💎 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

Python toolbox for gene expression-based prediction of metabolic alterations at genome-scale

Flux Balance Analysis of E. coli Core Model using COBRApy | Systems Biology & Data Science

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.

GUI for GEMCAT Algorithm

Rust reimplementation of gapseq — informed prediction and analysis of bacterial metabolic pathways and genome-scale networks. ~3× faster on pathway detection, in-process LP solver, single static binary.

Genome-scale metabolic model of mouse brain (iMiceBrain) and case study of Tricyclic pyrone drug

Reusable 4-tier soil microbiome screening pipeline — metagenomics, metabolic modeling, and community ecology for nitrogen fixation, carbon sequestration, bioremediation, and more

This repository explores the geometric stability of complex biochemical networks using the VNAE framework.

Context specific metabolic model generation. Done @ Dräger lab, MLU-Halle