Metasmith

Bioinformatic workflows that dynamically adapt to what you have and produce what you want.

Working Group: Pathways

Microbial metabolism serves as the gateway to manipulating matter at the molecular scale, exhibiting high programmable flexibility alongside inherent robustness. The underlying functions driving local biochemical fluxes are encoded within a diverse sequence landscape, forming a genetic archive that represents billions of years of evolutionary search. This archive is information-rich, yet the capacity to interface with it and model the correct assembly of biological parts to achieve desired metabolic phenotypes remains limited. Genome-scale metabolic models (GEMs) have achieved notable success on this frontier, but depend on a tall stack of supporting bioinformatics to generate prerequisite inputs and alleviate manual processing, and the absence of standardized contracts for bioinformatic tools impedes modular reuse of upstream dependencies across GEM construction and adjacent microbiome analyses. We have developed Metasmith, a workflow compiler that standardizes the interface of bioinformatics tools through formal input-output contracts. Its core innovation applies a novel type system combined with AI planning to model how bioinformatics tools can be chained together, enabling declarative generation of bioinformatics workflows executable in Nextflow. Our growing catalogue of integrated tools spans sequence assembly, functional annotation, metagenomic binning, ASV analysis, and GEM construction. Metasmith aims to streamline the design, execution, and sharing of bioinformatics analyses, advancing our understanding of microbial metabolism and beyond.

Project Links: https://github.com/hallamlab/Metasmith