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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

SBML support 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