BiGGR

BiGGR is an R software package to streamline the process of metabolic flux analysis, catering to the systems biology community's need for analyzing flux distributions within biochemical networks.BiGGR offers a user-friendly alternative to proprietary software options, allowing for integrating flux analysis with gene expression data handling tools and recognizing the importance of the R computing environment within the scientific community.

This software leverages public metabolic reconstruction databases, incorporating comprehensive resources like the BiGG database and the Recon2 human metabolism reconstruction as SBML (Systems Biology Markup Language) objects. BiGGR allows users to construct models by querying for specific pathways, genes, or reactions and then applying linear inverse modeling algorithms to estimate fluxes through maximizing or minimizing objective functions.

A significant feature of BiGGR is its capability to assess the uncertainty in flux estimates by sampling the constrained flux space, thus generating ensembles of feasible flux configurations that conform to experimental data within defined precision limits. Additionally, BiGGR offers automatic visualization tools for metabolic networks, employing hypergraphs to represent metabolic pathways with hyperedge widths indicative of the estimated flux values.

BiGGR supports importing and exporting models in SBML format, ensuring compatibility with various modeling and analysis tools across the field. Introducing a novel algorithm, Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA), within BiGGR, enables the prediction of flux changes based on gene expression variations, such as those occurring in diseases like Alzheimer's.