Welcome to refineGEMs!

refineGEMs is a Python-based toolbox for the curation and analysis of genome-scale metabolic models (GEMS).

Overview

This documentation provides information on how to install the toolbox, how to use it - either via command line or code - and provides different examples of use cases. Furthermore, it provides detailed information about the in-build media database and the code behind the modules.

Quick access to main sites

Connections to other tools

refineGEMs also provides access points for other tools:

• Reporting the MEMOTE score or generating a complete MEMOTE report

• Updating the SBO-Term annotations based on SBOannotator[1]

• Balancing the masses and charges with MassChargeCuration (MCC)[2]

• Correcting a biomass objective function with BOFdat

Licence and visual assets

The refineGEMs source code is distributed under the MIT licence. The project logos are licensed separately under CC BY 4.0; see the brand usage guide for attribution, colours, minimum size, clear space, and acceptable modifications.

Project-created documentation graphics are also licensed separately under CC BY 4.0; see the documentation graphics licence for covered assets and third-party exclusions.

Contributing

Bug reports, feature requests, documentation improvements, and pull requests are welcome. The repository provides GitHub issue templates; see Development for contribution guidance and review notes.

How to cite

When using refineGEMs, please cite the latest publication:

Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. Front. Bioinform., oct 2023. doi:10.3389/fbinf.2023.1214074.

Contents:

• Installation
  • Via pip
  • Via Docker
• Usage
  • Access points
  • The media database
• About different applications
  • Model refinement
  • Model annotation
  • Analysis and simulation
  • Media
• Media & Subsets
  • Content of the Database
  • Working with the Data
• Third-party databases and tools
  • Databases
  • Tools
  • Compliance notes for maintainers
• Content of refineGEMs
  • Subpackages
  • refineGEMs.cmd_access module
• Help and FAQ
  • Help
  • Known Issues and Bugs
  • FAQ
• Logo licence and brand usage
  • Approved Logo Assets
  • Colours
  • Minimum Size
  • Clear Space
  • Acceptable Modifications
• Documentation graphics licence
  • Covered Graphics
  • Future Graphics
• Notes for developers
  • Installation for developers
  • Contributing via GitHub
  • Additional packages required for development
  • Updating the requirements.txt
  • Todo Tree extension
  • Debugging switches
  • Guidelines for code documentation
  • Information about working on the media database

[1]

Nantia Leonidou, Elisabeth Fritze, Alina Renz, and Andreas Dräger. Sboannotator: a python tool for the automated assignment of systems biology ontology terms. Bioinformatics, 2023. URL: https://doi.org/10.1093/bioinformatics/btad437, doi:10.1093/bioinformatics/btad437.

[2]

Reihaneh Mostolizadeh, Finn Mier, and Andreas Dräger. Mcc: automated mass and charge curation at the genome scale applied to <i>c. tuberculostearicum</i>. Microbiology Spectrum, 14(2):e03200–24, 2026. URL: https://journals.asm.org/doi/abs/10.1128/spectrum.03200-24, doi:10.1128/spectrum.03200-24.