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SysBioChalmers / ecModels

A container for all enzyme constrained models created by GECKO.
Creative Commons Attribution 4.0 International
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update eciYali based on 4.1.1 #71

Closed automator-metatlas closed 3 years ago

automator-metatlas commented 3 years ago 
MATLAB is selecting SOFTWARE OPENGL rendering.

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   GECKO: Adding enzyme constraints to a genome-scale model
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Getting genome-scale model ready... Done!

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Generating ecModel:
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Retrieving EC numbers....................... Done!
Matching kcats....................... Done!
Adding enzymes to reactions................................ Done!
Improving model with curated data............................................ Done!

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Generating ecModel with shared pool assumption (ecModel_batch):
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prot_abundance file is empty or not available. A default value of f=0.5 is set instead
Matching data to enzymes in model... Done!
Total protein amount measured = 0 g/gDW
Total enzymes measured = 0 enzymes
Enzymes in model with 0 g/gDW = 0 enzymes
Total protein amount not measured = 0.5493 g/gDW
Total enzymes not measured = 647 enzymes
Total protein in model = 0.5493 g/gDW
The ECmodel is not overconstrained.
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Fitting sigma factor....................... Done!
[Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click <a href="matlab:opengl('problems')">here</a>.] 
Saving simulation results files...
File successfully saved.
Sigma factor (fitted for growth on glucose): 0.49

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Saving models:
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Saving eciYali4.1.1:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.
Saving eciYali_batch4.1.1:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.
mihai-sysbio commented 3 years ago

The file changes look like normal pipeline run, so this PR will be closed in favor of a new one.