Ecoli 0.2.0 - #32
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feat (model): curations Carrao 2024, including python code for model changes
feat (model): remove GLYCK and correct previous GLYCK2 gene reaction rule b3124 removal
fix (model): improves model indentation consistency (automatically through with cobrapy)
feat (model): curations Mao 2022
fix (model): improves model indentation consistency (automatically through cobrapy)
feat (model): curation Bernstein 2023
fix (model): improves model indentation consistency (automatically through with cobrapy)
feat (model): curation XYLI2 removal
feat: XYLI2 removal investigation on impact on related metabolites. Conclusion: No dead-end reactions produced -> keep all metabolites involved in XYLI2
feat (model): XYLI1 annotation update
feat: GLYCK removal investigation on impact on related metabolites. Conclusion: No dead-end reactions produced -> keep all metabolites involved in GLYCK
feat: complete collection of deprications
### Main improvements in this PR: - Implemented changes suggested by @cdebuck as outlined in issue #29 - Update annotation information for XYLI1 found to be outdated in issue #31 **I hereby confirm that I have:** - [x] Tested my code on my own computer for running the model - [x] Selected `develop` as a target branch
### Main improvements in this PR: - Implemented change from Bernstein 2023 as outlined in issue #27 **I hereby confirm that I have:** - [x] Tested my code on my own computer for running the model - [x] Selected `develop` as a target branch
### Main improvements in this PR: - Implemented changes from Mao 2022 as outlined in issue #25 **I hereby confirm that I have:** - [x] Tested my code on my own computer for running the model - [x] Selected `develop` as a target branch
chore: move deprecated reactions to model/reactions folder
chore: fix spelling
feat: add Carrao deprecated reaction to deprecated file
### Main improvements in this PR: - Implemented changes from Carrao 2024 as outlined in issue #21 **I hereby confirm that I have:** - [x] Tested my code on my own computer for running the model - [x] Selected `develop` as a target branch
mihai-sysbio
self-requested a review
August 29, 2025 12:17
| id: "Ecoli-GEM" | ||
| name: "The Consensus Genome-Scale Metabolic Model of Escherichia coli" | ||
| date: "2025-06-16" | ||
| version: "" |
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How about adding a suggestive name for this file?
Suggested change
| version: "" | |
| version: "deprecated" |
mihai-sysbio
approved these changes
Aug 29, 2025
chore: removed duplicate deprications as they are stored in depricated_complete_collection
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A note on the missing |
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Main improvements in this PR:
Curations based on @cdebuck findings:
Curations based on Bernstein 2023:
Curations based on Mao 2022:
Curations based on Carrao 2024:
I hereby confirm that I have: