Published October 16, 2026 | Version 0.1.3
Software Open

gpuGEM: GPU-based solving of linear optimisation problems over genome-scale metabolic models

Authors/Creators

  • 1. School of Medicine, University of Galway, University Rd, Galway, Ireland; Digital Metabolic Twin Centre, University of Galway, Galway, Ireland; Institute for Clinical Trials, University of Galway, Galway, Ireland
  • 2. School of Medicine, University of Galway, University Rd, Galway, Ireland; Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
  • 3. School of Medicine, University of Galway, University Rd, Galway, Ireland; Digital Metabolic Twin Centre, University of Galway, Galway, Ireland; School of Microbiology, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland; APC Microbiome Ireland, Cork, Ireland

Description

gpuGEM solves the linear programmes arising in constraint-based modelling of genome-scale metabolic networks on NVIDIA GPUs, wrapping the cuOpt PDLP first-order solver behind a COBRA-compatible interface.

The repository includes application/, a self-contained causal-gene prioritisation workflow: given a patient's blood biomarker pattern it ranks inherited-metabolic-disease genes by the flux reduction each one induces in the Harvey whole-body metabolic model (81,094 reactions, 56,452 metabolites). The model data, the pipeline and the reference results are all deposited, so the published application results can be reproduced from this archive alone.

This deposit accompanies the gpuGEM manuscript. See README.md for installation and application/README.md for the application.

Notes

Farid Zare and Timothy Hulshof contributed equally to this work (joint first authors). This study was funded by grants from the European Research Council (ERC) under the European Union's Horizon Europe research and innovation programme (grant agreement #101125633) to IT, the Science Foundation Ireland under Grant number 12/RC/2273P2, and the Horizon Europe grant Recon4IMD (#101080997). This work was further supported by the Swiss State Secretariat for Education, Research and Innovation, SERI (grant 23.00232), and UK Research and Innovation, UKRI (grants 10083717 and 10080153).

Files

Digital-Metabolic-Twin-Centre/gpuGEM-v0.1.3.zip

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Additional details

Related works

Is supplement to
https://github.com/Digital-Metabolic-Twin-Centre/gpuGEM (URL)

Funding

European Commission
AVATAR - Enabling personalised diagnosis, treatment, and stratification through whole-body metabolic modelling of an individual's genome, metabolome, and metagenome. 101125633
European Commission
Recon4IMD - Reconstruction and Computational Modelling for Inherited Metabolic Diseases 101080997

Software

Repository URL
https://github.com/Digital-Metabolic-Twin-Centre/gpuGEM