Table 1

Comparison of MicrobesFlux and other web-based fluxomics software
MicrobesFlux FAME Model SEED Webcoli BioMet Toolbox
Model generation Database KEGG KEGG RAST iJR904 None
Number of organisms 1,194 ~780 ~5,000 1 NA
Embedded functions for model reconstruction1 Inflow/outflow introduction
Biomass production implementation
Automated generation of biomass composition2
Heterologous pathways
Knock out pathways
Reactant/product Modification
Automated mass balance
Automated compound charging and charge balance
Transport reactions with coupling to ATP and proton translocation3
Prediction of reaction directionality/reversibility based on thermodynamics4
Gene-Protein-Reaction associations
Reaction compartments
Flux analysis FBA
FBA with customized objective function
Dynamic FBA
Flux Variability Analysis
Output Pathway visualization
SBML output

1: The embedded functions, as developed in MicrobesFlux, FAME and Webcoli, are the functional modules that are directly incorporated into the web-based software to provide human-computer interaction and to minimize users’ programming work. Model SEED can achieve the model reconstruction via manual programming on a SBML-formatted metabolic model, instead of using the embedded functions [22].

2: The biomass composition needs to be manually inputted in MicrobesFlux and FAME. Model SEED can automatically generate one template biomass composition for different organisms. Webcoli has fixed the biomass composition of E.coli in the system.

3: The transport reactions (i.e., inflow/outflow) can be coupled to ATP and proton translocation manually in MicrobesFlux, FAME, and Webcoli.

4: None of the software included in Table 1 predicts the reaction directionality/reversibility based on thermodynamics.

5: Gap-fill is achieved manually in MicrobesFlux and FAME. Model SEED uses a computational algorithm to achieve semi-automatic gap-fill.

Feng et al.

Feng et al. BMC Systems Biology 2012 6:94   doi:10.1186/1752-0509-6-94

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