excel file, and export to SBML when desired:

exportModel(modelSce, 'modelSce.xml');

Load the complementary template

The R. toruloides model is loaded the same way. It was written by RAVEN, so it has no redundant compartment suffix to clean up:

modelRhto = importModel('rhto.xml', true);
modelRhto.id = 'rhto';

It can be useful to store intermediate states of the MATLAB workspace so you can resume later:

save('scrap/importModels.mat')
% load('scrap/importModels.mat')

Next: Draft from homology.