Subsystems not recognized by getModelSubSystems()

Michel_Lavoie

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Sep 26, 2018, 2:57:03 PM9/26/18

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Hi all,

I am looking at a cobra model (called pti) of a phytoplanktonic species with a list of subsystems. However, it appears that the field pti.subsystems cannot be printed with the function getModelSubSystems(pti). When I run the function (se below), I get an array of letters and strange characters. I noticed that the subsystems, which can be found in the table in matlab (in the field pti.subSystems), were not enclosed with apostrophes, although when I type pti.subSystems, I can print all the subSystems associated with all reactions. No matter if I add apostrophe at the start and at the end of the subsystems, it does not solve the problem and the function getModelSubSystems() does not work. Would you have any idea to solve this?

Thank you very much,

Michel

>> getModelSubSystems(pti)

ans =

55×1 char array

' '

'''

'('

')'

','

'-'

'/'

'1'

'3'

'6'

':'

';'

'A'

'B'

'C'

'D'

'E'

'F'

'G'

'H'

'I'

'L'

'M'

'N'

'O'

'P'

'R'

'S'

'T'

'U'

'V'

'a'

'b'

'c'

'd'

'e'

'f'

'g'

'h'

'i'

'k'

'l'

'm'

'n'

'o'

'p'

'q'

'r'

's'

't'

'u'

'v'

'w'

'x'

'y'

You can see below the 'SystemConfigReport'.

>> generateSystemConfigReport

> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2018

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done.

> Checking if the repository is tracked using git ... Done.

> Checking if curl is installed ... Done.

> Checking if remote can be reached ... Done.

> Initializing and updating submodules (this may take a while)... Done.

> Adding all the files of The COBRA Toolbox ... Done.

> Define CB map output... set to svg.

> TranslateSBML is installed and working properly.

> Configuring solver environment variables ...

- [----] ILOG_CPLEX_PATH: --> set this path manually after installing the solver ( see instructions )

- [*---] GUROBI_PATH: /Library/gurobi752/mac64/matlab

- [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )

- [----] MOSEK_PATH: --> set this path manually after installing the solver ( see instructions )

Done.

> Checking available solvers and solver interfaces ... Done.

> Setting default solvers ... Done.

> Saving the MATLAB path ... Done.

- The MATLAB path was saved in the default location.

> Summary of available solvers and solver interfaces

Support LP MILP QP MIQP NLP

----------------------------------------------------------------------

gurobi active 1 1 1 1 -

ibm_cplex active 0 0 0 - -

tomlab_cplex active 0 0 0 0 -

glpk active 1 1 - - -

mosek active 0 - 0 - -

matlab active 1 - - - 1

cplex_direct active 0 0 0 0 -

dqqMinos active 1 - - - -

pdco active 1 - 1 - -

quadMinos active 1 - - - -

qpng passive - - 1 - -

tomlab_snopt passive - - - - 0

gurobi_mex legacy 0 0 0 0 -

lindo_old legacy 0 - - - -

lindo_legacy legacy 0 - - - -

lp_solve legacy 1 - - - -

opti legacy 0 0 0 0 0

----------------------------------------------------------------------

Total - 7 2 3 1 1

+ Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.

> You can solve LP problems using: 'gurobi' - 'glpk' - 'matlab' - 'dqqMinos' - 'pdco' - 'quadMinos' - 'lp_solve'

> You can solve MILP problems using: 'gurobi' - 'glpk'

> You can solve QP problems using: 'gurobi' - 'pdco' - 'qpng'

> You can solve MIQP problems using: 'gurobi'

> You can solve NLP problems using: 'matlab'

> Checking for available updates ...

> There are 6429 new commit(s) on <master> and 0 new commit(s) on <develop> [c72a7b @ master]

> You can update The COBRA Toolbox by running updateCobraToolbox() (from within MATLAB).

Elapsed time is 143.438534 seconds.

-----------------------------------------------------------------------------------------------------

MATLAB Version: 9.4.0.813654 (R2018a)

MATLAB License Number: 310290

Operating System: Mac OS X Version: 10.13.6 Build: 17G65

Java Version: Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

-----------------------------------------------------------------------------------------------------

MATLAB Version 9.4 (R2018a)

Simulink Version 9.1 (R2018a)

Aerospace Toolbox Version 2.21 (R2018a)

Bioinformatics Toolbox Version 4.10 (R2018a)

Communications System Toolbox Version 6.6 (R2018a)

Computer Vision System Toolbox Version 8.1 (R2018a)

Control System Toolbox Version 10.4 (R2018a)

Curve Fitting Toolbox Version 3.5.7 (R2018a)

DSP System Toolbox Version 9.6 (R2018a)

Database Toolbox Version 8.1 (R2018a)

Embedded Coder Version 7.0 (R2018a)

Financial Toolbox Version 5.11 (R2018a)

Fixed-Point Designer Version 6.1 (R2018a)

Fuzzy Logic Toolbox Version 2.3.1 (R2018a)

Global Optimization Toolbox Version 3.4.4 (R2018a)

Image Acquisition Toolbox Version 5.4 (R2018a)

Image Processing Toolbox Version 10.2 (R2018a)

Instrument Control Toolbox Version 3.13 (R2018a)

MATLAB Coder Version 4.0 (R2018a)

MATLAB Compiler Version 6.6 (R2018a)

MATLAB Compiler SDK Version 6.5 (R2018a)

Mapping Toolbox Version 4.6 (R2018a)

Model Predictive Control Toolbox Version 6.1 (R2018a)

Neural Network Toolbox Version 11.1 (R2018a)

Optimization Toolbox Version 8.1 (R2018a)

Parallel Computing Toolbox Version 6.12 (R2018a)

Partial Differential Equation Toolbox Version 3.0 (R2018a)

RF Toolbox Version 3.4 (R2018a)

Robust Control Toolbox Version 6.4.1 (R2018a)

Signal Processing Toolbox Version 8.0 (R2018a)

Simscape Version 4.4 (R2018a)

Simscape Multibody Version 5.2 (R2018a)

Simscape Power Systems Version 6.9 (R2018a)

Simulink Coder Version 8.14 (R2018a)

Simulink Control Design Version 5.1 (R2018a)

Simulink Desktop Real-Time Version 5.6 (R2018a)

Statistics and Machine Learning Toolbox Version 11.3 (R2018a)

Symbolic Math Toolbox Version 8.1 (R2018a)

System Identification Toolbox Version 9.8 (R2018a)

Wavelet Toolbox Version 5.0 (R2018a)

> Default shell : /bin/bash

> Version of shell : GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin17)

> Architecture : MACI64

> MATLAB folder : /Applications/MATLAB_R2018a.app

> COBRA Toolbox root : /Users/mlavoie/cobratoolbox

> git version : git version 2.15.2 (Apple Git-101.1)

> curl version : curl 7.54.0 (x86_64-apple-darwin17.0)

> CBT_LP_SOLVER : gurobi

> CBT_MILP_SOLVER : gurobi

> CBT_QP_SOLVER : gurobi

> CBT_MIQP_SOLVER : gurobi

> CBT_NLP_SOLVER : matlab

> GUROBI_PATH : /Library/gurobi752/mac64/matlab

> ILOG_CPLEX_PATH :

> TOMLAB_PATH :

> MOSEK_PATH :

> ----------------------------------- END OF CONFIGURATION REPORT -----------------------------------

Thomas Pfau

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Sep 27, 2018, 1:02:19 AM9/27/18

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Dear Michel,

Where did you obtain that model from and how did you import the model.

The output you get looks very much as if the model does not adhere to the model field definitions, and was not loaded via readCbModel.

Best

Thomas

On 2018-09-26 20:57, 'Michel_Lavoie' via COBRA Toolbox wrote:

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Michel_Lavoie

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Sep 27, 2018, 6:06:12 AM9/27/18

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Hi Thomas,

I found the model (iLB1025.mat) from the supplemental information of a publication (Levering et al 2016). Then, I loaded the model using the command load('iLB1025.mat') and was not able to get Subsystems with the command 'getModelSubSystems'. I also tried to read the model (iLB1025.xml) with the function 'readCbModel()' (see below) and then look at the subsystems, but in this case, I can see in the table (the field model.subSystems) that there are no subSystems and the function does not work. I think this is normal because in the .xml file there are no subsystems. I attached both files to this message. You can download the files in the supporting information S3 zip file at : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859558/. I could not attach the files to this message since I got an error message. Would you know how to fix this problem?

Thanks,

Michel

>> model = readCbModel('iLB1025.xml')

The model contains 17 errors.

