BaMFA

BaMFA implements Bayesian metabolic flux analysis to infer genome-scale intracellular flux distributions and quantify their uncertainties using exchange and intracellular (^13C) labeling measurements under steady-state constraints and objective-function considerations.

Key Features:

• Probabilistic Modeling: Uses a Bayesian framework to infer full flux vector distributions for genome-scale metabolic networks.
• Integration with Measurements: Integrates exchange and intracellular flux measurements, including ^13C labeling data, together with steady-state assumptions and objective-function considerations.
• Flux Couplings and Covariances: Couples all fluxes jointly in a truncated multivariate posterior distribution to reveal informative flux couplings and characterize genome-scale flux covariances.
• Enhanced Flux Inference: Enables inference of additional intracellular unobserved fluxes relative to conventional methods, demonstrated on Clostridium acetobutylicum with ^13C data.
• COBRA compatibility: Is COBRA-compatible for use with COBRA-based metabolic model formulations.

Scientific Applications:

• Systems biology: Characterizing genome-scale flux distributions and their uncertainties in metabolic network analyses.
• Bioinformatics: Integrating experimental flux measurements with probabilistic models for computational metabolic analysis.
• Metabolic engineering: Informing engineering strategies by revealing flux couplings and uncertainty in target pathways.
• Disease modeling: Quantifying metabolic flux uncertainty to support hypotheses about altered metabolism in disease contexts.
• Synthetic biology: Assessing flux distributions and dependencies to guide design and optimization of engineered metabolic networks.

Methodology:

Formulates flux inference within a Bayesian framework that integrates exchange and intracellular (including ^13C) measurements, steady-state constraints, and objective-function considerations to infer full flux distributions via a truncated multivariate posterior distribution coupling all fluxes.