💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis

A bioinformatics tool that integrates gene expression data with metabolic models for pathway-level disease analysis. Extends Metabolitics for more comprehensive systems biology analysis.

A paper on using event sourcing in computational systems biology.