Error while using OptKnock

[Bhushan Dhamale]

I am testing a few of the functions of the COBRA toolbox from the Schellenberger et al, 2011, Nature Protocol paper examples.
When I run the OptKnock function, I get the error message:

Reference to non-existent field 'rxnList'.
Error in setConstraintsIrrevModel (line 38)
constrProcessed = false*ones(length(constrOpt.rxnList),1);
Error in OptKnock (line 133)
constrOptIrrev = setConstraintsIrrevModel(constrOpt,model,modelIrrev,rev2irrev);

What might be done to remedy this problem?

P.S. I am attaching the live script and HTML files for reference.

[Thomas Pfau]

You missed a line from the protocol there:

>> constrOpt.rxnList = {‘Biomass_Ecoli_core_N(w/GAM)-Nmet2’, ‘ATPM’};

Best
Thomas

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[Ronan M.T. Fleming]

Why not use v3?

https://arxiv.org/abs/1710.04038

On 14 November 2017 at 21:35, Thomas Pfau <thoma...@uni.lu> wrote:

You missed a line from the protocol there:

>> constrOpt.rxnList = {‘Biomass_Ecoli_core_N(w/GAM)-Nmet2’, ‘ATPM’};

Best
Thomas

On 2017-11-14 18:14, Bhushan Dhamale wrote:

I am testing a few of the functions of the COBRA toolbox from the Schellenberger et al, 2011, Nature Protocol paper examples.
When I run the OptKnock function, I get the error message:

Reference to non-existent field 'rxnList'.
Error in setConstraintsIrrevModel (line 38)
constrProcessed = false*ones(length(constrOpt.rxnList),1);
Error in OptKnock (line 133)
constrOptIrrev = setConstraintsIrrevModel(constrOpt,model,modelIrrev,rev2irrev);

What might be done to remedy this problem?

P.S. I am attaching the live script and HTML files for reference.

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Campus Belval, Biotech II 115
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Tel: (+352) 46 66 44 5309
Email: thoma...@uni.lu

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[Bhushan Dhamale]

Silly me!
Sorry about that.

On inserting the constrOpt.rxnList, I get the following output for optKnockSol.rxnList:

ans = 5×1 cell array

{'GLUDy' } {'GLUSy' } {'ICDHyr' } {'NADTRHD'} {'PFL' }

However, the paper mentions ALCD2x, FUM, GLUDY, ME2, PYK in the knockout list.
Why am I getting 4 different reactions?

[Bhushan Dhamale]

Hello Ronan,
I was unaware of this.
Thank you for bringing it to my notice.
This will definitely be of great help to me.

Best,
Bhushan

On Wednesday, November 15, 2017 at 11:41:58 AM UTC+5:30, Ronan M.T. Fleming wrote:

Why not use v3?

https://arxiv.org/abs/1710.04038

On 14 November 2017 at 21:35, Thomas Pfau <thoma...@uni.lu> wrote:

You missed a line from the protocol there:

>> constrOpt.rxnList = {‘Biomass_Ecoli_core_N(w/GAM)-Nmet2’, ‘ATPM’};

Best
Thomas

On 2017-11-14 18:14, Bhushan Dhamale wrote:

I am testing a few of the functions of the COBRA toolbox from the Schellenberger et al, 2011, Nature Protocol paper examples.
When I run the OptKnock function, I get the error message:

Reference to non-existent field 'rxnList'.
Error in setConstraintsIrrevModel (line 38)
constrProcessed = false*ones(length(constrOpt.rxnList),1);
Error in OptKnock (line 133)
constrOptIrrev = setConstraintsIrrevModel(constrOpt,model,modelIrrev,rev2irrev);

What might be done to remedy this problem?

P.S. I am attaching the live script and HTML files for reference.

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Campus Belval, Biotech II 115
6 avenue du Swing
L-4367 Belvaux
Tel: (+352) 46 66 44 5309
Email: thoma...@uni.lu

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[Thomas Pfau]

I can't tell you for sure, but:
The set returned by the current function gives a better by-product excretion with a lower biomass production to the solution in the paper. It might be that at some point the tradeoff was changed or that the model (ecoli_core) was slightly altered.
Now there is an additional change from back then:

The rev field was deprecated. EColiCore has multiple reactions with a rev field of 1 (indicating a reversible reaction) but a lower bound of 0 (indicating irreversibility), thus contradicting each other.

So this could be another issue thats playing into this change.

Best

Thomas

[Bhushan Dhamale]

Hello Thomas,
Thank you for clearing that up.

Where might I be able to find the meaning of the fields contained within the optKnock structure array?

Best,
Bhushan

[Thomas Pfau]

Have a look at the function documentation. The output is essentially the solution structure returned by solveCobraMILP when solving the OptKnock problem.

2 fields are added:

rxnList (the knock out reactions, if there is a suggested knockout)

fluxes (the fluxes of the suggested solution.

Best

Thomas

[Ronan M.T. Fleming]

https://github.com/opencobra/cobratoolbox/tree/master/tutorials/additionalTutorials/optKnock

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Campus Belval, Biotech II 115
6 avenue du Swing
L-4367 Belvaux
Tel: (+352) 46 66 44 5309
Email: thoma...@uni.lu

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