https://github.com/robaina/marinegems

A repository of reference genome-scale metabolic models of marine microbes
https://github.com/robaina/marinegems

marine-biology metabolic-models microbial-communities microbial-ecology systems-biology

Last synced: about 1 year ago
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A repository of reference genome-scale metabolic models of marine microbes

• Host: GitHub
• URL: https://github.com/robaina/marinegems
• Owner: Robaina
• License: apache-2.0
• Created: 2024-07-23T18:29:13.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-08-26T12:16:15.000Z (almost 2 years ago)
• Last Synced: 2025-04-06T10:38:01.849Z (about 1 year ago)
• Topics: marine-biology, metabolic-models, microbial-communities, microbial-ecology, systems-biology
• Language: Jupyter Notebook
• Homepage:
• Size: 1.66 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# A repository of reference genome-scale metabolic models of marine microbes

__Reconstruction of GEMs from core models__

e.g. Synechococcus,

1. Start with generic model with minimal imports

2. Obtain set of imports from MAG

3. Add import reactions and required pathways to utilized imported compounds if not present in generic model

4. Add imports/exports required for the model to work (e.g. minerals, etc.)