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https://github.com/robaina/galapagos_cgem
https://github.com/robaina/galapagos_cgem
Last synced: 2 days ago
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- Host: GitHub
- URL: https://github.com/robaina/galapagos_cgem
- Owner: Robaina
- Created: 2024-07-23T13:01:54.000Z (4 months ago)
- Default Branch: master
- Last Pushed: 2024-07-25T10:37:39.000Z (3 months ago)
- Last Synced: 2024-10-17T19:38:33.045Z (20 days ago)
- Language: Jupyter Notebook
- Size: 17 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Reconstructing a cGEM for the most abundant marine microbial species in Galápagos
__Plan__:
1. Select GEMs for the most abundant marine microbial species in the dataset, represented by their families in [S3 Table](cgem_galapagos/data/Table_3.XLSX)
2. Build cGEM and analyze with MICOM
3. Input abundances to the cGEM as well as key environmental parameters: DOC, DIC, NO3, PO4, maybe chlorophyll as well
4. Analyze community changes (interactions) and growth rates for the four main scenarios: 2015, 2016, east and west, summarized in this [table](cgem_galapagos/outputs/Galapagos_Archipelago_Key_Changes.tsv).
__Data__:
1. Chlorophyll for small fraction (< 5 µm) and large fraction (> 5 µm), for bacterioplankton and phytoplankton, respectively.
__References__:
1. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.575194/full