💎 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

Machine learning pipeline for genome-scale metabolic engineering and intervention ranking in E. coli using COBRApy and FBA.

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

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

Species-agnostic pipeline that builds a pangenome-reference metabolic model and rapidly derives consistent, gap-filled strain-specific genome-scale models from bacterial genomes.

Hands-on workshop for genome-scale metabolic model reconstruction using gapseq with Google Colab.

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.

COBRApy JSON reconstruction of CHOmpact — a reduced metabolic model of CHO cells with IgG product quality outputs (Jiménez del Val et al. 2023).

A paper on using event sourcing in computational systems biology.

GUI for GEMCAT Algorithm

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

Lernprojekt zum Umgang mit dem **CellNetAnalyzer (CNA)** in MATLAB. Ziel ist es, den Import und die Analyse eines stöchiometrischen Modells zu demonstrieren.

A lightweight, retro-compatible Python virtual pet simulator implementing a formal hybrid Sensing-to-Action Cycle under Thermodynamic Constraints (SATC) dynamical system.

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

Growth-Based Classification of COVID-19 Using E. coli Metabolic Sensors

Copy of SPICEM (Spatial Inference of Cellular Environments via Metabolic Modeling) repository for sharing