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draeger-lab / refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
https://refinegems.readthedocs.io/en/latest/
MIT License
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Enhance biomass standardisation #112

Open GwennyGit opened 8 months ago

GwennyGit commented 8 months ago

Discussed in https://github.com/draeger-lab/refinegems/discussions/87

Originally posted by **GwennyGit** June 29, 2023 The paper ‘Standardising biomass reactions and ensuring complete mass balance in genome-scale metabolic models’ from 2017[[1]](#1) provides scripts to standardise biomass reactions. These scripts could be integrated into the module `biomass.py`, currently only available on the development branch. I already wrote to one of the corresponding authors of the paper[[1]](#1). As I did not hear back from the corresponding author, I will ask the head of the group if we can integrate their scripts. --- new status: got feedback from the authors. They agree to let us integrate their parts into refinegems and are happy to help with any questions that might occur. *** [1] Siu H J Chan and others, Standardising biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, Volume 33, Issue 22, November 2017, Pages 3603–3609, https://doi.org/10.1093/bioinformatics/btx453