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MetaFlux -- Quantitative Metabolic Modeling Component of Pathway Tools

The MetaFlux component of Pathway Tools enables construction of quantitative metabolic models using flux-balance analysis. Models can be derived from a Pathway/Genome Database, and existing models in SBML format can be imported into MetaFlux. A benefit of steady-state modeling over kinetic modeling is that steady-state models do not require the thousands of parameters needed by the kinetic-modeling approach.

MetaFlux is distributed as part of Pathway Tools, which can be obtained via the Download link on the left menu.

Applications of steady-state metabolic models include the following.

  • Model-driven discovery
    • Discover incompleteness in reconstructed metabolic network
    • Guide gene reannotations
  • Prediction of cellular phenotypes
    • Predict conditional gene essentiality
    • Predict growth under varying nutrient conditions
    • Predict growth rates
  • Metabolic engineering
    • Explore gene-deletion and gene-addition strategies
    • Test effects of pathway additions
    • Determine media supplementation strategies
  • Analysis of metabolic network properties
    • Predict network robustness
  • Evolutionary comparisons of metabolic networks
    • Understand epistatic interactions and mutational effects
    • Provide insights into evolutionary trajectories
  • Models of interspecies interactions
    • Model the exchange of metabolites
    • Determine costs/benefits for different types of commensalism
MetaFlux has a number of advantages over other FBA-related metabolic modeling tools:

Fast model development: PathoLogic tool enables network reconstruction from annotated genome in hours-to-days. MetaFlux enables draft model reconstruction within 1 month. MetaFlux multiple-gap filler suggests addition of reactions, secretions, nutrients to complete model, and tells the user which biomass metabolites cannot be produced. Reaction balance checker ensures mass balance of all reactions.

Literate Modeling Ensures Facile Inspection of Models: Literate modeling means a model is highly inspectable via the multiple visualization tools in Pathway Tools:pathway display, reaction display, metabolite display, and genome browser. Predicted metabolic fluxes can be visualized on the metabolic map viewer.

Metabolic Model is Coupled with Pathway/Genome Database: Because the metabolic model is generated directly from the Pathway/Genome Database, all database edits are immediately reflected in the metabolic model. No need to separately curate genome database and metabolic model; both are updated in one place. The metabolic model is developed in the context of a rich array of supporting information including the complete genome, curated regulatory network, and chemical structures of most metabolites.

Ease of use: MetaFlux can be run via a graphical user interface or a Lisp API.

Technical specs:

  • Optimization solver: SCIP
  • Import/export from SBML
  • Solving mode: Run individual FBA simulations
  • Development mode: Gap filler suggests missing reactions, secretions, metabolites.
  • Knock-out mode: Run selected gene knockouts, all gene knockouts, all reaction knockouts
  • Runs on MacOS, Windows, Linux