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Table 1 FBA software comparison. Features comparison of applications discussed in this article focusing on their ability to integrate regulatory networks analyses into FBA

From: FlexFlux: combining metabolic flux and regulatory network analyses

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Regulated FBA

Software

Free

Metabolic

Regulatory

Graphical

Command line for

Dynamic

Steady state

ODEs

EFM

 

dependencies

networks

networks

interface

batch processing

    

FlexFlux

Yes

Yes

Yes

Yes

Yes

Yes (Time

Yes

No

No

      

dependent FBA)

(RSA + FBA)

  

Cell net analyser

No

Yes

Only for export

Yes

Yes

No

No

Yes

Yes

COBRA

No

Yes

No

No

Yes

Yes

No

No

No

      

(Dynami-cRFBA)

   

COBRApy

Yes

Yes

No

No

Yes

No

No

No

No

OptFlux

Yes

Yes

No

Yes

No

No

No

No

Yes

SurreyFBA

Yes

Yes

No

Yes

Yes

No

No

No

Yes

FASIMU

Yes

Yes

No

No

Yes

No

No

No

No

SBRT

Yes

Yes

No

Yes

Yes

No

No

No

Yes

  1. ODEs Ordinary Differential Equations, EFM Elementary Flux Modes