Moritz E. Beber

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

The paper introduces nf-core/taxprofiler, a pipeline for automated metagenomic taxonomic classification and profiling using multiple tools and databases.

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

The paper identifies challenges in metabolic modeling standards and proposes a gold standard framework through community feedback.

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.