Error encountered during read.

model =

struct with fields:

S: [1704×2156 double]

mets: {1704×1 cell}

b: [1704×1 double]

csense: [1704×1 char]

rxns: {2156×1 cell}

lb: [2156×1 double]

ub: [2156×1 double]

c: [2156×1 double]

osenseStr: 'max'

genes: {1025×1 cell}

rules: {2156×1 cell}

geneNames: {1025×1 cell}

compNames: {6×1 cell}

comps: {6×1 cell}

proteins: {1025×1 cell}

metCharges: [1704×1 double]

metFormulas: {1704×1 cell}

metNames: {1704×1 cell}

rxnNames: {2156×1 cell}

subSystems: {2156×1 cell}

description: 'iLB1025.xml'

modelVersion: [1×1 struct]

modelID: 'pti'

>> getModelSubSystems(model)

ans =

0×0 empty cell array

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Thomas Pfau

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Sep 27, 2018, 6:20:24 AM9/27/18

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Dear Michel,

Please always load models (also .mat models) using readCbModel (yes, the function can read .mat files).
There are plenty of models around which have sometimes very odd fields and readCbModel does take care of most of the known problems. If you use load, it is very likely that your model struct will not be compatible with the Toolbox.

Best

Thomas

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Thomas Pfau

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Sep 27, 2018, 6:35:56 AM9/27/18

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Dear Michel,

I had a look at the model:

One issue is that the metCHEBIID field in the model has inconsistent formats (empty strings and numbers) which are not currently handled by the toolbox.

I submitted a PR to add this adjustment to readCbModel.

Until that is in, I would suggest to run convertOldStyleModel on the loaded model (loaded with load), as readCbModel will reject the model. The model will still not pass verifyModel because of the metChEBIID field, but you can use it for most purposes.

Best

Thomas

Michel_Lavoie

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Sep 27, 2018, 6:41:37 AM9/27/18

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Hi Thomas,

I tried the function 'readCbModel()' to read a .mat file and it did not work (see below) even though when I load the model using load() I can do flux balance analysis and the model seems functional.

>> model = readCbModel('iLB1025bon.mat')

Error using readCbModel (line 229)

There were no valid models in the mat file.\n Please load the model manually via ' load iLB1025bon.mat'

and check it with verifyModel() to validate it

I just saw your new email telling me to try 'convertOldStyleModel()'. I tried it (see below) and it seems to work !!!

Thank you very much Thomas for your very valuable help,

Michel

>> pti = convertOldStyleModel(pti)

pti =

struct with fields:

id: 'iLB1025'

description: 'Metabolic network reconstruction of Phaeodactylum tricornutum'

rxns: {2156×1 cell}

rxnNames: {2156×1 cell}

grRules: {2156×1 cell}

rules: {2156×1 cell}

c: [2156×1 double]

S: [1704×2156 double]

lb: [2156×1 double]

ub: [2156×1 double]

subSystems: {2156×1 cell}

rxnECNumbers: {2156×1 cell}

rxnKEGGID: {2156×1 cell}

rxnNotes: {2156×1 cell}

proteinAssociation: {2156×1 cell}

rxnsLocalization: {2156×1 cell}

rxnReferences: {2156×1 cell}

rxnGeneMat: [2156×1025 double]

genes: {1025×1 cell}

mets: {1704×1 cell}

metNames: {1704×1 cell}

metComps: [1704×1 double]

metFormulas: {1704×1 cell}

metKEGGID: {1704×1 cell}

metChEBIID: {1704×1 cell}

metInChIString: {1704×1 cell}

b: [1704×1 double]

comps: {6×1 cell}

compNames: {6×1 cell}

rxnConfidenceScores: [2156×1 double]

metCharges: [1704×1 double]

osenseStr: 'max'

csense: [1704×1 char]

