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

BMC Bioinformatics

Table 1 Feature Comparison.

	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 [32–34]	+	+	+	+	-	-
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]	+	-	-	-	-	-

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.

ISSN: 1471-2105