Published January 14, 2020
| Version 1.0.0
Dataset
Open
Artifacts for q2-micom
Description
This repository hosts artifacts for use with q2-micom and MICOM. In particular it provides summarized metabolic model databases and growth media.
Model databases
Model databases are provided for family, genus and species ranks. AGORA is a manually curated database of 818 high quality metabolic reconstructions. Raw data was obtained from https://www.vmh.life/.
CarveME is an automatically reconstructed database but offers much more organisms (>5K strains). Raw data was obtained from https://github.com/cdanielmachado/embl_gems.
Diets
We currently only provide an average western diet which is only compatible with AGORA.
Files
Files
(1.1 GB)
| Name | Size | Download all |
|---|---|---|
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md5:20ce58f32bed50181004f0a4a2a97934
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10.1 MB | Download |
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md5:bb08b2ca4761f2f64c82ba926bf9c39f
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21.1 MB | Download |
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md5:ddec06f45acb24774ba68dda97ff2804
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50.0 MB | Download |
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md5:b4d104c8ef1ce12a737ff84c5cb43c8b
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68.6 MB | Download |
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md5:41386026ec4232feb472502ad92f8753
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264.3 MB | Download |
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md5:59f08a29ae4075570c1c300552982770
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693.1 MB | Download |
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md5:ab1602ec728a95105b420354b5b30a93
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7.2 kB | Download |
Additional details
Related works
- Cites
- Journal article: 10.1038/nbt.3703 (DOI)
- Journal article: 10.1093/nar/gky537 (DOI)
- Journal article: 10.1038/nbt.4212 (DOI)
References
- Diener et. al. Additional data related to https://doi.org/10.1101/361907.