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opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
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model summary C-Flux meaning #1211

Closed Shlomit840 closed 2 years ago

Shlomit840 commented 2 years ago

Checklist

Question

Hi I need an explanation of C-Flux meaning in model summary. if the objective is growth, is the C-Flux shows what percentage of the biomass carbon comes from every compound? in the example below, all the carbon for the biomass seems to be from bz, (benzoate). but its flux is extremely low. other carbon-containing compounds have high fluxes but don't have C-Flux. How is it possible?

model.summary()

Objective

1.0 Growth = 13.315904571948098

Uptake

Metabolite Reaction Flux C-Number C-Flux bz_e EX_bz_e 0.001332 7 100.00% <--- source for all biomass carbon? ca2_e EX_ca2_e 0.06931 0 0.00% cl_e EX_cl_e 0.06931 0 0.00% cobalt2_e EX_cobalt2_e 0.001332 0 0.00% cu2_e EX_cu2_e 0.009441 0 0.00% fe2_e EX_fe2_e 0.1934 0 0.00% k_e EX_k_e 2.599 0 0.00% mg2_e EX_mg2_e 0.1155 0 0.00% mn2_e EX_mn2_e 0.009201 0 0.00% nh4_e EX_nh4_e 149.1 0 0.00% o2_e EX_o2_e 1000 0 0.00% octane_e EX_octane_e 132.8 0 0.00% pi_e EX_pi_e 13.13 0 0.00% so4_e EX_so4_e 3.337 0 0.00% zn2_e EX_zn2_e 0.004541 0 0.00%

Secretion

Metabolite Reaction Flux C-Number C-Flux 4hba_e EX_4hba_e -0.002969 7 0.00% co2_e EX_co2_e -493.9 1 100.00% h2o_e EX_h2o_e -869.8 0 0.00% h_e EX_h_e -128.9 0 0.00%

Midnighter commented 2 years ago

Uptake corresponds to your medium definition. Those are all exchange reactions. I don't see any other carbon containing metabolite in the uptake reactions shown here so this makes sense to me.

Why the uptake rate for benzoate is so low, I cannot say without knowing more about the constraints in the model. I'm also concerned by the extremely high nitrate and oxygen uptake rates. Your secretion rates are also extremely high. It looks like your model might contain some mass imbalances or infeasible cycles.

Shlomit840 commented 2 years ago

Thank you for the quick response. In this model summary there is octane with flux 132.8, and C-Flux 0 . Octane is a big carbon source. Why it is not used for biomass carbon? (Assuming C-Flux is the flux for biomass, and not for energy). Shlomit

From: Moritz E. Beber @.> Sent: Tuesday, May 3, 2022 1:47 PM To: opencobra/cobrapy @.> Cc: Shlomit Medina @.>; Author @.> Subject: Re: [opencobra/cobrapy] model summary C-Flux meaning (Issue #1211)

Uptake corresponds to your medium definition. Those are all exchange reactions. I don't see any other carbon containing metabolite in the uptake reactions shown here so this makes sense to me.

Why the uptake rate for benzoate is so low, I cannot say without knowing more about the constraints in the model. I'm also concerned by the extremely high nitrate and oxygen uptake rates. Your secretion rates are also extremely high. It looks like your model might contain some mass imbalances or infeasible cycles.

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Midnighter commented 2 years ago

In this model summary there is octane with flux 132.8, and C-Flux 0 .

Oh yeah, I missed that. My guess is that the molecular formula for octane is not annotated on the metabolite so COBRApy has no way of knowing that there are carbon atoms in it.

Shlomit840 commented 2 years ago

Yes This was the problem. The formula of octane was missing. Anyway, I want to verify, the C-Flux is the C that is going to the biomass, right?

Thank you Shlomit

From: Moritz E. Beber @.> Sent: Tuesday, May 3, 2022 5:33 PM To: opencobra/cobrapy @.> Cc: Shlomit Medina @.>; Author @.> Subject: Re: [opencobra/cobrapy] model summary C-Flux meaning (Issue #1211)

In this model summary there is octane with flux 132.8, and C-Flux 0 .

Oh yeah, I missed that. My guess is that the molecular formula for octane is not annotated on the metabolite so COBRApy has no way of knowing that there are carbon atoms in it.

— Reply to this email directly, view it on GitHubhttps://github.com/opencobra/cobrapy/issues/1211#issuecomment-1116172651, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMGR3HXIBZ3BGAAYNY3G7WDVIE2K7ANCNFSM5U6CE3KQ. You are receiving this because you authored the thread.Message ID: @.***>

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Midnighter commented 2 years ago

Anyway, I want to verify, the C-Flux is the C that is going to the biomass, right?

In general, the summary just shows uptake flux by the model. In most cases, when biomass is the objective and there are no other sinks consuming carbon-based molecules, you can compute a biomass yield on your input, yes. You also have a large CO2 secretion flux so clearly not all of your carbon is integrated into biomass.

Shlomit840 commented 2 years ago

Ok Thank you very much for the answers. Shlomit

מאת: Moritz E. Beber @.***> ‏‏נשלח: יום רביעי 04 מאי 2022 12:56:29 ‏‏אל: opencobra/cobrapy עותק: Shlomit Medina; Author ‏‏נושא: Re: [opencobra/cobrapy] model summary C-Flux meaning (Issue #1211)

Anyway, I want to verify, the C-Flux is the C that is going to the biomass, right?

In general, the summary just shows uptake flux by the model. In most cases, when biomass is the objective and there are no other sinks consuming carbon-based molecules, you can compute a biomass yield on your input, yes. You also have a large CO2 secretion flux so clearly not all of your carbon is integrated into biomass.

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Midnighter commented 2 years ago

One clarification, you can, of course, always compute your yields but you cannot simply assume that all carbon goes to biomass. You have to check your model for that.