|Comparison of MicrobesFlux and other web-based fluxomics software|
|MicrobesFlux||FAME||Model SEED||Webcoli||BioMet Toolbox|
|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||○|
|Knock out pathways||●||●||●|
|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|
|FBA with customized objective function||●||●|
|Flux Variability Analysis||●|
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 .
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