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fba

fba[model, objective]
performs flux-balance analysis (FBA) on model.
fba[model, objective, bounds]
performs flux-balance analysis (FBA) using additional flux constraints.
  • The following options can be given:
OptFlagMax"Min" (Minimization) or "Max" (Maximization)
SolverLinearProgrammingChoose from all supported solvers, i.e. LinearProgramming, GurobiSolve, GLPKStandalone, CPLEXStandalone
LooplessFalseSet True if loopless FBA should be performed
EXAMPLESCLOSE ALL
Basic Examples   (1)
Perform flux-balance analysis and maximize Biomass flux
The biomass reaction can not carry any flux. Inspecting the model constraints reveals that all exchange reactions can only secrete.
Change the model's constraints to simulate glucose mininmal media condtions and require a certain ATP maintainance flux
Now the biomass reaction can carry a flux
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Click for copyable input
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Click for copyable input
Perform flux-balance analysis and maximize Biomass flux
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Click for copyable input
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The biomass reaction can not carry any flux. Inspecting the model constraints reveals that all exchange reactions can only secrete.
In[4]:=
Click for copyable input
Out[4]=
In[5]:=
Click for copyable input
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Change the model's constraints to simulate glucose mininmal media condtions and require a certain ATP maintainance flux
In[6]:=
Click for copyable input
Now the biomass reaction can carry a flux
In[7]:=
Click for copyable input
Out[7]=
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Generalizations & Extensions   (1)
Determine active reactions using FBA
Determine all genes in the model that are associated with the active reactions
Genes not associated with any active reaction
Perform single gene knockout analysis
Set Inteterminate biomass fluxes is to 0. and sort the result
Visualize the result (show only gene deletion that had an effect on)