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feat: include gap-filling step
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haowang-bioinfo committed Dec 12, 2020
1 parent 737152c commit b7a4c06
Showing 1 changed file with 6 additions and 2 deletions.
8 changes: 6 additions & 2 deletions code/masterScriptMouseGEM.m
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
%
%
% PURPOSE: This script is for reconstruction of the Mouse-GEM, by using
% the Human-GEM as template and taking in account mouse-specific
% the Human-GEM as template and taking into account mouse-specific
% pathways/reactions.
%
%
@@ -37,7 +37,6 @@
% get ortholog pairs from human to mouse
mouseOrthologPairs = extractAllianceGenomeOrthologs('human2MouseOrthologs.json');
mouseGEM = getModelFromOrthology(ihuman, mouseOrthologPairs);
mouseGEM.id = 'Mouse-GEM';



@@ -68,9 +67,14 @@
[mouseGEM, modelChanges] = addMetabolicNetwork(mouseGEM, rxnsToAdd, metsToAdd);


%% Gap-filling for biomass formation
[mouseGEM, gapfillNetwork]=gapfill4Biomass(mouseGEM,ihuman);
% Added 0 reactions for gap-filling


%% Save the model into mat, yml, and xml

mouseGEM.id = 'Mouse-GEM';
save('../model/Mouse-GEM.mat', 'mouseGEM');
writeHumanYaml(mouseGEM, '../model/Mouse-GEM.yml');
exportModel(mouseGEM, '../model/Mouse-GEM.xml');

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