SBbadger

SBbadger is a software tool developed for generating synthetic biochemical reactions or metabolic networks. It's designed to fill the gap in the development and benchmarking of computational tools for the inference, optimization, and simulation of biochemical reaction networks. Traditional approaches for assembling benchmark models, such as collection from literature, subnetwork extraction, or de novo generation, often fall short in representing the diversity and complexity of natural biochemical networks or in providing a sufficient volume of models for rigorous statistical analysis.

SBbadger addresses these limitations by allowing users to define degree distributions, choose from multiple kinetic formalisms, and specify a range of other properties to tailor the generated networks closely to the characteristics of biological systems. This capability enables the creation of benchmark model sets that not only mirror the properties of natural biochemical systems but also support the kinetics and model structures commonly targeted by computational analysis and inference software.