Skip to main content

Table 1 Feature Comparison.

From: FASIMU: flexible software for flux-balance computation series in large metabolic networks

  FASIMU COBRA OptFlux SBRT BioSPICE Pathway
Analyser
SBML import [41] + + + + + +
Flatfile import + + + + + -
SBML export [41] + + + + - -
expa export [45] + + + - + -
Metatool export [46, 47] + - + + - -
Biomass maximization [1] + + + + + +
Flux minimization [29] + - - - - -
Regulatory network - - - + - -
MOMA [13] + - + - + +
ROOM [31] + - + - - -
Fitness maximization [30] + - - - - -
Expression profile match [18, 19] + - - - - -
FVA [3234] + + + + - -
MFA [35] + - + + - -
Thermodynamic feasiblity [17] + - - - - -
Batch computation & scripting + + - - - -
Description language + - - + - -
Graphical user interface - - + + + -
Not depend on commercial software + - + + + -
Solver selection 4 5 1 2 1 1
User documentation + + + + - -
Built-in visualization - - + - - -
Interaction with CellDesigner [42] - - + - - -
Interaction with Cytoscape [27] + - + - - -
Interaction with BiNA [26] + - - - - -
  1. Feature comparison of recent programs focusing on flux-balance optimization. +/- denote the existance/absence of the feature. The row solver selection indicates the number of solver programs to choose from.