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

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
• Usage
  • Access points
  • The media database
• About different applications
  • Model refinement
  • Model annotation
  • Analysis and simulation
  • Further examples
• Media & Subsets
  • Content of the Database
  • Working with the Data
• Content of refineGEMs
  • Subpackages
  • refineGEMs.cmd_access module
• Help and FAQ
  • Help
  • Known Issues and Bugs
  • FAQ
• Notes for developers
  • Installation for developers
  • Additional packages required for development
  • Updating the requirements.txt
  • 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. bioRxiv, February 2023. URL: https://doi.org/10.20944/preprints202302.0317.v1, doi:10.20944/preprints202302.0317.v1.

[2]

Finnem and Reihaneh Mostolizadeh. Biomathsys/masschargecuration: v0.1. January 2023. URL: https://doi.org/10.5281/zenodo.7525185, doi:10.5281/zenodo.7525185.