>> getModelSubSystems(pti)

ans =

89×1 cell array

{'Aldehyde degradation' }

{'Amino acid metabolism: Alanine, Aspartate and Glutamate metabolism' }

{'Amino acid metabolism: Aminoacyl-tRNA biosynthesis' }

{'Amino acid metabolism: Asparagine metabolism' }

{'Amino acid metabolism: Cysteine and Methionine metabolism' }

{'Amino acid metabolism: Glycine, Serine and Threonine metabolism' }

{'Amino acid metabolism: Histidine metabolism' }

{'Amino acid metabolism: Homocysteine biosynthesis' }

{'Amino acid metabolism: Homoserine biosynthesis' }

{'Amino acid metabolism: Lysine biosynthesis' }

{'Amino acid metabolism: Lysine degradation' }

{'Amino acid metabolism: Phenylalanine metabolism' }

{'Amino acid metabolism: Phenylalanine, Tyrosine, Tryptophan biosynthesis'}

{'Amino acid metabolism: Proline and Arginine metabolism' }

{'Amino acid metabolism: Tryptophan metabolism' }

{'Amino acid metabolism: Tyrosine metabolism' }

{'Amino acid metabolism: Valine, Leucine and Isoleucine biosynthesis' }

{'Amino acid metabolism: Valine, Leucine and Isoleucine degradation' }

{'Amino sugar metabolism' }

{'Ascorbate metabolism' }

{'Betaine lipid biosynthesis' }

{'Biosynthesis of steroids: Steroid synthesis' }

{'Biosynthesis of steroids: Terpenoid backbone synthesis' }

{'Biosynthesis of steroids: Ubiquinone/Terpenoid-quinone biosynthesis' }

{'Butanoate metabolism' }

{'Calvin-Benson cycle' }

{'Carbon fixation' }

{'Cardiolipin biosynthesis' }

{'Carotenoid biosynthesis' }

{'Cofactor biosynthesis: Biotin biosynthesis' }

{'Cofactor biosynthesis: Carnitine biosynthesis' }

{'Cofactor biosynthesis: Folate biosynthesis' }

{'Cofactor biosynthesis: Lipoate biosynthesis' }

{'Cofactor biosynthesis: Nicotinate and Nicotinamide metabolism' }

{'Cofactor biosynthesis: Pantothenate and CoA biosynthesis' }

{'Cofactor biosynthesis: Regeneration' }

{'Cofactor biosynthesis: Riboflavin biosynthesis' }

{'Cofactor biosynthesis: Thiamine (B1)' }

{'Cofactor biosynthesis: Vitamin B6' }

{'Fatty acid biosynthesis' }

{'Fatty acid biosynthesis, mitochondria' }

{'Fatty acid biosynthesis: Long chain omega-3 synthesis' }

{'Fatty acid degradation, mitochondria' }

{'Fatty acid degradation, peroxisome' }

{'Fructose and mannose metabolism' }

{'Galactoglycerolipid metabolism' }

{'Galactose metabolism' }

{'Glycolysis/Gluconeogenesis/Entner-Doudoroff pathway' }

{'Glyoxylate cycle; TCA cycle; Dicarboxylate metabolism' }

{'Inositol phosphate metabolism' }

{'Metabolism of other amino acids: Glutathione metabolism' }

{'Metabolism of other amino acids: Selenoamino acid metabolism' }

{'Metabolism of other amino acids: beta-Alanine metabolism' }

{'Modeling: ATP maintenance' }

{'Modeling: Biomass' }

{'Modeling: Demand' }

{'Modeling: Exchange reaction' }

{'Modeling: Sink' }

{'N-Glycan biosynthesis' }

{'Nitrogen metabolism' }

{'Nucleotide metabolism: Purine metabolism' }

{'Nucleotide metabolism: Pyrimidine metabolism' }

{'Nucleotide sugar metabolism' }

{'Oxidative phosphorylation' }

{'Pentose interconversions' }

{'Pentose phosphate pathway' }

{'Phosphoglycerolipid metabolism' }

{'Photosynthesis' }

{'Phylloquinone biosynthesis' }

{'Plastoquinol biosynthesis' }

{'Porphyrin and chlorophyll metabolism' }

{'Pyruvate metabolism' }

{'Sphingolipid metabolism' }

{'Starch and sucrose metabolism' }

{'Sulfolipid biosynthesis' }

{'Sulfolipid metabolism' }

{'Sulfur metabolism' }

{'TCA cycle' }

{'Transport, chloroplast' }

{'Transport, cytosol' }

{'Transport, extracellular' }

{'Transport, fatty acids' }

{'Transport, mitochondria' }

{'Transport, peroxisome' }

{'Transport, thylakoid' }

{'Transport, triacylglycerol' }

{'Triacylglycerol biosynthesis' }

{'Triacylglycerol degradation' }

{'Urea cycle' }

Le jeudi 27 septembre 2018 01:02:19 UTC-4, Thomas Pfau a écrit :

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