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SysBioChalmers / ecModels

A container for all enzyme constrained models created by GECKO.
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update ecMouseGEM based on 2021-04-05-19-25 #80

Closed automator-metatlas closed 3 years ago

automator-metatlas commented 3 years ago 
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                                                                               November 23, 2020

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***************************************************************
   GECKO: Adding enzyme constraints to a genome-scale model
***************************************************************

Getting genome-scale model ready...[Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

  - grRule #MA-R00080: Atp6v0b and Atp6v0c and Atp6v0e and Atp6v1a and Atp6v1d and Atp6v1f and Atp6v1h and ((Atp6v0a1 and Atp6v0d1) or (Atp6v0a1 and Atp6v0d2) or (Atp6v0a2 and
  Atp6v0d1) or (Atp6v0a2 and Atp6v0d2) or (Atp6v0a4 and Atp6v0d1) or (Atp6v0a4 and Atp6v0d2) or (Atp6v0d1 and Tcirg1) or (Atp6v0d2 and Tcirg1)) and ((Atp6v1b1 and Atp6v1c1 and
  Atp6v1e1 and Atp6v1g1) or (Atp6v1b1 and Atp6v1c1 and Atp6v1e1 and Atp6v1g2) or (Atp6v1b1 and Atp6v1c1 and Atp6v1e2 and Atp6v1g1) or (Atp6v1b1 and Atp6v1c2 and Atp6v1e1 and
  Atp6v1g1) or (Atp6v1b2 and Atp6v1c1 and Atp6v1e1 and Atp6v1g1) or (Atp6v1b1 and Atp6v1c1 and Atp6v1e1 and Atp6v1g3) or (Atp6v1b1 and Atp6v1c1 and Atp6v1e2 and Atp6v1g2) or
  (Atp6v1b1 and Atp6v1c2 and Atp6v1e1 and Atp6v1g2) or (Atp6v1b1 and Atp6v1c2 and Atp6v1e2 and Atp6v1g1) or (Atp6v1b2 and Atp6v1c1 and Atp6v1e1 and Atp6v1g2) or (Atp6v1b2 and
  Atp6v1c1 and Atp6v1e2 and Atp6v1g1) or (Atp6v1b2 and Atp6v1c2 and Atp6v1e1 and Atp6v1g1) or (Atp6v1b1 and Atp6v1c1 and Atp6v1e2 and Atp6v1g3) or (Atp6v1b1 and Atp6v1c2 and
  Atp6v1e1 and Atp6v1g3) or (Atp6v1b1 and Atp6v1c2 and Atp6v1e2 and Atp6v1g2) or (Atp6v1b2 and Atp6v1c1 and Atp6v1e1 and Atp6v1g3) or (Atp6v1b2 and Atp6v1c1 and Atp6v1e2 and
  Atp6v1g2) or (Atp6v1b2 and Atp6v1c2 and Atp6v1e1 and Atp6v1g2) or (Atp6v1b2 and Atp6v1c2 and Atp6v1e2 and Atp6v1g1) or (Atp6v1b1 and Atp6v1c2 and Atp6v1e2 and Atp6v1g3) or
  (Atp6v1b2 and Atp6v1c1 and Atp6v1e2 and Atp6v1g3) or (Atp6v1b2 and Atp6v1c2 and Atp6v1e1 and Atp6v1g3) or (Atp6v1b2 and Atp6v1c2 and Atp6v1e2 and Atp6v1g2) or (Atp6v1b2 and
  Atp6v1c2 and Atp6v1e2 and Atp6v1g3))

 This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

  - (G1 or G2) and (G3 or G4)

 For these cases modify the grRules manually, writing all the possible combinations e.g.

  - (G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

 For other cases modify the correspondent grRules avoiding:

  1) Overall container brackets, e.g.
        "(G1 and G2)" should be "G1 and G2"

  2) Single unit enzymes enclosed into brackets, e.g.
        "(G1)" should be "G1"

  3) The use of uppercases for logical operators, e.g.
        "G1 OR G2" should be "G1 or G2"

  4) Unbalanced brackets, e.g.
        "((G1 and G2) or G3" should be "(G1 and G2) or G3"
] 
[> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In preprocessModel (line 40)
In enhanceGEM (line 51)] 
[Warning:
Conflicting grRules where found for several reactions (check the above lines). GECKO will ignore these grRules to avoid introduction of potentially wrong enzyme constrains for
such cases. It is recommended to check your original GEM and fix these grRules manually with the guidance provided by the function "standardizeGrRules.m" in the RAVEN toolbox.
] 
[> In preprocessModel (line 42)
In enhanceGEM (line 51)] 
 Done!

==================
Generating ecModel:
==================
Retrieving EC numbers...................................................................................................................................... Done!
Matching kcats...................................................................................................................................... Done!
Adding enzymes to reactions.................................................................................................................................................................................................... Done!
Improving model with curated data... Done!
Removing repeated rxn: MA-R02404 & MA-R10410_REV
Removing repeated rxn: MA-R10410 & MA-R02404_REV

==============================================================
Generating ecModel with shared pool assumption (ecModel_batch):
==============================================================
prot_abundance file is empty or not available. A default value of f=0.5 is set instead

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Constrained ecModel is feasible
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 = 0.50572 g/gDW
Total enzymes not measured = 3021 enzymes
Total protein in model = 0.50572 g/gDW

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The ECmodel is not overconstrained.
***************************************************************
Fitting sigma factor...
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. 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>.] 

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Saving simulation results files...
File successfully saved.
Sigma factor (fitted for growth on glucose): 0.27

=============
Saving models:
=============
IVANDOMENZAIN commented 3 years ago

@mihai-sysbio things are going well with ecMouseGEM, just need to debug the SBML files generation step. But it seems that we need to renew one of the licenses, I think that it is the GUROBI one, as the warning is displayed in the steps in which the GECKO pipeline should solve multiple LP problems.

mihai-sysbio commented 3 years ago

Thanks @IVANDOMENZAIN for mentioning this. The Gurobi license had EXPIRATION=2021-04-12. We should now be good until EXPIRATION=2021-06-06.